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Warning: Undefined array key "media" in /var/www/html/allbio/feed.php on line 385 AllBio public
http://www.allbioinformatics.eu/
Sat, 27 Apr 2024 13:01:17 +0000FeedCreator 1.8http://www.allbioinformatics.eu/lib/tpl/A_Centered_Perspective/images/favicon.icoAllBio
http://www.allbioinformatics.eu/
public:activities
http://www.allbioinformatics.eu/doku.php?id=public:activities&rev=1549962286&do=diff
<h1 class="sectionedit1" id="allbio_activities">AllBio Activities</h1>
<div class="level1">
<p>
All AllBio partners will organize within the next 6 months local or national events to disseminate the idea of the AllBio project and invite for collaborations within AllBio. Further, these events should also help to understand and analyse problems in bioinformatics processes within plan sciences, microbiology and livestock research. AllBio will collect, also during these events, <a href="http://www.allbioinformatics.eu/doku.php?id=public:test_cases" class="wikilink1" title="public:test_cases" data-wiki-id="public:test_cases">Test Cases</a> AllBio will be involved to solve.
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio Activities","hid":"allbio_activities","codeblockOffset":0,"secid":1,"range":"13-497"} -->
<h1 class="sectionedit2" id="ontology">Ontology</h1>
<div class="level1">
<p>
The first, and probably most important, task of WP4 will be the coordination of the ontology activities. A crucial step on the path to generalise bioinformatics facilities that were originally developed for activities in the (post-) human genome era will be the harmonisation of the ontologies for data and methods that have so far mainly been developed independently in the various life-science fields. At the highest levels, the ontologies are likely to easily be made to agree, but it is important to cope with a multitude of small problems, such as the simple facts that bacterial genomes do not have introns, or that fungal genomes encode a variety of unique products reflecting biochemical/ biophysical/ morphological/ reproductive/ genetic characteristics distinct from humans and plants, or that plant genomes can be enormous (up to 40 times larger than the human genome and very repetitive owing to polyploidy).
</p>
<p>
<strong>AllBio will organize in March 2012 an Initial Ontology Workshop</strong> for 25-40 participants to ensure that the project partners and the external collaborators get access to the information needed to make their facilities operate within the framework of the EDAM ontology. This workshop will also function to make the EDAM team aware of aspects from the bacterial and plant worlds they might have missed and will need to incorporate in EDAM.
</p>
</div>
<!-- EDIT{"target":"section","name":"Ontology","hid":"ontology","codeblockOffset":0,"secid":2,"range":"498-1884"} -->
<h1 class="sectionedit3" id="webservice">WebService</h1>
<div class="level1">
<p>
The combination of web services and workflow managers such as Taverna, Chipster and Galaxy have proven
to be a powerful combination for prototyping bioinformatics programs and pipelines. Often, a workflow is all that is needed to get the job done permanently. The AllBio partners have extensive experience both with workflow-management software (in particular, Taverna, Galaxy and CHIPSTER) and with the creation of web service enabled tools. A programme of activities towards the use of workflow-management software in the bioinformatics activities in the target areas is provided in WP3. Software from within the consortium will be made available as Web services that can be used by workflow-management software; workflow-management training courses are being organised routinely by UNIMAN; examples of workflows that include AllBio produced Web services will be placed on the AllBio portal by individual partners as the tools become available. Many international projects, today, are directed towards systems biology or other holistic approaches.
</p>
<p>
For the AllBio communities with less experience of developing and deploying web service enabled tools,
an <strong>initial workshop will be organised by RUNMC in May 2012</strong>, and a complementary advanced version of the
workshop in month September 2013 offering training for 25-40 participants. These workshops will provide seminars on web service technology, ‘hands on’ practice on deploying web services, and also ‘clinics’ to help those with existing services to use the appropriate ontologies and interchange schemas.
</p>
</div>
<!-- EDIT{"target":"section","name":"WebService","hid":"webservice","codeblockOffset":0,"secid":3,"range":"1885-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:agm2
http://www.allbioinformatics.eu/doku.php?id=public:agm2&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_consortium_meeting">AllBio Consortium Meeting</h2>
<div class="level2">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aagm2&media=public:dsc_5008_2.jpg" class="media" title="public:dsc_5008_2.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=600&tok=e24e0b&media=public:dsc_5008_2.jpg" class="media" loading="lazy" alt="" width="600" /></a>
</p>
</div>
<h5 id="day_one">Day One</h5>
<div class="level5">
<p>
Arrival: 29th Sept.
</p>
<p>
Start at lunch time,
12:00 - 18:00 points 1-5
</p>
<p>
dinner
</p>
</div>
<h5 id="day_two">Day Two</h5>
<div class="level5">
<p>
9:00-16:00 Writing the white paper
</p>
<p>
then all can leave early enough to be back home that day.
</p>
</div>
<h5 id="agenda_points">Agenda points</h5>
<div class="level5">
<ol>
<li class="level1"><div class="li"> deliverables</div>
</li>
<li class="level1"><div class="li"> organisation of writing the reports (we need two of them, the year 3</div>
</li>
<li class="level1"><div class="li"> report and the final one)</div>
</li>
<li class="level1"><div class="li"> financial statements (if possible with the presence of your financial people)</div>
</li>
<li class="level1"><div class="li"> links to other projects (e.g. GOBLET, BioCatalogue, Images…)</div>
</li>
<li class="level1"><div class="li"> future activities arising from AllBio</div>
</li>
<li class="level1"><div class="li"> writing the white paper</div>
</li>
</ol>
</div>
<h5 id="location">Location</h5>
<div class="level5">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aagm2&media=public:hampshirehotel.png" class="media" title="public:hampshirehotel.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=400&tok=cf8f0d&media=public:hampshirehotel.png" class="mediaright" align="right" loading="lazy" alt="" width="400" /></a>
Amsterdam, Netherland
</p>
<p>
<a href="http://www.hampshire-hotels.com/hampshire-hotel-rembrandt-square-amsterdam" class="urlextern" title="http://www.hampshire-hotels.com/hampshire-hotel-rembrandt-square-amsterdam" rel="ugc nofollow">Hampshire Hotel</a>
</p>
<p>
Rembrandt Square Amsterdam
</p>
<p>
Amstelstraat 17
</p>
<p>
1017 DA - Amsterdam
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio Consortium Meeting","hid":"allbio_consortium_meeting","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:agm2012
http://www.allbioinformatics.eu/doku.php?id=public:agm2012&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_annual_general_meeting_2012">AllBio Annual General Meeting 2012</h2>
<div class="level2">
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=31bf14&media=public:allbio_agm_2012.jpg" class="medialeft" align="left" loading="lazy" alt="" width="500" />
</p>
<p>
The AllBio first AGM took place in the Eden Hotel in Amsterdam, the Netherlands hosting at least one member of the partners.
</p>
<p>
The meeting was guided by the chair Erik Bongcam-Rudloff having firstly an overview of the actions and results of the first project year and then a discussion about the year 2 actions and results we need to achieve.
</p>
<p>
An important argument was the <a href="http://www.allbioinformatics.eu/doku.php?id=public:bioinf" class="wikilink1" title="public:bioinf" data-wiki-id="public:bioinf">Bioinformatics Workshop</a> in Milan, Italy, 12-14 December 2012 where test case providers and bioinformaticans will create woring groups and discuss the possible solutions of some test cases.
</p>
<p>
<em>
</em>
<em>
</em>
<em>
The AGM will take place 21 September 2012 in Amsterdam, Netherlands in the Hotel Eden (<a href="http://www.edenamsterdamhotel.com/" class="urlextern" title="http://www.edenamsterdamhotel.com/" rel="ugc nofollow">http://www.edenamsterdamhotel.com/</a>)
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio Annual General Meeting 2012","hid":"allbio_annual_general_meeting_2012","codeblockOffset":0,"secid":1,"range":"41-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:agm2013
http://www.allbioinformatics.eu/doku.php?id=public:agm2013&rev=1549962286&do=diff
<h3 class="sectionedit1" id="allbio_agm_2013">AllBio AGM 2013</h3>
<div class="level3">
<p>
27 September 2013 London
</p>
<p>
<a href="http://www3.hilton.com/en/hotels/united-kingdom/hilton-london-heathrow-airport-LHRAPTW/index.html" class="urlextern" title="http://www3.hilton.com/en/hotels/united-kingdom/hilton-london-heathrow-airport-LHRAPTW/index.html" rel="ugc nofollow">HILTON LONDON HEATHROW AIRPORT</a> at Terminal 4
</p>
<p>
Time: 10:00-17:00
</p>
<p>
10:00-10:15 Welcome
</p>
<p>
10:15-11:00 Presentations of hack-a-thon results and experiences
</p>
<p>
11:00-11:15 Coffee Break
</p>
<p>
11:15-12:00 Summary of the hack-a thon results/experiences
</p>
<p>
12:00-12:30 Suggestion to write a white paper
</p>
<p>
12:30-13:30 Lunch
</p>
<p>
13:30-15:30 Official AGM procedure with presentations from each WP including intensive discussion of the remaining deliverables
</p>
<p>
15:30-16:00 Coffee Break
</p>
<p>
16:00-17:00 Design of the last year
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aagm2013&media=public:bioinfo:dsc_2215.jpg" class="media" title="public:bioinfo:dsc_2215.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=e74bca&media=public:bioinfo:dsc_2215.jpg" class="media" loading="lazy" alt="" width="200" /></a>
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:bigdata
http://www.allbioinformatics.eu/doku.php?id=public:bigdata&rev=1549962286&do=diff
<h2 class="sectionedit1" id="managing_big_data">Managing Big Data</h2>
<div class="level2">
<p>
<strong>July 9 - 11 2014</strong>
<strong>Berlin, Germany</strong>
</p>
<p>
In collaboration with <strong><a href="http://project.isbe.eu" class="urlextern" title="http://project.isbe.eu" rel="ugc nofollow">ISBE</a></strong> and <strong><a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">SeqAhead</a></strong>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Abigdata&media=public:logos.png" class="media" title="public:logos.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=400&tok=f8f33f&media=public:logos.png" class="media" loading="lazy" alt="" width="400" /></a>
</p>
</div>
<!-- EDIT{"target":"section","name":"Managing Big Data","hid":"managing_big_data","codeblockOffset":0,"secid":1,"range":"13-214"} -->
<h3 class="sectionedit2" id="allbio_tutorial_new_methods_in_genome_annotation">AllBio Tutorial "New methods in genome annotation"</h3>
<div class="level3">
<p>
<br/>
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio Tutorial \"New methods in genome annotation\"","hid":"allbio_tutorial_new_methods_in_genome_annotation","codeblockOffset":0,"secid":2,"range":"215-276"} -->
<h3 class="sectionedit3" id="seqahead_workshop_setting_the_standards_for_analysing_and_integrating_big_data">SeqAhead Workshop "Setting the standards for analysing and integrating big data"</h3>
<div class="level3">
<p>
<br/>
</p>
<p>
Modern life sciences are facing a rapidly increasing amount of data produced worldwide. The diversity and heterogeneity of the data calls for standardized formats for the data itself, its description and its context (the metadata), as well as for the processes during generation and processing of the data, the Standard Operating Procedures (SOPs). Standardization is important to enable researchers to exchange and integrate the data and resulting models and to relate corresponding data to each other.
The rapid development of modern technologies, especially the Next Generation Sequencing (NGS) technologies, allows the generation of biological data with increasing speed and precision. Standards and SOPs, therefore, become an increasingly critical issue specifically in large scale, distributed or applied approaches assuring that data can be accessed, integrated, shared, and compared. The development of quality control and standards are key drivers for efficient and successful large-scale research pipelines in the life sciences.
The workshop will bring together experimentalists and modellers, as well as representatives from national and international standardization bodies and data management experts. It will include discussions of the current state of standardization in the different fields of the life sciences. The aim is to identify overlaps, possible interoperability and interfacing options between the corresponding standards.
</p>
<p>
<strong>The organising team:</strong>
</p>
<ul>
<li class="level1"><div class="li"> Martijn J. Moné VU University Amsterdam (NL)</div>
</li>
<li class="level1"><div class="li"> Susanne Hollmann University of Potsdam (D)</div>
</li>
<li class="level1"><div class="li"> Martin Golebiewski HITS (D)</div>
</li>
<li class="level1"><div class="li"> Babette Regierer LifeGlimmer GmbH (D)</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Contact: (+49) 331-977-702811 plantsys@uni-potsdam.de</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:managing_big_data_flyer_ws_july_2014_berlin.pdf" class="media mediafile mf_pdf" title="public:managing_big_data_flyer_ws_july_2014_berlin.pdf (368.5 KB)">Flyer</a></strong></div>
</li>
</ul>
<p>
<strong>Program</strong>
</p>
</div>
<h4 id="workshop_seqahead_setting_the_standards_for_analysing_and_integrating_big_data">Workshop SeqAhead Setting the standards for analysing and integrating big data</h4>
<div class="level4">
<p>
<br/>
<strong>Wednesday, July 9, 2014</strong>
</p>
<ul>
<li class="level1"><div class="li"> 09:30-10:00 Welcome and Introduction</div>
</li>
<li class="level1"><div class="li"> 10:00-11:15 Session 1: Data Generation</div>
</li>
<li class="level1"><div class="li"> 11:15-11:45 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 11:45-13:00 Session 2: Data Standards</div>
</li>
<li class="level1"><div class="li"> 13:00-14:00 Lunch</div>
</li>
<li class="level1"><div class="li"> 14:00-15:30 Session 3: Data Integration</div>
</li>
<li class="level1"><div class="li"> 15:30-16:00 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 16:30-18:00 Session 4: Data Processing</div>
</li>
<li class="level1"><div class="li"> 18:00-18:30 Discussion and formation of groups for breakout sessions</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Get together Thursday, July 10, 2014</div>
</li>
<li class="level1"><div class="li"> 09:00-10:30 Breakout sessions</div>
</li>
<li class="level1"><div class="li"> 10:30-11:00 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 11:00-13:30 Presentations of the results & Discussion of a roadmap</div>
</li>
<li class="level1"><div class="li"> Closing remarks </div>
</li>
</ul>
</div>
<h4 id="tutorial_allbio_new_methods_in_genome_annotation">Tutorial AllBio New methods in genome annotation</h4>
<div class="level4">
<p>
<br/>
Hands-on training in new computational methods in next generation sequencing and genome annotation
</p>
<ul>
<li class="level1"><div class="li"> 15:00 - 18:00 Lectures</div>
</li>
</ul>
<p>
<strong>Friday, July 11, 2014</strong>
</p>
<ul>
<li class="level1"><div class="li"> 09:00 - 17:00 Hands on training*</div>
</li>
</ul>
<ol>
<li class="level1"><div class="li"> genome annotation automatic pipelines</div>
</li>
<li class="level1"><div class="li"> specific metabolic pathways gene discovery</div>
</li>
<li class="level1"><div class="li"> co-expression correlation network construction</div>
</li>
</ol>
<p>
*please bring your own laptop with you
</p>
</div>
<!-- EDIT{"target":"section","name":"SeqAhead Workshop \"Setting the standards for analysing and integrating big data\"","hid":"seqahead_workshop_setting_the_standards_for_analysing_and_integrating_big_data","codeblockOffset":0,"secid":3,"range":"277-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:bioinf
http://www.allbioinformatics.eu/doku.php?id=public:bioinf&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="bioinformatics_workshop_evaluation_of_test_cases">Bioinformatics Workshop "Evaluation of Test Cases"</h2>
<div class="level2">
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=350&tok=e5a706&media=public:duomo_milano2.jpg" class="medialeft" align="left" loading="lazy" alt="" width="350" />
</p>
<p>
<strong>12 - 14 December 2012</strong>
</p>
<p>
<strong>Milan, Italy</strong>
</p>
<p>
Venue: BEST WESTERN PREMIER Cristoforo Colombo <a href="http://www.hotelcristoforocolombo.it/" class="urlextern" title="http://www.hotelcristoforocolombo.it/" rel="ugc nofollow">http://www.hotelcristoforocolombo.it/</a>
</p>
<p>
<br/>
<br/>
The aim of the Bioinformatics Workshop “Evaluation of Test Cases” is to join the biologists who submitted the <a href="http://www.allbioinformatics.eu/doku.php?id=public:test_cases" class="wikilink1" title="public:test_cases" data-wiki-id="public:test_cases">test cases</a> with the (bio)informaticians who might be able to propose solutions for these bioinformatics challenges.
</p>
<p>
These group could then build communities who will work together to solve these test cases in first hand but will also be nucleus for jointly develop proposals for the <a href="http://ec.europa.eu/research/horizon2020/index_en.cfm?pg=home&video=none" class="urlextern" title="http://ec.europa.eu/research/horizon2020/index_en.cfm?pg=home&video=none" rel="ugc nofollow">Horizon 2020</a> calls.
</p>
</div>
<h5 id="programme">Programme</h5>
<div class="level5">
<p>
(<a href="http://www.allbioinformatics.eu/doku.php?id=public:bioinfo:update" class="wikilink1" title="public:bioinfo:update" data-wiki-id="public:bioinfo:update">see updates of the event</a>)
</p>
<p>
<strong><em class="u">12 December 2012</em></strong>
</p>
<ul>
<li class="level1"><div class="li"> 13:00 - 14:00 Registration and Lunch</div>
</li>
<li class="level1"><div class="li"> 14:00 - 14:30 Welcome by the chair Erik Bongcom-Rudloff and the local organizer Andreas Gisel</div>
</li>
<li class="level1 node"><div class="li"> 14:30 - 18:00 Presentation of the 15 selected test cases - each 10 plus some questions</div>
<ol>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc1" class="wikilink1" title="public:loadedtestcases:tc1" data-wiki-id="public:loadedtestcases:tc1">FAIRE-seq data analyser</a></strong> - Amin Omidbakhshfard (University of Potsdam, Germany)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc2" class="wikilink1" title="public:loadedtestcases:tc2" data-wiki-id="public:loadedtestcases:tc2">Identification of large structural variations</a></strong> - TBD</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc3" class="wikilink1" title="public:loadedtestcases:tc3" data-wiki-id="public:loadedtestcases:tc3">Discovery of gene regulatory networks</a></strong> - Nooshin Omranian (Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc4" class="wikilink1" title="public:loadedtestcases:tc4" data-wiki-id="public:loadedtestcases:tc4">Primer design for ChIP-PCR studies</a></strong> - Prashant Garapati (Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany) </div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc5" class="wikilink1" title="public:loadedtestcases:tc5" data-wiki-id="public:loadedtestcases:tc5">Integrative Omics analysis workflow</a></strong> Karl Göran Andersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc6" class="wikilink1" title="public:loadedtestcases:tc6" data-wiki-id="public:loadedtestcases:tc6">Bacterial Comparative Genomics</a></strong> - Laurent Falquet Swiss Institute of Bioinformatics, Lausanne, Switzerland)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc7" class="wikilink1" title="public:loadedtestcases:tc7" data-wiki-id="public:loadedtestcases:tc7">Processing an un-annotated genome</a></strong> - TBD</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc8" class="wikilink1" title="public:loadedtestcases:tc8" data-wiki-id="public:loadedtestcases:tc8">Discover non-coding RNA in yeast</a></strong> - TBD</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9" class="wikilink1" title="public:loadedtestcases:tc9" data-wiki-id="public:loadedtestcases:tc9">Pathway analysis of a poorly annotated but sequenced plant genome</a></strong> - Erik Alexandersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc10" class="wikilink1" title="public:loadedtestcases:tc10" data-wiki-id="public:loadedtestcases:tc10">Gene prediction modelling for plants</a></strong> - TBD</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc11" class="wikilink1" title="public:loadedtestcases:tc11" data-wiki-id="public:loadedtestcases:tc11">Genome assembly of heterozygous diploid data</a></strong> -TBD</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12" class="wikilink1" title="public:loadedtestcases:tc12" data-wiki-id="public:loadedtestcases:tc12">Functional annotation of the potato genome</a></strong> - Erik Alexandersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc13" class="wikilink1" title="public:loadedtestcases:tc13" data-wiki-id="public:loadedtestcases:tc13">Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones</a></strong> - Annalisa Giampetruzzi (Institute of Plant Virology CNR, Bari, Italy)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc14" class="wikilink1" title="public:loadedtestcases:tc14" data-wiki-id="public:loadedtestcases:tc14">Improved cell factories</a></strong> - Mikko Arvas (VTT Technical Research Centre of Finland, Espoo, Finland)</div>
</li>
<li class="level2"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc15" class="wikilink1" title="public:loadedtestcases:tc15" data-wiki-id="public:loadedtestcases:tc15">Genetics, Genomics and Evolution of prolific breeds of domestic
sheep (Ovis aries)</a></strong> - Juha Kantanen (MTT Agrifood Research Finland, Jokioinen, Finland)</div>
</li>
</ol>
</li>
<li class="level1"><div class="li"> 16:20 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 18:00 Coach</div>
</li>
</ul>
<p>
<strong><em class="u">13 December 2012</em></strong>
</p>
<ul>
<li class="level1"><div class="li"> 09:00 - 11:30 Topic wise parallel sessions to discuss the test cases</div>
</li>
</ul>
<div class="table sectionedit2"><table class="inline">
<thead>
<tr class="row0">
<th class="col0">⇒ We will divide the work in 4 parallel groups, one for each of the following topics:</th>
</tr>
</thead>
<tr class="row1">
<td class="col0">- data formats / standardization and workflows</td>
</tr>
<tr class="row2">
<td class="col0">- scalability of tools (multi genome comparison/data compression)</td>
</tr>
<tr class="row3">
<td class="col0">- non model organisms and multiploidy</td>
</tr>
<tr class="row4">
<td class="col0">- visualization and training</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table","secid":2,"range":"3393-3669"} --><div class="table sectionedit3"><table class="inline">
<thead>
<tr class="row0">
<th class="col0">⇒ The 4 groups will analyze (according to the topic) each test case to identify</th>
</tr>
</thead>
<tr class="row1">
<td class="col0">1.) the difficulties or the current limitations affecting the test case</td>
</tr>
<tr class="row2">
<td class="col0">2.) the existing tools required (with or without adaptation)</td>
</tr>
<tr class="row3">
<td class="col0">3.) the missing tools required</td>
</tr>
<tr class="row4">
<td class="col0">4.) keep minutes of discussion</td>
</tr>
<tr class="row5">
<td class="col0">5.) prepare a summary for discussion</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table1","secid":3,"range":"3671-3996"} --><ul>
<li class="level1"><div class="li"> 10:30 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 11:30 - 13:00 Reporting of the different sessions and general discussions</div>
</li>
</ul>
<div class="table sectionedit4"><table class="inline">
<thead>
<tr class="row0">
<th class="col0">⇒ Each group will report in 15min the results of their session</th>
</tr>
</thead>
<tr class="row1">
<td class="col0">a) is there a common trait in several test cases?</td>
</tr>
<tr class="row2">
<td class="col0">b) are there common tools required or missing?</td>
</tr>
<tr class="row3">
<td class="col0">c) can we split test cases according to operations?</td>
</tr>
<tr class="row4">
<td class="col0">d) can we group test cases?</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table2","secid":4,"range":"4102-4352"} --><ul>
<li class="level1"><div class="li"> 13:00 - 14:00 Lunch</div>
</li>
<li class="level1"><div class="li"> 14:00 - 15:30 Presentations of relevant data analysis tools</div>
</li>
</ul>
<ol>
<li class="level1"><div class="li"> Oren Tzfadia (Weizmann Institute of Science, Tel Aviv, Israel) - The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways</div>
</li>
<li class="level1"><div class="li"> Dimitris Vlachakis (Biomedical Research Foundation, Academy of Athens, Greece) - Recipes to make the most out of your wetlab data in less than 10 minutes.</div>
</li>
<li class="level1"><div class="li"> Jacques van Helden (Université Libre de Bruxelles, Bruxelles, Belgium) - A quick tour of Regulatory Sequence Analysis Tools (RSAT) and Network Analysis Tools (NeAT)</div>
</li>
<li class="level1"><div class="li"> Tatyana Goldberg (Technische Universität, München, Germany) - Loctree2 predicts localization for all domains of life</div>
</li>
<li class="level1"><div class="li"> Domenica D’Elia (Institute for Biomedical Tachnology, Bari, Italy) and Gianvito Pio (University of Bari, Italy) - HOCCLU2: a data mining tool for easily handling interactions data and discovering regulatory networks</div>
</li>
<li class="level1"><div class="li"> Bruno Contreras Moreira (CSCI, Zaragoza, Spain) - Introducing get_homologues and footprintDB</div>
</li>
<li class="level1"><div class="li"> Petri Klemelä (IT Center for Science, Helsinki, Finland) - Chipster: user-friendly analysis software for high-throughput data</div>
</li>
<li class="level1"><div class="li"> Paul Kersey (European Bioinformatics Institute, Hinxton, <abbr title="Gigabyte">GB</abbr>) - Ensembl beyond humans: genomic resources for animals, plants and microbes</div>
</li>
<li class="level1"><div class="li"> Mikko Arvas (VTT Technical Research Centre of Finland) - Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species</div>
</li>
<li class="level1"><div class="li"> Marco Masseroli (Politecnico di Milano, Milan, Italy) - Genomic and Proteomic Knowledge Base (GPKB) & Bio Search Computing (Bio-SeCo)</div>
</li>
</ol>
<ul>
<li class="level1"><div class="li"> 15:30 - 18:30 Parallell session for test cases specific discussions in light of the results of the topics-wise discussions</div>
</li>
</ul>
<div class="table sectionedit5"><table class="inline">
<thead>
<tr class="row0">
<th class="col0">⇒ We will divide again the work in 3 parallel sessions. Each session will analyze 5 test cases (random distribution).</th>
</tr>
</thead>
<tr class="row1">
<td class="col0">For each test case we need:</td>
</tr>
<tr class="row2">
<td class="col0">- identification of tools</td>
</tr>
<tr class="row3">
<td class="col0">- a SWOT analysis (Strength, Weaknesses, Opportunities and Threats)</td>
</tr>
<tr class="row4">
<td class="col0">- a preliminary work plan for a follow-up activity</td>
</tr>
<tr class="row5">
<td class="col0">- propose other collaborators for the follow-up activity</td>
</tr>
<tr class="row6">
<td class="col0">- keep minutes of discussion</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table3","secid":5,"range":"6107-6498"} -->
<p>
* 16:20 Coffee Break
</p>
<p>
<strong><em class="u">14 December 2012</em></strong>
</p>
<ul>
<li class="level1"><div class="li"> 09:00 - 11:00 Cross-presentation of the results from the test case discussions</div>
</li>
</ul>
<div class="table sectionedit6"><table class="inline">
<thead>
<tr class="row0">
<th class="col0">⇒ Selection of test cases (or operations) in 3 categories and discussion of the work plan</th>
</tr>
</thead>
<tr class="row1">
<td class="col0">a) relatively easy, workflow exists or can be adapted within weeks</td>
</tr>
<tr class="row2">
<td class="col0">b) more difficult, some tools are missing, workflows are partial, need months to adapt</td>
</tr>
<tr class="row3">
<td class="col0">c) very difficult, scalability problem, tools completely missing, requires new developments (projects over years)</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table4","secid":6,"range":"6635-7002"} --><ul>
<li class="level1"><div class="li"> 10:30 Coffee Break</div>
</li>
<li class="level1"><div class="li"> 11:00 - 13:00 Organization of the follow-up events to approach the solutions of some test cases</div>
</li>
</ul>
<div class="table sectionedit7"><table class="inline">
<tr class="row0">
<td class="col0">a) create work groups to prepare the hack-a-thon events</td>
</tr>
<tr class="row1">
<td class="col0">b) decide number of events and divide test cases or operations, plan a soon solution of one test case</td>
</tr>
<tr class="row2">
<td class="col0">c) collect emails and skype accounts</td>
</tr>
<tr class="row3">
<td class="col0">d) decide upon video meetings schedule and chairperson</td>
</tr>
<tr class="row4">
<td class="col0">e) keep minutes of discussion and decisions</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table5","secid":7,"range":"7129-7433"} --><ul>
<li class="level1"><div class="li"> 13:00 - 14:00 Lunch and end of the workshop</div>
</li>
</ul>
<p>
<br/>
<br/>
<br/>
The topics were extracted as common problems from all proposed test cases are the following:
</p>
<ul>
<li class="level1"><div class="li"> multiploidy</div>
</li>
<li class="level1"><div class="li"> data formats / standardization</div>
</li>
<li class="level1"><div class="li"> workflows</div>
</li>
<li class="level1"><div class="li"> scalability of tools (multi genome comparison/data compression)</div>
</li>
<li class="level1"><div class="li"> non model organisms</div>
</li>
<li class="level1"><div class="li"> visualization</div>
</li>
<li class="level1"><div class="li"> best practice / guide line</div>
</li>
<li class="level1"><div class="li"> data to biology and biology to data</div>
</li>
<li class="level1"><div class="li"> training</div>
</li>
</ul>
</div>
<h5 id="contact_us">Contact Us</h5>
<div class="level5">
<p>
If you are willing and able to help to work on one of the <a href="http://www.allbioinformatics.eu/doku.php?id=public:test_cases" class="wikilink1" title="public:test_cases" data-wiki-id="public:test_cases">test cases</a> and interested to create a working group capable to develop a proposal for future EU calls, please contact <strong>andreas.gisel[at]ba.itb.cnr[dot]it</strong> with the subject <strong>AllBio Bioinfo</strong>.
</p>
</div>
<h5 id="organising_committee_and_local_organisers">Organising committee and local organisers</h5>
<div class="level5">
<p>
Erik Bongcam-Rudloff,
Gert Vriend,
Laurent Falquet,
Teresa Attwood,
Eija Korpelainen,
Jacques van Helden,
Thomas Svensson,
Bernd Müller-Röber,
Susanne Hollmann,
Babette Regierer,
Paul Kersey,
Andreas Gisel
</p>
<p>
Angelica Tulipano,
Flavio Licciulli,
Sabino Liuni,
Domenica D'Elia
</p>
</div>
<!-- EDIT{"target":"section","name":"Bioinformatics Workshop \"Evaluation of Test Cases\"","hid":"bioinformatics_workshop_evaluation_of_test_cases","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:cnr
http://www.allbioinformatics.eu/doku.php?id=public:cnr&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="consiglio_nazionale_delle_ricerche_italy">CONSIGLIO NAZIONALE DELLE RICERCHE Italy</h2>
<div class="level2">
<p>
<strong><a href="http://www.itb.cnr.it" class="urlextern" title="http://www.itb.cnr.it" rel="ugc nofollow">www.itb.cnr.it</a></strong>
</p>
<p>
The ITB is the largest institute of its kind in Italy and was established to pioneer new types of cross-disciplinary biomedical research by bringing biology, engineering, medicine, and the basic sciences together. This is achieved by means of collaborations between industry and basic scientists and clinicians from a broad range of disciplines. One of the most important aims of its research mission is translating fundamental discoveries into new technologies.The Core Research Overview and the major focuses of the institute are: Cancer/Stem Cell research, Neurodegenerative Diseases, Cardiovascular medicine and Immunology combined with the development of high-throughput bioscience research such as Micro-Array and Proteomic-based technologies, novel high-throughput sequencing projects and Bioinformatics.
</p>
</div>
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<h3 class="sectionedit2" id="dr_andreas_gisel">Dr. Andreas Gisel</h3>
<div class="level3">
<p>
<strong><a href="http://www.ba.itb.cnr.it/gisel" class="urlextern" title="http://www.ba.itb.cnr.it/gisel" rel="ugc nofollow">www.ba.itb.cnr.it/gisel</a></strong>
</p>
<p>
Andreas Gisel has a degree in Biology from the Swiss Federel Institute of Technology, Zurich, Switzerland and got his PhD in Biochemistry and Molecular Biology for the same Institute. After a postdoc at US Berkeley and in Novartis SA in 2008 he got a permanent senior researcher position at ITB in Bari. He is a member of the executive board of EMBnet, the editorial board of the EMBnet.journal and member of the technical committee of IGI, the Italian GRID infrastructure. In two European project he covers leading positions as work group chair of the COST Action ‘<a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">SeqAhead</a>’, a network for NGS data analysis and work package leader of the FP7 project ‘AllBio’.
His main research interests are sequence analysis of NGS data focusing mainly on the analysis and discovery of smallRNA such as miRNA, applied gene ontology and distributed and GPU oriented bioinformatics applications.
His recent research activities are in collaboration with the plant groups in Italy and Spain working on virus and viroid infected crop plants such as orange, olive tree, wine grape to investigate the pathogen - host interaction via RNA interference.
</p>
<p>
Another collaboration on a similar topic he has with the pharmaceutical department at the University of Bari investigating the diagnostic and therapeutic aspect of miRNA in diverse cancers.
</p>
<p>
In the field of applied gene ontology he developed during the recent years a GRID based search algorithm to propose functional analogue gene products using the gene ontology as the gene product description which is compared. The search data are stored in a relational database and accessible on <a href="http://engine.ba.itb.cnr.it" class="urlextern" title="http://engine.ba.itb.cnr.it" rel="ugc nofollow">engine.ba.itb.cnr.it</a>.
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Tulipano A, Marangi C, Angelini L, Donvito G, Cuscela G, Maggi GP, Gisel A
GRID distribution supports clustering validation of large mixed microarray data sets.
EMBnet.journal 17 (1): 18-25
<a href="http://journal.embnet.org/index.php/embnetjournal/article/view/205/481" class="urlextern" title="http://journal.embnet.org/index.php/embnetjournal/article/view/205/481" rel="ugc nofollow">LINK</a>
</p>
<p>
Ruiz-Ruiz S, Navarro B, Gisel A, Peña L, Navarro L, Moreno P, Di Serio F, Flores R
Citrus tristeza virus infection induces the accumulation of viral small RNAs (21- 24-nt) mapping preferentially at the 3’-terminal region of the genomic RNA and affects the host small RNA profile.
Plant Mol Biol. 2011 Feb 15
<a href="http://www.ncbi.nlm.nih.gov/pubmed/21327514" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/21327514" rel="ugc nofollow">LINK</a>
</p>
<p>
Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction.
Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J.
PLoS One. 2009 Nov 5;4(11):e7686.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/19890399" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/19890399" rel="ugc nofollow">LINK</a>
</p>
<p>
Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis.
Di Serio F, Gisel A, Navarro B, Delgado S, Martínez de Alba AE, Donvito G, Flores R.
PLoS One. 2009 Oct 21;4(10):e7539.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/19847296" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/19847296" rel="ugc nofollow">LINK</a>
</p>
<p>
Gene analogue finder: a GRID solution for finding functionally analogous gene products.
Tulipano A, Donvito G, Licciulli F, Maggi G, Gisel A.
BMC Bioinformatics. 2007 Sep 3;8:329.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/17767718" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/17767718" rel="ugc nofollow">LINK</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"Dr. Andreas Gisel","hid":"dr_andreas_gisel","codeblockOffset":0,"secid":2,"range":"952-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:congress
http://www.allbioinformatics.eu/doku.php?id=public:congress&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="allbio_congressbroadening_the_bioinformatics_infrastructure_to_unicellular_animal_and_plant_science">AllBio Congress: "Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science"</h1>
<div class="level1">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Acongress&media=public:firenze1.png" class="media" title="public:firenze1.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:firenze1.png" class="mediacenter" loading="lazy" title="Firenze Michelangelo Square" alt="Firenze Michelangelo Square" /></a>
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio Congress: \"Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science\"","hid":"allbio_congressbroadening_the_bioinformatics_infrastructure_to_unicellular_animal_and_plant_science","codeblockOffset":0,"secid":1,"range":"51-227"} -->
<h3 class="sectionedit2" id="florence_italy">Florence, Italy</h3>
<div class="level3">
</div>
<!-- EDIT{"target":"section","name":"Florence, Italy","hid":"florence_italy","codeblockOffset":0,"secid":2,"range":"228-253"} -->
<h3 class="sectionedit3" id="june_2014">11 - 13 June 2014</h3>
<div class="level3">
<p>
<br/>
</p>
<p>
<em class="u"><strong><color red>see more at the official <a href="http://allbioinformatics.eu/florence2014/" class="urlextern" title="http://allbioinformatics.eu/florence2014/" rel="ugc nofollow">AllBio Conference site</a>!!!!</color></strong></em>
</p>
<p>
<br/>
</p>
</div>
<h5 id="venueac_hotel_firenze">Venue: AC Hotel Firenze</h5>
<div class="level5">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Acongress&media=public:achotelfirenze.png" class="media" title="public:achotelfirenze.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=9f1da6&media=public:achotelfirenze.png" class="mediaright" align="right" loading="lazy" title="AC Hotel Firenze" alt="AC Hotel Firenze" width="200" /></a>
<a href="http://www.marriott.com/hotels/travel/flrfi-ac-hotel-firenze/" class="urlextern" title="http://www.marriott.com/hotels/travel/flrfi-ac-hotel-firenze/" rel="ugc nofollow">http://www.marriott.com/hotels/travel/flrfi-ac-hotel-firenze/</a>
</p>
<p>
We will soon set up a special web site for this event with registration and more detailed information.
</p>
<p>
Stay in Contact!!
</p>
</div>
<!-- EDIT{"target":"section","name":"11 - 13 June 2014","hid":"june_2014","codeblockOffset":0,"secid":3,"range":"254-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:contact
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anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:csc
http://www.allbioinformatics.eu/doku.php?id=public:csc&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="csc_-_it_center_for_science_finland">CSC - IT CENTER FOR SCIENCE Finland</h2>
<div class="level2">
<p>
<strong><a href="http://www.csc.fi" class="urlextern" title="http://www.csc.fi" rel="ugc nofollow">www.csc.fi</a></strong>
</p>
<p>
CSC - IT Center for Science is a non-profit company administered by the Ministry of Education, Science and Culture. It provides academia, research institutes and companies with IT support and Finland's widest selection of scientific software and databases and a powerful supercomputing environment. CSC also actively participates in European research infrastructure projects such as ELIXIR (European Life Sciences Infrastructure for Biological Information) and PRACE (The Partnership for Advanced Computing in Europe). In terms of bioinformatics services CSC provides software, databases, user support and training at a national level. The bioinformatics courses cover different areas such as next generation sequencing data analysis, microarray data analysis,R programming and protein modeling.
</p>
</div>
<!-- EDIT{"target":"section","name":"CSC - IT CENTER FOR SCIENCE\tFinland","hid":"csc_-_it_center_for_science_finland","codeblockOffset":0,"secid":1,"range":"39-927"} -->
<h3 class="sectionedit2" id="dr_eija_korpelainen">Dr Eija Korpelainen</h3>
<div class="level3">
<p>
studied biochemistry at the University of Turku, Finland and received her PhD from University of Adelaide, Australia in 1996. After working as an EMBO post doctoral fellow at the University of Helsinki, she joined CSC in 2001. In her role as bioinformatics specialist Dr Korpelainen has provided nation-wide bioinformatics services including training, user support and software development. As an example of the latter, she has directed the development of <a href="http://chipster.csc.fi/" class="urlextern" title="http://chipster.csc.fi/" rel="ugc nofollow">Chipster</a>. Chipster enables biologists to access a comprehensive collection of up-to-date analysis tools, combine them to automatic, sharable workflows, and visualise results interactively. Chipster is open source and it is used in many institutes around the world for analysing and visualising next generation sequencing, microarray and proteomics data. In addition to her current position as Chipster product manager, Dr Korpelainen runs data analysis courses in Finland and abroad, and participates in international bioinformatics projects such as the COST Action <a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">SeqAhead</a>, a network for NGS data analysis, where she chairs the Software working group.
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Niemenmaa M, Kallio A, Schumacher A, Klemelä P, <strong>Korpelainen E</strong>, Heljanko K. <br/>
Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud <br/>
Bioinformatics. 2012 Feb 2.
</p>
<p>
Elo LL, Kallio A, Laajala TD, Hawkins RD, <strong>Korpelainen E</strong>, Aittokallio T. <br/>
Optimized detection of transcription factor-binding sites in ChIP-seq experiments<br/>
Nucleic Acids Res. 2012 Jan;40(1):e1.
</p>
<p>
Kallio MA, Tuimala JT, Hupponen T, Klemelä P, Gentile M, Scheinin I, Koski M, Käki J, <strong>Korpelainen EI</strong>. <br/>
Chipster: user-friendly analysis software for microarray and other high-throughput data<br/>
BMC Genomics. 2011 Oct 14;12:507.
</p>
<p>
Juhila J, Sipilä T, Icay K, Nicorici D, Ellonen P, Kallio A, <strong>Korpelainen E</strong>, Greco D, Hovatta I.<br/>
MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus<br/>
PLoS One. 2011;6(6):e21495.
</p>
<p>
Elo LL, Hiissa J, Tuimala J, Kallio A, <strong>Korpelainen E</strong>, Aittokallio T. <br/>
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets<br/>
Brief Bioinform. 2009 Sep;10(5):547-55.
</p>
</div>
<!-- EDIT{"target":"section","name":"Dr Eija Korpelainen","hid":"dr_eija_korpelainen","codeblockOffset":0,"secid":2,"range":"928-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:ebi
http://www.allbioinformatics.eu/doku.php?id=public:ebi&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="european_molecular_biology_laboratory_united_kingdom">EUROPEAN MOLECULAR BIOLOGY LABORATORY United Kingdom</h2>
<div class="level2">
<p>
<a href="http://www.ebi.ac.uk" class="urlextern" title="http://www.ebi.ac.uk" rel="ugc nofollow">http://www.ebi.ac.uk</a>
</p>
<p>
The European Bioinformatics Institute (EBI) is an academic research institute located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK), part of the European Molecular Biology Laboratory (EMBL).
</p>
<p>
The EBI's mission:
</p>
<ul>
<li class="level1"><div class="li"> To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress</div>
</li>
<li class="level1"><div class="li"> To contribute to the advancement of biology through basic investigator-driven research in bioinformatics</div>
</li>
<li class="level1"><div class="li"> To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators</div>
</li>
<li class="level1"><div class="li"> To help disseminate cutting-edge technologies to industry</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"EUROPEAN MOLECULAR BIOLOGY LABORATORY\tUnited Kingdom","hid":"european_molecular_biology_laboratory_united_kingdom","codeblockOffset":0,"secid":1,"range":"39-804"} -->
<h3 class="sectionedit2" id="prof_paul_kersey">Prof. Paul Kersey</h3>
<div class="level3">
<p>
<a href="http://www.ebi.ac.uk/Information/Staff/person_maintx.php?s_person_id=267" class="urlextern" title="http://www.ebi.ac.uk/Information/Staff/person_maintx.php?s_person_id=267" rel="ugc nofollow">Dr. Paul Kersey</a> leads the Ensembl Genomes team at the EBI, which provides services for genome-scale data from non-vertebrate species, primarily through the use of the Ensembl software platform. The team integrates data from across the taxonomic space, and collaborates closely with particular groups involved in genome annotation and the development of domain-specific resources. The team particulates in the WormBase, VectorBase and PomBase consortia (developing resources for nematodes, insect vectors of human pathogens, and the model fungus fission yeast) respectively, and coordinates the PhytoPath project (for plant pathogens), and the EC FP7 consortia Microme (focused on microbial pathways) and transPLANT (focused on plant genomics). Particular areas of interest include genome assembly, comparative genomics and variation.
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
WormBase 2012: more genomes, more data, new website
Karen Yook, Todd W Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J Chen, Paul Davis, Norie de la Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian Grove, Kevin Howe, Snehalata Kadam, Ranjana Kishore, Raymond Lee, Yuling Li, Hans-Michael Muller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul Kersey, John Spieth, Lincoln Stein, Paul W Sternberg
Nucleic Acids Research 40 D735-D741 2012.
</p>
<p>
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
Paul J Kersey, Daniel M Staines, Daniel Lawson, Eugene Kulesha, Paul Derwent, Jay C Humphrey, Daniel ST Hughes, Stephan Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew Yates, Ewan Birney
Nucleic Acids Research 40 D91-97 2012.
</p>
<p>
PomBase: a comprehensive online resource for fission yeast
Valerie Wood, Midori A Harris, Mark D McDowall, Kim Rutherford, Brendan W Vaughan, Daniel M Staines, Martin Aslett, Antonia Lock, Jürg Bähler, Paul J Kersey, Stephen G Oliver
Nucleic Acids Research 40 D695-699 2012.
</p>
<p>
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Dent A Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Faas, Hung On Ken Yu, Buffalo Vince, Daniel R Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha, Ariyaratne Wing-Kin Sung, Zemin Ning, Matthias Haimel, Jared T Simpson, Nuno A Fronseca, İnanç Birol, T Roderick Docking, Isaac Y Ho, Daniel S Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C Schatz, David R Kelly, Adam M Phillippy, Sergey Koren, Shiaw-Pyng Yang, Wei Wu, Wen-Chi Chou, Anuj Srivastava, Timothy I Shaw, J Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T Dimon, Victor Solovyev, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan MacLean, Fangfang Xia, Ruibang Luo, L Zhenyu, Yinlong Xie, Binghang Liu, Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, Paul J Kersey, Richard Durbin, Shaun D Jackman, Jarrod A Chapman, Xiaoqiu Huang, Joseph L DeRisi, Mario Caccamo, Yingrui Li, David B Jaffe, Richard Green, David Haussler, Ian Korf, Benedict Paten
Genome Res. 2011. 21: 2224-2241
</p>
<p>
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Xiangchao Gan, Oliver Stegle, Jonas Behr, Joshua G Steffen, Philipp Drewe, Katie L Hildebrand, Rune Lyngsoe, Sebastian J Schultheiss, Edward J Osborne, Vipin T Sreedharan, André Kahles, Regina Bohnert, Géraldine Jean, Paul Derwent, Paul Kersey, Eric J Belfield, Nicholas P Harberd, Eric Kemen, Christopher Toomajian, Paula X Kover, Richard M Clark, Gunnar Rätsch, Richard Mott
Nature 2011. 477:419-423.
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Paul Kersey","hid":"prof_paul_kersey","codeblockOffset":0,"secid":2,"range":"805-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:eccb-ulb
http://www.allbioinformatics.eu/doku.php?id=public:eccb-ulb&rev=1549962286&do=diff
<h5 id="eccb_2014_tutorial">ECCB 2014 Tutorial</h5>
<div class="level5">
<p>
<br/>
</p>
</div>
<h3 class="sectionedit1" id="analysis_of_cis-regulatory_motifs_from_high-throughput_sequences">Analysis of Cis-Regulatory Motifs from High-Throughput sequences</h3>
<div class="level3">
<p>
There are still some places available for this tutorial:
</p>
<p>
Date: Saturday Sept 6, 2014
Place: Forum building of the Faculty of Medicine of Strasbourg
Time: 9am – 5.30pm (registration starts from 8am)
</p>
<p>
Contact e-mail: mthomas@biologie.ens.fr
</p>
<p>
More details: <a href="http://www.eccb14.org/program/tutorials/cis-r" class="urlextern" title="http://www.eccb14.org/program/tutorials/cis-r" rel="ugc nofollow">http://www.eccb14.org/program/tutorials/cis-r</a>
</p>
<p>
How to register: <a href="http://www.eccb14.org/registration" class="urlextern" title="http://www.eccb14.org/registration" rel="ugc nofollow">http://www.eccb14.org/registration</a>
</p>
<p>
Registration includes lunch & coffee breaks on the day of the workshop
and the tutorial material (.pdf and/or print). ECCB Tutorial rates:
110 € (academic) or 60 € (student)
</p>
</div>
<h5 id="short_description">Short description</h5>
<div class="level5">
<p>
This tutorial aims at introducing the theoretical principles and
giving practical skills to use specialized software tools to extract
motifs from full-scaled NGS datasets (typically covering tens of Mb).
</p>
</div>
<h5 id="teachers">Teachers</h5>
<div class="level5">
<ul>
<li class="level1"><div class="li"> Jacques van Helden, Aix-Marseille Université (France)</div>
</li>
<li class="level1"><div class="li"> Morgane Thomas-Chollier, Ecole Normale Supérieure (France)</div>
</li>
<li class="level1"><div class="li"> Carl Herrmann, University Heidelberg (Germany).</div>
</li>
<li class="level1"><div class="li"> Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada)</div>
</li>
</ul>
</div>
<h5 id="description">Description</h5>
<div class="level5">
<p>
Next Generation Sequencing led to the development of novel methods
(ChIP-seq, FAIRE-seq, Clip-seq, ) to acquire massive data about
diverse signals involved in genome regulation and function
(cis-regulation, chromatin conformation, RNA maturation,
recombination, replication, …).
</p>
<p>
Extracting relevant information from the raw data requires not only
specialized software tools, but also a good understanding of their
principles and parameters.
</p>
<p>
In this tutorial we will demonstrate how to analyze ChIP-seq data
using the Regulatory Sequence Analysis Tools (RSAT,
<a href="http://www.rsat.eu/" class="urlextern" title="http://www.rsat.eu/" rel="ugc nofollow">http://www.rsat.eu/</a>), via their different ways of access:
web-interface, command-line, and web-services.
</p>
<p>
This tutorial aims at introducing the theoretical principles and
giving practical skills to use specialized software tools to extract
motifs from full-scaled NGS datasets (typically covering tens of Mb).
</p>
</div>
<h5 id="contents">Contents</h5>
<div class="level5">
<p>
The tutorial will be organized in 2 half days:
</p>
<p>
1) Analysis of cis-regulatory elements with the Regulatory Sequence
Analysis Tools (RSAT): methods and website utilization
(<a href="http://www.rsat.eu/" class="urlextern" title="http://www.rsat.eu/" rel="ugc nofollow">http://www.rsat.eu/</a>).
</p>
<p>
2) Using RSAT in command-line and via web services (SOAP/WSDL).
</p>
<p>
Topics:
- Motif discovery in NGS peak sets.
- Impact of the background models.
- Comparison between motifs.
- Motif enrichment in peak sequences.
- Evaluating the quality of motifs extracted from NGS peaks.
- Building control sets to estimate the rates of false positives.
</p>
</div>
<h5 id="topics_not_covered">Topics not covered</h5>
<div class="level5">
<p>
Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak
calling, functional enrichment of peaks, other tools for pattern
discovery and matching).
</p>
</div>
<h5 id="target_audience">Target audience</h5>
<div class="level5">
<p>
The course is addressed to bioinformaticians and biologists. The
afternoon will require being familiar with the Unix shell (Linux) and
basic programming skills (Perl or Python) to implement clients for web
services.
</p>
</div>
<h5 id="in_practice">In practice</h5>
<div class="level5">
<ul>
<li class="level1"><div class="li"> Participants will need to bring their own laptop.</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> All command-line programs will be run on the IFB cloud platform</div>
</li>
</ul>
<p>
(<a href="https://cloud.france-bioinformatique.fr/" class="urlextern" title="https://cloud.france-bioinformatique.fr/" rel="ugc nofollow">https://cloud.france-bioinformatique.fr/</a>) managed by Christophe
Blanchet (IBCP, Lyon, France). Each participant will be given a
(free) account to access this cloud and thereby a fully functional
virtual machine with RSAT.
</p>
<ul>
<li class="level1"><div class="li"> Wireless internet will be available at the conference venue.</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> An indicative reading list will be available a few weeks before the</div>
</li>
</ul>
<p>
tutorial.
</p>
<ul>
<li class="level1"><div class="li"> The hands-on will be organized in a cookbook mode: we will</div>
</li>
</ul>
<p>
distribute protocols explaining the steps to solve selected test
cases.
</p>
<ul>
<li class="level1"><div class="li"> For the practicals, we ensure that there is no need to transfer data</div>
</li>
</ul>
<p>
from the conference room to the servers.
</p>
</div>
<h5 id="funding">Funding</h5>
<div class="level5">
<p>
This tutorial is funded by the <strong>ALLBIO</strong> project
(<a href="http://www.allbioinformatics.eu/" class="urlextern" title="http://www.allbioinformatics.eu/" rel="ugc nofollow">http://www.allbioinformatics.eu/</a>), whose goal is to establish the
link between bioinformatics and biologist communities who express
uncovered needs for other fields than human genomics (microbial,
plant, livestock).
</p>
</div>
<!-- EDIT{"target":"section","name":"Analysis of Cis-Regulatory Motifs from High-Throughput sequences","hid":"analysis_of_cis-regulatory_motifs_from_high-throughput_sequences","codeblockOffset":0,"secid":1,"range":"29-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:eu-us
http://www.allbioinformatics.eu/doku.php?id=public:eu-us&rev=1549962286&do=diff
<h3 class="sectionedit1" id="allbio_participates_the_eu-us_animal_biotechnology_working_group">AllBio participates the EU-US Animal Biotechnology Working Group</h3>
<div class="level3">
<p>
The EU-US Animal Biotechnology Working Group, part of the EU-US task force on biotechnology, organizes a workshop on “A potential shared international cyber-infrastructure” 12 - 13 September 2012 at Hinxton, <abbr title="Gigabyte">GB</abbr>. This event is organized in connection with the life stock meeting organized by EBI (<a href="http://www.ebi.ac.uk/~laura/livestock_meeting_2012.html" class="urlextern" title="http://www.ebi.ac.uk/~laura/livestock_meeting_2012.html" rel="ugc nofollow">http://www.ebi.ac.uk/~laura/livestock_meeting_2012.html</a>).
</p>
<p>
The EU Commission invited AllBio to participate this workshop and will be represented by the AllBio coordinator Erik Bongcam-Rudloff. He will present during the second day of the event “Test cases will describe complex bio-informatics problems. AllBio present the solutions of some Test Cases”
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:events
http://www.allbioinformatics.eu/doku.php?id=public:events&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="events">Events</h2>
<div class="level2">
</div>
<!-- EDIT{"target":"section","name":"Events","hid":"events","codeblockOffset":0,"secid":1,"range":"51-70"} -->
<h3 class="sectionedit2" id="to_come">To come</h3>
<div class="level3">
<ul>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:val" class="wikilink1" title="public:val" data-wiki-id="public:val">Validation and Training Workshops</a></strong> click to see more</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"To come","hid":"to_come","codeblockOffset":0,"secid":2,"range":"71-164"} -->
<h3 class="sectionedit3" id="passed">Passed</h3>
<div class="level3">
<ul>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:agm2" class="wikilink1" title="public:agm2" data-wiki-id="public:agm2">AllBio Consortium Meeting</a></strong> 29 - 30 September 2014</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.tgac.ac.uk/allbio-open-science-reproducibility-best-practice-workshop/" class="urlextern" title="http://www.tgac.ac.uk/allbio-open-science-reproducibility-best-practice-workshop/" rel="ugc nofollow">Open Science & Reproducibility Best Practice Workshop</a></strong> 15 - 17 September 2014, Norwich, UK</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://web.csc.fi/english/csc/courses/archive/chipseq2014" class="urlextern" title="http://web.csc.fi/english/csc/courses/archive/chipseq2014" rel="ugc nofollow">ChIP- and DNase-seq data analysis workshop</a></strong>, 16 - 19 September 2014, CSC, Helsinki, Finland</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:eccb-ulb" class="wikilink1" title="public:eccb-ulb" data-wiki-id="public:eccb-ulb">Analysis of Cis-Regulatory Motifs from High-Throughput sequences</a></strong>, 6 Sept 2014 Strasbourg, France</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.iscb.org/ngs2014-program/ngs2014-tutorials" class="urlextern" title="http://www.iscb.org/ngs2014-program/ngs2014-tutorials" rel="ugc nofollow">AllBio Tutorial on "Non-coding RNA data analysis"</a></strong> during NGS2014, an ISCB event - 4 June 2014, Barcelona Spain</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:congress" class="wikilink1" title="public:congress" data-wiki-id="public:congress">AllBio Congress</a></strong> - 11 - 13 June 2014, Florence, Italy</div>
</li>
<li class="level1"><div class="li"> <strong>AllBio Workshop: <a href="http://www.allbioinformatics.eu/doku.php?id=public:valid-ulb" class="wikilink1" title="public:valid-ulb" data-wiki-id="public:valid-ulb">Analyzing thousands of bacterial genomes:
gene annotation, metabolism, regulation</a></strong> - 23 - 25 June 2014, Marseille, France</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://allbioinformatics.eu/bari2014/" class="urlextern" title="http://allbioinformatics.eu/bari2014/" rel="ugc nofollow">Epigenetics, coding and non-coding RNAs- Challenging NGS data</a></strong> - 25 - 27 June 2014, Bari, Italy</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.ebi.ac.uk/training/course/Agri-Omics" class="urlextern" title="http://www.ebi.ac.uk/training/course/Agri-Omics" rel="ugc nofollow">AllBio Plant and Pathogen Bioinformatics training course - 8. - 11. July 2014 - EBI, Hinxton, GB</a></strong> </div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:bigdata" class="wikilink1" title="public:bigdata" data-wiki-id="public:bigdata">Managing Big Data - AllBio Tutorial "New methods in genome annotation"</a></strong> 9 - 11 July 2014, Berlin, Germany</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:valid-ki" class="wikilink1" title="public:valid-ki" data-wiki-id="public:valid-ki">AllBio Metagenome data analysis! - 21. - 23. May 2014 - Science for Life Laboratory, Stockholm, Sweden</a></strong> </div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://teacher.bmc.uu.se/ALLBIO2014/" class="urlextern" title="http://teacher.bmc.uu.se/ALLBIO2014/" rel="ugc nofollow">Bioinformatics approaches to Identify causative sequence variants in farm animals</a></strong> Training course, Uppsala Sweden, 12 - 16. May 2014 <a href="http://www.allbioinformatics.eu/doku.php?id=public:valid-slu" class="wikilink1" title="public:valid-slu" data-wiki-id="public:valid-slu">Images</a><a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aevents&media=public:dsc_4589.jpg" class="media" title="public:dsc_4589.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=9897d1&media=public:dsc_4589.jpg" class="mediaright" align="right" loading="lazy" alt="" width="200" /></a></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://teacher.bmc.uu.se/BIGDATA/Managing_Big_Data.pdf" class="urlextern" title="http://teacher.bmc.uu.se/BIGDATA/Managing_Big_Data.pdf" rel="ugc nofollow">Managing Big Data: Setting the standards for analysing and integrating big data</a></strong> Workshop: 28-29 April and tutorials: 29-30 April 2014, University of Potsdam, Campus Golm Karl-Liebknecht-Str. 24-25 House 25 Room D 002. Germany</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://web.csc.fi/english/csc/courses/archive/rnaseq2014" class="urlextern" title="http://web.csc.fi/english/csc/courses/archive/rnaseq2014" rel="ugc nofollow">RNA-seq data analysis workshop</a></strong> 8th - 10th January 2014, Espoo, Finland</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:hack6" class="wikilink1" title="public:hack6" data-wiki-id="public:hack6">HACKATHON2 Test Cases #9 and #12</a></strong> - 27-29 November - Alnarp, Sweden</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:tc5-15" class="wikilink1" title="public:tc5-15" data-wiki-id="public:tc5-15">HACKATHON Test Cases 5 and 15</a></strong> - 7-8 October - Uppsala, Sweden</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:agm2013" class="wikilink1" title="public:agm2013" data-wiki-id="public:agm2013">AllBio AGM</a></strong> - 27 September - London, UK</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:workiscb" class="wikilink1" title="public:workiscb" data-wiki-id="public:workiscb">AllBio at ISCB2013</a></strong> - 29 August 2013 - Copenhagen, Denmark</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:hack3" class="wikilink1" title="public:hack3" data-wiki-id="public:hack3">Hackathon session #3: Test Case #2</a></strong> - 28 - 30 August 2013 - Nijmegen, the Netherlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:hack4" class="wikilink1" title="public:hack4" data-wiki-id="public:hack4">Hackathon session #4: Test Cases #9 and #12</a></strong> - 19 - 21 September 2013 - Amsterdam, the Netherlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:hack2" class="wikilink1" title="public:hack2" data-wiki-id="public:hack2">Hackathon session #2: Test Cases #8 and #13</a></strong> - 18 - 19 April 2013 - Bari, Italy</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.seqahead.it/cost-bari-2013/" class="urlextern" title="http://www.seqahead.it/cost-bari-2013/" rel="ugc nofollow">AllBio and SeqAhead joint workshop on "NGS and non-coding RNA data analysis"</a></strong> April 17 - 18 2013, Bari, Italy</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:hack" class="wikilink1" title="public:hack" data-wiki-id="public:hack">Hackathon session #1: Test Cases #1 and #2</a></strong> - 18-20 March 2013 - Amsterdam, The Netherlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:plantomicsebi" class="wikilink1" title="public:plantomicsebi" data-wiki-id="public:plantomicsebi">AllBio sponsored EBI course on data resources and tools for plant-omics</a></strong> - 18-22 February 2013 - Hinxton, United Kingdom</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:bioinf" class="wikilink1" title="public:bioinf" data-wiki-id="public:bioinf">Bioinformatics Workshop "Evaluation of Test Cases"</a></strong> - 12 -14 December 2012 Milan, Italy</div>
</li>
<li class="level1"><div class="li"> Networking Meeting - 29 -30 November 2012 Amsterdam, Nederlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:onto1" class="wikilink1" title="public:onto1" data-wiki-id="public:onto1"> AllBio Ontology Workshop: “Using Biomedical Ontologies for Improved Bioinformatics Databases Interoperability”</a></strong> - 3-5 October 2012 Garching (Munich), Germany</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:plantpathebi" class="wikilink1" title="public:plantpathebi" data-wiki-id="public:plantpathebi">AllBio sponsored EBI PhytoPath Training Course</a></strong> - 19-20 September 2012 - Hinxton, United Kingdom</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:agm2012" class="wikilink1" title="public:agm2012" data-wiki-id="public:agm2012">AllBio Annual Genereal Meeting</a></strong> - 21 September 2012 - Amsterdam, the Netherlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:localeventsitb" class="wikilink1" title="public:localeventsitb" data-wiki-id="public:localeventsitb">Local community building event Italy</a></strong> - June 2012 Bari, Italy</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:testcaseanalysis" class="wikilink1" title="public:testcaseanalysis" data-wiki-id="public:testcaseanalysis">AllBio consortium Meeting: Test Case Analysis</a></strong> - 3 June Uppsala, Sweden </div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:localeventsslu" class="wikilink1" title="public:localeventsslu" data-wiki-id="public:localeventsslu">Local community building event Sweden</a></strong> - 3 May 2012 Uppsala, Sweden</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:localeventsrunmc" class="wikilink1" title="public:localeventsrunmc" data-wiki-id="public:localeventsrunmc">Local community building event Netherlands</a></strong> - 10 April 2012 Utrecht, Netherlands</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:initial_ontology" class="wikilink1" title="public:initial_ontology" data-wiki-id="public:initial_ontology">Initial Ontology Workshop</a></strong> - March 2012</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:localeventssib" class="wikilink1" title="public:localeventssib" data-wiki-id="public:localeventssib">Local community building event Switzerland </a></strong> - 30 March 2012</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:localevents" class="wikilink1" title="public:localevents" data-wiki-id="public:localevents">Local events for AllBio community building</a></strong> - February - June 2012</div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:kick-off" class="wikilink1" title="public:kick-off" data-wiki-id="public:kick-off">Kick-off meeting</a></strong> in Brussels - 10 November 2011</div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"Passed","hid":"passed","codeblockOffset":0,"secid":3,"range":"165-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:febs
http://www.allbioinformatics.eu/doku.php?id=public:febs&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h3 class="sectionedit1" id="pathogen-host-interactions_of_major_animal_infectious_diseases_and_zoonoses">Pathogen-host-interactions of major animal infectious diseases and zoonoses</h3>
<div class="level3">
<p>
<strong>Island of Spetses, Greece, 9-15 September 2012</strong>
</p>
<p>
Advanced lecture course intended for Ph.D. students and postdoctoral scientists
</p>
<p>
<strong>Registration: <a href="http://www.kas.unibe.ch/FEBS2012/" class="urlextern" title="http://www.kas.unibe.ch/FEBS2012/" rel="ugc nofollow">http://www.kas.unibe.ch/FEBS2012/</a></strong>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:spetses_flyer.pdf" class="media mediafile mf_pdf" title="public:spetses_flyer.pdf (89.1 KB)">spetses_flyer.pdf</a>
</p>
</div>
<h4 id="aim_of_the_conference">Aim of the conference</h4>
<div class="level4">
<p>
Infections of domestic and wild animals are shaped by co-evolution between host and pathogen, unlike the usual experimental rodent models. In recent years, the genetics of several animal species, as well as that of their pathogens, has reached a level that permits the study of host-pathogen interactions at the molecular level. The aim of the course is to provide a forum for discussions of bacterial, viral and parasitic infections in their natural animal hosts. Emphasis will be on examples and approaches that are at the frontier of current knowledge, including genomics, bioinformatics and structural biology. In addition, key molecular mechanisms underlying host and tissue specificity leading to the emergence of new microbial infections will be discussed. Bringing together top scientists that work on viral, bacterial or parasitic infections will not only stimulate scientific interaction, but will demonstrate to the students that being able to integrate knowledge acquired in the “viral, bacterial and parasitic worlds” is essential for a successful career in host- pathogen research.
The FEBS 2012 summer-school is organized as an intensive lecture and training course limited to 60 successful applicants in the fields of animal or zoonotic pathogen-host interaction research.
</p>
<p>
<strong>Organizers:</strong> Joachim Frey, Institute of Veterinary Bacteriology, and Ernst Peterhans, Institute of Veterinary Virology, Universität Bern, Switzerland; Julian Rood and Ben Adler, ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Melbourne, Australia; Efstathios S. Gonos, National Hellenic Research Foundation, Athens, Greece
</p>
</div>
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http://www.allbioinformatics.eu/doku.php?id=public:hack&rev=1549962286&do=diff
<h3 class="sectionedit1" id="hackathon_session_1test_cases_1_and_2">Hackathon session #1: Test Cases #1 and #2</h3>
<div class="level3">
<p>
March 18-20 2013 ALLBIO will organize three meetings in parallel in Hotel Eden in Amsterdam. One meeting will be an EMBRACE-style technology workshop on computing interoperability issues for the life-sciences. The other two will be hackathons for two of the ALLBIO testcases. The idea is to have breakfast, lunch, dinner, and two short sessions all-together to generate synergy.
We have ensured ample access to the Amsterdam super computer at SARA called Lisa. Lisa does not have the fastest chips, but she has very many of them. We will get an account about a month in advance to start installing things if needed.
</p>
<p>
<strong>Location</strong><br/>
Eden hotel<br/>
Amstel 144<br/>
1017 AE Amsterdam<br/>
T: +31 (0)20 5307830 <br/>
F: +31 (0)20 5307819 <br/>
</p>
<p>
And if you want to pre-enjoy the luxury of this place, look at:
</p>
<pre class="code"> www.edenhotelamsterdam.com
www.edenrembrandtsquare.com
www.floamsterdam.com </pre>
</div>
<h5 id="hackathons">Hackathons</h5>
<div class="level5">
<p>
<br/>
<strong>Coordination</strong><br/>
Gert Vriend<br/>
Gregoire Rossier<br/>
</p>
<p>
The three day <strong>schedule</strong> will be (very roughly, hackathons tend to live their own life…):
</p>
<pre class="code"> Monday 18
13-14 lunch
14-14:30 Introduction (Gert, Greg; joint with other hackathon)
14:30-15 Problem specific introduction (Endre)
15-18 Getting on with it
18-19 Time to dress up for dinner
19-24 Get together in the local Italian restaurant with other two meetings
Tuesday 19
9-10 Recap and planning
10-13 Hacking
13-14 Lunch
14-16 If needed, help from the EMBRACEionists
16-18 Hacking
18-19 Time to dress up for dinner
19-24 Get together in the local non-Italian restaurant with other two meetings
Wednesday 20
9-10 Recap and planning
10-13 Hacking
13-14 Lunch
14-16 Recap and writing final report </pre>
</div>
<h5 id="hackathon_test_case_1faire-seq_data_analyser">Hackathon / Test case #1: FAIRE-seq data analyser</h5>
<div class="level5">
<p>
Location Board 1, Eden hotel
</p>
<p>
<strong>Participants</strong><br/>
Endre Barta (TC leader)<br/>
Amin Omidbakhshfard (TC proposer)<br/>
Matti Kankainen<br/>
Nooshin Omranian<br/>
Attila Horvath<br/>
</p>
<p>
<strong>Project description</strong><br/>
Basically our case is about to develop a pipeline for FAIRE-seq analysis. I have earlier developed a pipeline for ChIP-seq analysis (see the reference below), which we are using now in the University of Debrecen for hundreds of samples successfully. During the Milano meeting we have discussed that in generally we can use the same tools for FAIRE-seq as in the case of ChIP-seq analysis. During the hackathon we would try different programs for example for peak calling and for denovo motif finding by using of the real data. Amin promised me sending the link to download the data in advance for being able to try it. It would be needed for writing the description.<br/>
In the meanwhile we had also discussed it with Eija and concluded that the best solution would be to integrate the pipeline in some extent into the Chipster or at least use tools already integrated in Chipster for the analysis. I will contact Eija later this week and we will further discuss it.
As for the hardware requirements, as a minimum, having access to a good internet connection would be enough to connect to the Chipster server in the CSC and to our server (for the command line work) in the University of Debrecen. Having a small linux server available on site (in case we will be working in a hotel) would be a benefit, but we should then install basic NGS tools and /or the chipster server (it is possible to use the chipster virtual machine).<br/>
I have a PhD student Gergely Nagy, who is working on developing such pipelines. He will work also on the data and he would also come to Amsterdam if possible.
</p>
</div>
<h5 id="hackathon_test_case_2identification_of_large_structural_variations">Hackathon / Test case #2: Identification of large structural variations</h5>
<div class="level5">
<p>
Location Board 2, Eden hotel
</p>
<p>
<strong>Participants</strong><br/>
Yael Maoz (TC leader)<br/>
Jozefus Schippers (TC proposer)<br/>
Laurent Falquet<br/>
Dimitrios Vlachakis<br/>
Sophia Kossida<br/>
Shumaila Sayyab<br/>
Ilari Scheinin (Is already in Amsterdam, might drop by, Chipster expert)<br/>
</p>
<p>
<strong>Project description</strong>
</p>
<p>
<em>Overview</em><br/>
Although many tools designed for structural variation analysis there are no guidelines for bench scientists to help them choose the best tool for their particular data set. In this test case, a researcher is eager to identify large structural variants in multiple accessions of Arabidopsis. What is needed is a tool which can identify the type and quality of the sequencing reads, assemble them with regards to a reference genome, identify SNPs, short indels and large indels, and determine if any annotated genes are associated with the large indels. Lastly, it is desirable that the tool should have a user-friendly interface with which bench scientists can easily examine structural variants in their accession(s) of interest that need to be validated. The long term goal would be to scale up this process to analyse multiple genomes at a time (for example, multiple time points, treatments, or related individuals).<br/>
Rough Sketch of the Plan:<br/>
Initially we need to first identify which tools for analyzing SVs do the best analysis and provide the most information or closest to the outcome the researcher is looking for. Then we can work on incorporating the additional features requested (such as the gene annotation within INDELs) and how to make it into a user-friendly interface. So, to that end, we need test data. It is likely we will go with the Arabidopsis data (here and here) as it seems to be fairly well validated already even the large indels. At the first hackathon we will test multiple programs and see which performs best according to our needs. Another hackathon will deal with incorporating additional features and also allowing for multiple genome analysis in a single run (such as comparing 6 genome to each other and a reference at once). Lastly, we can look at incorporating all of this into a user friendly - click and go type program and setting up an online repository for the data.<br/>
</p>
<p>
<em>To Do List</em><br/>
1) Check quality of genomes and apply quality control as needed using fastq<br/>
2) Align reads using BWA<br/>
3) Quality check alignments<br/>
4) Run SV programs<br/>
5) Format output as needed for visualization<br/>
6) Test accuracy of output against data from <a href="http://genome.cshlp.org/content/22/3/508.full" class="urlextern" title="http://genome.cshlp.org/content/22/3/508.full" rel="ugc nofollow">http://genome.cshlp.org/content/22/3/508.full</a> (Supp. Table 7)<br/>
7) Write up SWAT analysis<br/>
<br/>
<em>Technical Description</em><br/>
Using the genomic comparison previously performed on the Arabidopsis accessions Columbia and Landsberg as a test dataset, we will run and evaluate 12 structural variation analysis programs aligning Landsberg (Ler) to the reference genome Columbia (Col) - see Data section below.<br/>
We will need the following SV programs installed (with parallelizing capabilities when possible):<br/>
</p>
<p>
Delly<br/>
InGap (Java)<br/>
BreakDancer<br/>
GenomeSTRIP<br/>
Tigra-SV<br/>
GASV<br/>
Hydra<br/>
SVMerge<br/>
SVDetect<br/>
CNVSeq<br/>
CNVnator<br/>
SVM2<br/>
<br/>
Additionally we will need BWA, samtools, fastqc, picard, perl, python, java and R. We estimate that we will need 512 <abbr title="Gigabyte">GB</abbr> as we will be generating lots of intermediary files using the tools. We would like to run these as jobs (qsub or bsub) on a cluster. It would be great if the set up would allow us to copy the files to a temporary directory while running the job so that each job can independently use the same data.<br/>
Data:<br/>
4 Ler genomes of Arabidopsis thaliana that were obtained with Illumina PE and MP sequencing (200bp to 5Kbp libraries): <a href="http://www.1001genomes.org/projects/MPISchneeberger2011/index.html" class="urlextern" title="http://www.1001genomes.org/projects/MPISchneeberger2011/index.html" rel="ugc nofollow">http://www.1001genomes.org/projects/MPISchneeberger2011/index.html</a> We will use the Col-0 line for the reference.<br/>
Background<br/>
We have recently published two articles on gene regulatory networks on the regulatory network guiding the insulin producing cells and the regulatory region analysis of Wnt5 genes, revealing the conservation of a regulatory module with putative implication in pancreas development.<br/>
1) Kapasa M, Vlachakis D, Kostadima M, Sotiropoulou G, Kossida S, Towards the elucidation of the regulatory network guiding the insulin producing cells, Genomics. 2012, 1(2), 35-47<br/>
2) Kapasa M, Arhondakis S, Kossida S, Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development, Biol Direct. 2010 4;5:49<br/>
</p>
</div>
<h5 id="the_embrace_meeting">The EMBRACE meeting</h5>
<div class="level5">
<pre class="code"> Monday 18
12-14 lunch
14-16 Introduction seminars of the new club members
16-18 Discussion on the outcome of the previous two meetings
18-19 Time to dress up for dinner
19-24 Get together in the local Italian restaurant
Tuesday 19
10-13 Seminars
13-14 Lunch
14-16 Helping out at the hackathons
16-18 Seminars
18-19 Time to dress up for dinner
19-24 Get together in the local non-Italian restaurant
Wednesday 20
09-11 Helping out at the hackathons
11-13 Final discussions (including one on the future of this series)
13-... Lunch </pre>
<p>
<strong>Participants</strong><br/>
Tanya Goldberg<br/>
Guy Yadav<br/>
Jan Krüger<br/>
Madis Rumming<br/>
Jose Maria Fernandez<br/>
Matus Kalas<br/>
Kristoffer Rapacki<br/>
Kalle Happonen<br/>
Jon Ison<br/>
Pawel Sztromwasser<br/>
Dmitry Repchevski<br/>
Gert Vriend<br/>
Tim te Beek<br/>
</p>
<p>
Seminars (puting them in some order will be the work of the first ten minutes of the meeting):<br/>
</p>
<p>
Jon Ison: EDAM ontology: update and plans<br/>
Jon Ison: BioMedBridges service registry (<a href="http://wwwdev.ebi.ac.uk/fgpt/toolsui/" class="urlextern" title="http://wwwdev.ebi.ac.uk/fgpt/toolsui/" rel="ugc nofollow">http://wwwdev.ebi.ac.uk/fgpt/toolsui/</a>)<br/>
Gert Vriend: The question domain, or in other words, why are we doing this?<br/>
Guy Yadav: Web service sustainability (survivability)<br/>
Madis Rumming: CeBiTec history, present, and future<br/>
Jan Krüger: Technological issues related to CeBiTec move to the Cloud<br/>
Kalle Happonen: Elixir and the Finish cloud-based delivery model for compute and capacity<br/>
Dmitry Repchevski: INB Semantic Web Registry (WSDL 2, WSDL2 RDF etc)<br/>
Kristoffer Rapacki: Danish ELIXIR Node<br/>
Matus Kalas: BioXSD take-off<br/>
Pawel Sztromwasser: Bergen experience with Amazon and the Finish Cloud<br/>
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:hack2
http://www.allbioinformatics.eu/doku.php?id=public:hack2&rev=1549962286&do=diff
<h3 class="sectionedit1" id="hack-a-thon_session_2_for_test_cases_8_and_13">Hack-a-thon session #2 for Test Cases #8 and #13</h3>
<div class="level3">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Ahack2&media=public:hack_bari.jpg" class="media" title="public:hack_bari.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=e8aa90&media=public:hack_bari.jpg" class="mediacenter" loading="lazy" alt="" width="500" /></a>
</p>
<p>
The AllBio Hack-a-thon was proceeded by a <a href="http://www.seqahead.it/cost-bari-2013/" class="urlextern" title="http://www.seqahead.it/cost-bari-2013/" rel="ugc nofollow">SeqAhead Workshop</a> on the topic of “NGS and non-coding RNA data analysis.
</p>
<p>
<br/>
</p>
<p>
AllBio bioinformatics hack-a-thon working on a test case selected by the AllBio community.
</p>
<div class="table sectionedit2"><table class="inline">
<tr class="row0">
<td class="col0">09:00 – 09:10</td><td class="col1">Andreas Gisel, CNR – ITB, Bari</td><td class="col2">Introduction</td>
</tr>
<tr class="row1">
<td class="col0">09:10 – 09:30</td><td class="col1">Annalisa Giampetruzzi, CNR – IVV, Bari</td><td class="col2">Presentation Test Case 13</td>
</tr>
<tr class="row2">
<td class="col0">09:30 – 10:00</td><td class="col1"> </td><td class="col2">Analysis of the workflow of Test Case 13</td>
</tr>
<tr class="row3">
<td class="col0">10:00 – 12:30</td><td class="col1 leftalign"> </td><td class="col2">Hack-a-thon (coffee break 11:00 – 11:30)</td>
</tr>
<tr class="row4">
<td class="col0">12:30 – 13:00</td><td class="col1 leftalign"> </td><td class="col2">Conclusion</td>
</tr>
<tr class="row5">
<td class="col0">13:00 – 14:00</td><td class="col1 leftalign" colspan="2"> </td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table","secid":2,"range":"349-673"} -->
<p>
<br/>
The hack-a-ton will be held with the precious collaboration of:
</p>
<ul>
<li class="level1"><div class="li"> Marc Friedlander, Centre for Genomic Regulation, Barcelona (Spain)</div>
</li>
<li class="level1"><div class="li"> Thomas J Hardcastle, University of Cambridge (United Kingdom)</div>
</li>
<li class="level1"><div class="li"> Vesselin Baev - University of Plovdiv (Bulgaria)</div>
</li>
<li class="level1"><div class="li"> Annalisa Giampetruzzi, IVV – CNR, Bari (Italy)</div>
</li>
<li class="level1"><div class="li"> Domenico Catalano, IGV – CNR, Bari (Italy)</div>
</li>
<li class="level1"><div class="li"> Angelica Tulipano, ITB – CNR, Bari (Italy)</div>
</li>
<li class="level1"><div class="li"> Flavio Licciulli, ITB – CNR, Bari (Italy)</div>
</li>
<li class="level1"><div class="li"> Domenica D’Elia, ITB – CNR, Bari (Italy)</div>
</li>
<li class="level1"><div class="li"> Andreas Gisel, ITB – CNR, Bari (Italy)</div>
</li>
</ul>
<p>
<br/>
</p>
<p>
The hackatin session #2 for test cas 8 and 13 will be a joint event with the SeqAhead workshop 17 - 18 Aprikl 2013 in Bari, Italy
</p>
</div>
<h5 id="test_cases">TEST CASES</h5>
<div class="level5">
<ol>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc8" class="wikilink1" title="public:loadedtestcases:tc8" data-wiki-id="public:loadedtestcases:tc8">Discover non-coding RNA in yeast</a></strong></div>
</li>
</ol>
<ol>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc13" class="wikilink1" title="public:loadedtestcases:tc13" data-wiki-id="public:loadedtestcases:tc13">Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones</a></strong></div>
</li>
</ol>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:hack3
http://www.allbioinformatics.eu/doku.php?id=public:hack3&rev=1549962286&do=diff
<h3 class="sectionedit1" id="hack-a-thon_session_3_for_test_case_2">Hack-a-thon session #3 for Test Case #2</h3>
<div class="level3">
</div>
<h5 id="august_2013_in_nijmegen_the_netherlands">28 - 30 August 2013 in Nijmegen, the Netherlands</h5>
<div class="level5">
<p>
<br/>
<br/>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc2" class="wikilink1" title="public:loadedtestcases:tc2" data-wiki-id="public:loadedtestcases:tc2">Test Case #2</a>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Ahack3&media=public:dsc_0220.jpg" class="media" title="public:dsc_0220.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=b96237&media=public:dsc_0220.jpg" class="medialeft" align="left" loading="lazy" title="First Hack-a-thon in Amsterdam" alt="First Hack-a-thon in Amsterdam" width="300" /></a>In August we organise the third hack-a-thon, which is actually the second round of the <a href="http://www.allbioinformatics.eu/doku.php?id=public:hack" class="wikilink1" title="public:hack" data-wiki-id="public:hack">first hack-a-thon</a>. This hack-a-thon will take place in Nijmegen at <a href="http://www.cmbi.ru.nl/" class="urlextern" title="http://www.cmbi.ru.nl/" rel="ugc nofollow">CMBI</a>.
</p>
<p>
The hotel is twenty minutes walking (or a few minutes by car) away.
</p>
<p>
<a href="http://www.hotelcourage.nl/sionshof/" class="urlextern" title="http://www.hotelcourage.nl/sionshof/" rel="ugc nofollow">Hotel Sionshof</a>
</p>
<p>
Nijmeegsebaan 53
6564 CC Nijmegen
the Netherlands
+31 (0)24 3227727
<br/>
<br/>
</p>
<p>
We will start Tuesday Aug 27 at 10.15 am.
</p>
<p>
The meeting ends Thursday Aug 29 at 17:00.
</p>
<p>
Food will be organised by the hosting institute throughout.
</p>
<p>
TC Leader: Yael Maoz
</p>
<p>
Participants:<br/>
Yael Maoz<br/>
Monika Brandt<br/>
Tobias Rausch<br/>
Yogesh Paudel<br/>
Laurant Falquet<br/>
Leon Mei<br/>
Wai Yi<br/>
Alexander Schoenhuth<br/>
</p>
<p>
<strong>Project description</strong>
</p>
<p>
Although many tools designed for structural variation analysis there are no guidelines for bench scientists to help them choose the best tool for their particular data set. In this test case, a researcher is eager to identify large structural variants in multiple accessions of Arabidopsis. What is needed is a tool which can identify the type and quality of the sequencing reads, assemble them with regards to a reference genome, identify SNPs, short indels and large indels, and determine if any annotated genes are associated with the large indels. Lastly, it is desirable that the tool should have a user-friendly interface with which bench scientists can easily examine structural variants in their accession(s) of interest that need to be validated. The long term goal would be to scale up this process to analyse multiple genomes at a time (for example, multiple time points, treatments, or related individuals).
</p>
<p>
<strong>Background from the first hackathon</strong>
</p>
<p>
In the first hackathon, a benchmarking study was performed on synthetic and biological data to test several existing structural variant analysis tools. However, these tools are largely limited to diploid genome analysis and are unable to identify large structural variants (>1Kb) in addition to being unable to identify more complex variants, such as inversions, translocations and copy number variants.
</p>
<p>
<strong>Objective of the second hackathon</strong>
</p>
<p>
Examining larger structural variants and incorporating additional types structural variants, including inversions, translocations and copy number variants into the analysis pipeline we had previously developed. Tools currently available to identify these types of variants include inGAP, SVdetect, CNVnator, CNVseq, DWACseq. We would use simulated data and perform biological testing on a small subset of the tetraploid wheat genome. Following successful testing of the synthetic and validation in a biological setting, we would convert the pipeline into a bench-scientist friendly graphical user interface.
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:hack4
http://www.allbioinformatics.eu/doku.php?id=public:hack4&rev=1549962286&do=diff
<h3 class="sectionedit1" id="hack-a-thon_session_4_for_test_cases_9_and_12">Hack-a-thon session #4 for Test Cases #9 and #12</h3>
<div class="level3">
</div>
<h5 id="september_2013_in_amsterdam_the_netherlands">19 - 21 September 2013 in Amsterdam, the Netherlands</h5>
<div class="level5">
<p>
<br/>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9" class="wikilink1" title="public:loadedtestcases:tc9" data-wiki-id="public:loadedtestcases:tc9">Test Case #9</a>
</p>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12" class="wikilink1" title="public:loadedtestcases:tc12" data-wiki-id="public:loadedtestcases:tc12">Test Case #12</a>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Ahack4&media=public:datacenter.jpeg" class="media" title="public:datacenter.jpeg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:datacenter.jpeg" class="medialeft" align="left" loading="lazy" alt="" /></a>In September we will organise the fourth hack-a-thon. This hack-a-thon will take place in Amsterdam at SARA.
</p>
<p>
Go to Google maps. Find Watergraafsmeer in Amsterdam and in Watergraafsmeer the Science Park. In the top right corner of the triangular half of the science park you find a boomerang-shaped building. That's it.
</p>
<p>
SARA and the eScience Centre share the building. Google places SARA at the location where we will get a room for the hack-a-thon, and if you search for eScience Centre Amsterdam you find the building where the eScience centre (who will help us too) and SARA (who will officially host us) are housed.
</p>
<p>
<a href="http://www.hotelcasa400.nl" class="urlextern" title="http://www.hotelcasa400.nl" rel="ugc nofollow">Hotel CASA 400</a>
Eerste Ringdijkstraat 4
1097 BC Amsterdam
</p>
<p>
TC Leaders: Oren Tzfadia and Erik Alexandersson
</p>
<p>
<strong>Participants:</strong><br/>
Monika Brandt<br/>
Agnieszka Danek (Silesian University of Technology, Gliwice, Poland)<br/>
Estelle Wera (SLU)<br/>
Itziar Frades (SLU)<br/>
Didi Amar (Weizmann Institute)<br/>
Tatyana Goldberg (Technische Universitaet Muenchen)<br/>
Erik Alexandersson (SLU)<br/>
Oren Tzfadia (Weizmann Institute)<br/>
Sanjeev Kumar Sharma (James Hutton Institut)<br/>
Gregoire Rossier (SIB)
</p>
<p>
It will start Thursday Sept 19 at 12:00 at SARA.
</p>
<p>
We will end Saturday with lunch (around 13).
</p>
<p>
<strong>Provisional program, schedule is flexible</strong>
</p>
<p>
<strong>
<em>Wednesday 18 September</em></strong><br/>
Arrival of first participants<br/>
</p>
<p>
<strong><em>Thursday 19 September</em></strong><br/>
morning: Arrival of participants<br/>
12:00: Lunch at SARA<br/>
12:45: Welcome and AllBio project overview (Greg)<br/>
<strong>13:00 - 18:00</strong> <strong>Hackathon part 1</strong><br/>
13:00: Introductory slides (Oren)<br/>
13:30: Overview of the test case (Erik)<br/>
13:45: Overview of the data sets, pre-processing and validation scheme (Didi, Oren)<br/>
14:20: Coffee break<br/>
14:35: Organize all data set on computers and SARA server. 1st round or pre-processing runs. In parallel, preparation of ‘gold standard’ discussion (Sanjeev, Erik)<br/>
16:15: Round table discussion on Potato metabolic genes as ‘gold standard’ for the annotation validation schemes (Sanjeev, Erik)<br/>
16:45: 1st round of the validation scheme scripts runs<br/>
17:45: Return to CASA hotel<br/>
18:15: Day 1 summary, write a wrap-up mini report (at the hotel)<br/>
20:00: Dinner at CASA hotel<br/>
</p>
<p>
<strong><em>Friday 20 September</em></strong><br/>
<8:30: Breakfast at CASA hotel<br/>
8:30: Taxi to SARA<br/>
<strong>9:00 - 12:45:</strong> <strong>Hackathon part 2</strong><br/>
9:00: Refine scripts after analysis of 1st round results. Re-running the validation score. Define ‘stable’ scores and scoring schemes<br/>
10:45: Coffee break<br/>
11:00: Round table discussion – preparing for writing the summary report and delineating bullet points for a manuscript road map<br/>
12:45: Lunch at SARA<br/>
<strong>13:30 - 18:00:</strong> <strong>Hackathon part 3</strong><br/>
13:30: Split to task sub-groups and run specific needed computational/biological analyses<br/>
16:00: Video conference (skype) with Kate Dreher from USA. Coffee provided<br/>
17:00: Continue running computational tasks and summarizing results<br/>
18:00: Taxi to CASA hotel<br/>
19:30 - 20:30 Free slot if needed<br/>
20:45: Walk for dinner at <a href="http://www.huizefrankendael.nl/en/home/" class="urlextern" title="http://www.huizefrankendael.nl/en/home/" rel="ugc nofollow">Restaurant Merkelbach</a> (Middenweg 72)<br/>
</p>
<p>
<em><strong>Saturday 21 September</strong></em><br/>
<8:45: Breakfast at CASA hotel<br/>
8:45: Check out<br/>
<strong>9:00 - 12:00:</strong> <strong>Hackathon part 4</strong> (hotel meeting room)<br/>
9:00: Recap video conference with Kate<br/>
9:45: Hackathon summary and perspectives<br/>
12:00: Lunch at CASA hotel<br/>
13:00: End of the event<br/>
</p>
<p>
<strong>Overview</strong>
</p>
<p>
For non-model organisms, genes predicted in the sequenced genome are relatively poorly functionally annotated. Instead, researchers have to rely on information derived from sequence identity to model organisms.
</p>
<p>
We aim to gather information from several complete sequenced plant genomes and bind/modify existing tools and pipelines for efficiently analyzing large scale ‘-omics data’. By that, we seek to generate a robust and automated framework to assign genes into functional categories, and classify them in a biological context such as biological pathways.
</p>
<p>
Another challenge is to compare, link and annotate transcript sequences derived from RNA-seq of not yet sequenced genomes with already sequenced genomes. The potato genome was sequenced last year and it is time to ripe for genome comparisons, function assignment of genes, transcriptome and proteomics analysis. During the sequencing project, the potato genome consortium run into several problems, due to sequence heterogeneity and eventually genome assembly could only be successfully done based on a homozygous doubled-monoploid potato clone (S. tuberosum group Phureja). The genome structure of this clone differs greatly from the cultivars that are commonly studied, i.e. crop potato cultivars grown for food or as starch for industrial use.
</p>
<p>
Currently, the OrthoMCL clusters are used for gene family analysis together with BLAST. Visualisation of ‘-omics’ data has been done in a commercial software, QluCore, but this does not handle multiple data types simultaneously well and does not visualise functional pathways. Gene predictions were done ab initio with parameters trained for A. thaliana and also based on sequence similarity with four other plant genomes. Functional annotation of predicted genes was done by identifying orthologous and paralogous gene families in 12 sequenced plant species by OrthoMCL.
</p>
<p>
Available data: RNA-seq (GSII Illumina pair.end reads) exist for 3 different potato cultivars and 3 wild potato species. In addition, gene expression data (Agilent microarray based on the 3.4 version of the potato genome) and secretome quantitative proteomics data from various states exist (all samples are from leaves).
</p>
<p>
<strong>Rough Sketch of the Plan before hack-a-thon:</strong>
</p>
<ul>
<li class="level1"><div class="li"> Share and review project “blue print” by all Hack-a-thiners.</div>
</li>
<li class="level1"><div class="li"> Data collection.</div>
</li>
<li class="level1"><div class="li"> Building virtual “warehouse” of relevant existing tools.</div>
</li>
<li class="level1"><div class="li"> Comprehensive related literature survey.</div>
</li>
<li class="level1"><div class="li"> Data pre-processing and protocols set up.</div>
</li>
<li class="level1"><div class="li"> Simulations of “dry” (practice) runs for optimizing “wet” (real) runs to be performed at the time of the hack-a-thon meeting in Amsterdam.</div>
</li>
<li class="level1"><div class="li"> Define computational needs (computer clusters, memory usage, and required packages installments).</div>
</li>
</ul>
<p>
During the hack-a-thon, we would like to test and evaluate ~5-6 annotations pipelines:
- Trinotate
- Blast2GO
- PotatoCyc
- OrthoMCL / InParanoid
- Phytozome
- KEGG
</p>
<p>
Two things are CRUCIAL for us to complete BEFORE going to Amsterdam: 1) Collecting outputs from each pipeline. 2) Parse the output of each pipeline to get a tab delimited file that looks like so: GeneID (Potato ID) Term (GO term ID OR E.C ID) Score (if available p-value/e-value).
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:hack6
http://www.allbioinformatics.eu/doku.php?id=public:hack6&rev=1549962286&do=diff
<h2 class="sectionedit1" id="hackathon2_test_cases_9_and_12">HACKATHON2 Test Cases #9 and #12</h2>
<div class="level2">
<p>
Promising results from the first hack-a-thon session in September (Amsterdam) encouraged us to organize a second session for for these 2 Test Cases #9 and #12. It will take place from 27 to 29 November in the Department of Plant Protection Biology of Sveriges lantbruksuniversitet (SLU), Alnarp, Sweden.
</p>
<p>
Venue: SLU Alnarp (8 km north of Malmö)<br/>
Hotel: Comfort Hotell, Carlsgatan 10C, 211 20 Malmö +46-40-33 04 40 (next to Malmö Central Station, <a href="http://goo.gl/maps/kYbRl" class="urlextern" title="http://goo.gl/maps/kYbRl" rel="ugc nofollow">http://goo.gl/maps/kYbRl</a>)
</p>
<p>
TC Leaders: Oren Tzfadia and Erik Alexandersson
</p>
<p>
<strong>Participants:</strong><br/>
Agnieszka Danek (Silesian University of Technology, Gliwice, Poland)<br/>
Estelle Wera (SLU)<br/>
Itziar Frades (SLU)<br/>
Didi Amar (Weizmann Institute)<br/>
Erik Alexandersson (SLU)<br/>
Oren Tzfadia (Weizmann Institute)<br/>
</p>
<p>
Remotely: Tatyana Goldberg, Kate Dreher<br/>
</p>
<p>
<strong>Software</strong>: Use of already set-up VM (surfSara, Amsterdam)
</p>
<p>
<strong>To-do list before the hack-a-thon:</strong><br/>
Finish outstanding workflows for comparison during hack-a-thon and visualization of outcome (Didi, Estelle, Itziar and Tanya).<br/>
Maintenance of VM (Agnieszka).
</p>
<p>
<strong>Hack-a-thon schedule:</strong><br/>
</p>
<p>
<strong>Tuesday 26 November</strong><br/>
Arrival Agnieszka (12:05 at Malmö airport) and Oren (evening Copenhagen Airport)<br/>
18:00 Meet and greet with Itziar and/or Estelle
</p>
<p>
<strong>Wednesday 27 November (Seminar room H-house)</strong><br/>
8:30 Pick-up at Comfort Hotell<br/>
9:00-12:00 Set-up, introduction to 2nd hack-a-thon and check of shell script<br/>
12:00-13:00 Lunch (and pick of Didi at Malmö Central Station) <br/>
13:00-14:00 Discussion on how and if to merge flows to one Diamond flow<br/>
14:00-18:00 Working on merging flows<br/>
19:00 Dinner in Malmö<br/>
</p>
<p>
<strong>Thursday 28 November (Morning: Kronliljan, Navet Afternoon: Lilla sessionssalen, Slottet)</strong><br/>
8:30 Pick-up at Comfort Hotell<br/>
9:00-12:00 Working on merging flows <br/>
12:00-13:00 Lunch<br/>
13:00-18:00 Adapting data for public use and accessibility<br/>
Free evening: Hack or Slack!<br/>
</p>
<p>
<strong>Friday 29 November (Seminar room H-house)</strong><br/>
8:30 Pick-up at Comfort Hotell<br/>
9:00-13:00 Deposition of data and finalizing figures<br/>
13:00-15:00 Lunch and tour of the park<br/>
15:00-16:00 Presentation Oren and discussion<br/>
16:00-17:00 Last push!<br/>
20:00 End of Hack-a-thon II dinner at “Från tryne till knorr” in Malmö<br/>
</p>
<p>
<strong>Saturday 30 November</strong><br/>
Departure Oren, Didi and Agnieszka
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:initial_ontology
http://www.allbioinformatics.eu/doku.php?id=public:initial_ontology&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<p>
<strong>AllBio will organize in March 2012 an Initial Ontology Workshop</strong> for 25-40 participants to ensure that the project partners and the external collaborators get access to the information needed to make their facilities operate within the framework of the EDAM ontology. This workshop will also function to make the EDAM team aware of aspects from the bacterial and plant worlds they might have missed and will need to incorporate in EDAM.
</p>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:ki
http://www.allbioinformatics.eu/doku.php?id=public:ki&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="karolinska_institutet_sweden">KAROLINSKA INSTITUTET Sweden</h2>
<div class="level2">
</div>
<!-- EDIT{"target":"section","name":"KAROLINSKA INSTITUTET\tSweden","hid":"karolinska_institutet_sweden","codeblockOffset":0,"secid":1,"range":"50-90"} -->
<h2 class="sectionedit2" id="scilifelab">SciLifeLAB</h2>
<div class="level2">
<p>
<a href="http://www.scilifelab.se/" class="urlextern" title="http://www.scilifelab.se/" rel="ugc nofollow">http://www.scilifelab.se/</a>
</p>
<p>
Science for Life Laboratory (SciLifeLab) is a national resource center dedicated to large scale bio-scientific research with focus on biomedicine, including genome and proteome profiling, bio-imaging and bioinformatics.
</p>
<p>
General information
SciLifeLab is a collaboration between four universities in Stockholm and Uppsala: Stockholm University, the Karolinska Institutet, the Royal Institute of Technology (KTH) and Uppsala University. The centre combines advanced technical know-how and state-of-the-art equipment with a broad knowledge in translational medicine and molecular bioscience. The vision is to make SciLifeLab a competitive centre for high-throughput biosciences with platforms in genomics, comparative genetics, proteomics, bioimaging and functional genomics as well as research communities (programs) in biology, medicine and environmental sciences. SciLifeLab will provide the technology needed for optimal usage of resources unique for Sweden and Scandinavia, among them clinical material in the form of biobanks and excellent medical records
</p>
</div>
<!-- EDIT{"target":"section","name":"SciLifeLAB","hid":"scilifelab","codeblockOffset":0,"secid":2,"range":"91-1201"} -->
<h3 class="sectionedit3" id="prof_thomas_svensson">Prof. Thomas Svensson</h3>
<div class="level3">
<p>
Facility Manager, Genome Bioinformatics at Science for Life Laboratory.
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Thomas Svensson","hid":"prof_thomas_svensson","codeblockOffset":0,"secid":3,"range":"1202-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:kick-off
http://www.allbioinformatics.eu/doku.php?id=public:kick-off&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="allbio_kick-off_meeting">AllBio Kick-off Meeting</h1>
<div class="level1">
</div>
<h4 id="report">Report</h4>
<div class="level4">
<p>
<br/>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=400&tok=7d903f&media=public:dsc_4579.jpeg" class="medialeft" align="left" loading="lazy" title="AllBio group picture" alt="AllBio group picture" width="400" /><br/>
</p>
<p>
The kick-off meeting was opened by the AllBio coordinator Erik Bongcam-Rudloff and the local organizer Jacques van Helden. Each Participant introduced himself and the institute she/he is asociated. Erik Bongcam-Rudloff and the chairs of the workgroups then presented AllBio.
</p>
<p>
As next the scientific officer Dr. Barend Verachtert took the word and congratulated for the project.
</p>
<p>
After some comments about the project AllBio, Dr. Barend Verachtert gave the participants an overview of the future aspects of KBBE and Horizon 2020 in general.
</p>
<p>
After lunch the participants discussed some topic to get the project started especially the form of the web site and the first community building meetings each partner will have to organize to disseminate the AllBio idea locally and collect ideas for Test cases.
</p>
</div>
<h4 id="agenda">Agenda</h4>
<div class="level4">
<p>
<br/>
</p>
<p>
<strong>10 November 2011, Brussels, Belgium</strong>
</p>
<p>
09:00 - 09:10 Welcome by the local organizer Jacques van Helden
</p>
<p>
09:10 - 09:55 Introduction to EU policies and perspectives Barend Verachtert
</p>
<p>
09:55 - 10:00 Welcome and introduction by the coordinator Erik Bongcam-Rudloff
</p>
<p>
10:00 - 10:30 Introduction of participants
</p>
<p>
10:30 - 11:00 Coffee break
</p>
<p>
11:00 - 12:00 Introduction to the AllBio project,
</p>
<ol>
<li class="level1"><div class="li"> Work Packages and expected results (impact!!!)</div>
</li>
<li class="level6"><div class="li"> Timeline of the overall project</div>
</li>
<li class="level6"><div class="li"> Communication strategy within the consortium</div>
</li>
<li class="level6"><div class="li"> Webpage setup</div>
</li>
</ol>
<p>
12:30 - 13:30 Lunch
</p>
<p>
13:30 - 14:30 Communication strategy with the scientific communities
</p>
<ol>
<li class="level1"><div class="li"> Local communities</div>
</li>
<li class="level7"><div class="li"> European level</div>
</li>
<li class="level7"><div class="li"> Upcoming events where we can/should present AllBio</div>
</li>
</ol>
<p>
14:30 - 15:30 Test cases – how to start? - First draft of a questionnaire
</p>
<p>
15:30 - 16:00 Coffee break
</p>
<p>
16:00 - 17:00 Next meetings
</p>
<ol>
<li class="level1"><div class="li"> Workshops</div>
</li>
<li class="level7"><div class="li"> Local events</div>
</li>
<li class="level7"><div class="li"> AGM</div>
</li>
</ol>
</div>
<!-- EDIT{"target":"section","name":"AllBio Kick-off Meeting","hid":"allbio_kick-off_meeting","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:loadedtestcases
http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="selected_test_cases">Selected Test Cases</h2>
<div class="level2">
<ol>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc1" class="wikilink1" title="public:loadedtestcases:tc1" data-wiki-id="public:loadedtestcases:tc1">FAIRE-seq data analyser</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc2" class="wikilink1" title="public:loadedtestcases:tc2" data-wiki-id="public:loadedtestcases:tc2">Identification of large structural variations</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc3" class="wikilink1" title="public:loadedtestcases:tc3" data-wiki-id="public:loadedtestcases:tc3">Discovery of gene regulatory networks</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc4" class="wikilink1" title="public:loadedtestcases:tc4" data-wiki-id="public:loadedtestcases:tc4">Primer design for ChIP-PCR studies</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc5" class="wikilink1" title="public:loadedtestcases:tc5" data-wiki-id="public:loadedtestcases:tc5">Integrative Omics analysis workflow</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc6" class="wikilink1" title="public:loadedtestcases:tc6" data-wiki-id="public:loadedtestcases:tc6">Bacterial Comparative Genomics</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc7" class="wikilink1" title="public:loadedtestcases:tc7" data-wiki-id="public:loadedtestcases:tc7">Processing an un-annotated genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc8" class="wikilink1" title="public:loadedtestcases:tc8" data-wiki-id="public:loadedtestcases:tc8">Discover non-coding RNA in yeast</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9" class="wikilink1" title="public:loadedtestcases:tc9" data-wiki-id="public:loadedtestcases:tc9">Pathway analysis of a poorly annotated but sequenced plant genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc10" class="wikilink1" title="public:loadedtestcases:tc10" data-wiki-id="public:loadedtestcases:tc10">Gene prediction modelling for plants</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc11" class="wikilink1" title="public:loadedtestcases:tc11" data-wiki-id="public:loadedtestcases:tc11">Genome assembly of heterozygous diploid data</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12" class="wikilink1" title="public:loadedtestcases:tc12" data-wiki-id="public:loadedtestcases:tc12">Functional annotation of the potato genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc13" class="wikilink1" title="public:loadedtestcases:tc13" data-wiki-id="public:loadedtestcases:tc13">Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones</a></strong></div>
</li>
</ol>
</div>
<!-- EDIT{"target":"section","name":"Selected Test Cases","hid":"selected_test_cases","codeblockOffset":0,"secid":1,"range":"41-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:localevents
http://www.allbioinformatics.eu/doku.php?id=public:localevents&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="local_events_for_allbio_community_building">Local events for AllBIO community building</h2>
<div class="level2">
<p>
Each <a href="http://www.allbioinformatics.eu/doku.php?id=public:partners" class="wikilink1" title="public:partners" data-wiki-id="public:partners">AllBio partner</a> will organise a local (or national) conference inviting representatives of the different life science communities (user communities). The aim of the local (national) conferences is the introduction of AllBio and the vision of the project and gather information of the communities about the bioinformatics needs in their area. These needs will be formulated as so calles <a href="http://www.allbioinformatics.eu/doku.php?id=public:test_cases" class="wikilink1" title="public:test_cases" data-wiki-id="public:test_cases">Test Cases</a> which will be submitted to the project.
The events will take place between February and May 2012.
</p>
</div>
<!-- EDIT{"target":"section","name":"Local events for AllBIO community building","hid":"local_events_for_allbio_community_building","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:localeventsitb
http://www.allbioinformatics.eu/doku.php?id=public:localeventsitb&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsitb&media=public:image001.jpg" class="media" title="public:image001.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=734482&media=public:image001.jpg" class="mediaright" align="right" loading="lazy" alt="" width="200" /></a>
</p>
<h5 id="first_italian_allbio_community_building_workshop_on">First Italian AllBio Community Building Workshop on</h5>
<div class="level5">
</div>
<h2 class="sectionedit1" id="bioinformatics_meets_biology">Bioinformatics Meets Biology</h2>
<div class="level2">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:allbio_italian_community-building_itb_last3.pdf" class="media mediafile mf_pdf" title="public:allbio_italian_community-building_itb_last3.pdf (4.5 MB)">allbio_italian_community-building_itb_last3.pdf</a>
</p>
<p>
The Italian community building event hosted more than 35 Participants from 11 different institutes.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsitb&media=public:p1110281-s.jpg" class="media" title="public:p1110281-s.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=565421&media=public:p1110281-s.jpg" class="media" loading="lazy" alt="" width="300" /></a>
</p>
<p>
Presentation of the AllBio project
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsitb&media=public:p1110304-s.jpg" class="media" title="public:p1110304-s.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=f99e69&media=public:p1110304-s.jpg" class="media" loading="lazy" alt="" width="300" /></a>
</p>
<p>
Discussion of a presented test case
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsitb&media=public:p1110312-s.jpg" class="media" title="public:p1110312-s.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=9457a1&media=public:p1110312-s.jpg" class="media" loading="lazy" alt="" width="300" /></a>
</p>
<p>
Presentation of another test case
</p>
</div>
<h4 id="programme">Programme</h4>
<div class="level4">
<ul>
<li class="level1"><div class="li"> 9:00 – 10:00 Registration and Coffee</div>
</li>
<li class="level1"><div class="li"> 10:00 – 10:30 <a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:allbioitaly2.pptx" class="media mediafile mf_pptx" title="public:allbioitaly2.pptx (2.2 MB)">AllBio – Andreas Gisel</a></div>
</li>
<li class="level1"><div class="li"> 10:30 – 13:00 4 Test Case Presentations</div>
</li>
</ul>
<ol>
<li class="level1"><div class="li"> Patrizia Stifanelli </div>
</li>
<li class="level1"><div class="li"> Stefano Castellana </div>
</li>
<li class="level1"><div class="li"> Francesco Calabrese </div>
</li>
<li class="level1"><div class="li"> Chrysovalentinos Pousis</div>
</li>
</ol>
<ul>
<li class="level1"><div class="li"> 13:00 – 14:00 Lunch</div>
</li>
<li class="level1"><div class="li"> 14:00 – 17:00 Round Table Discussion</div>
</li>
</ul>
<p>
<br/>
<br/>
</p>
<p>
Broadening the Bioinformatics Infrastructure
to unicellular, animal, and plant science
</p>
<p>
<color red>CHANGE OF DATE AN VENUE </color>
</p>
<p>
<color red>26 June 2012 </color>
</p>
<p>
<color red>Sala Congressi 1 floor </color>
</p>
<p>
<color red>Area CNR Bari </color>
</p>
<p>
<color red>Via Amendola 122 </color>
</p>
<ul>
<li class="level1"><div class="li"> 09 – 10 registration and coffee</div>
</li>
<li class="level1"><div class="li"> 10 - 13 Selected presentations</div>
</li>
<li class="level1"><div class="li"> 13 – 14 Lunch</div>
</li>
<li class="level1"><div class="li"> 14 – 17 Round table discussions of test cases</div>
</li>
</ul>
<p>
<del>26 - 27 June 2012</del>
</p>
<p>
Institute for Biomedical Technologies, Bari
</p>
</div>
<h4 id="about_allbio">About AllBio</h4>
<div class="level4">
<p>
AllBio is a European Coordination and Support Action which concerts the efforts of 10 bioinformatics academic Institutes to generalise and broaden the applicability of the many existent human-centric bioinformatics facilities to life science research fields related to unicellular organisms, plants, or animals (<a href="http://www.allbioinformatics.eu" class="urlextern" title="http://www.allbioinformatics.eu" rel="ugc nofollow">www.allbioinformatics.eu</a>).
</p>
<p>
These activities require that the partners start to structure and coordinate their collaborations with national biologists and bioinformaticians in ALL life sciences fields and carry these collaborations to an international level.
</p>
</div>
<h4 id="workshop">Workshop</h4>
<div class="level4">
<p>
<strong>We hereby would like to invite you to attend the AllBio community-building event in Bari, which will take place on 26 and 27 June 2012.</strong>
</p>
<p>
As interdisciplinary Italian community we would like to work with you on detecting gaps in existing tools and workflows to handle biological data. While presenting and discussing your data analysis approaches we will identify your needs, what methods you have tried before and how you would ideally see the results of your data analysis. This information will help to create AllBio test cases. These test cases will then be forwarded to the AllBio consortium to define which challenges will be supported and coordinated to solve many highly relevant bioinformatics problems in as many disciplines as possible.
</p>
<p>
<strong>AllBio will be able to financially support a limited number of participants to this workshop and therefore we would like to ask you to submit a short abstract to be selected among the supported participants.</strong>
</p>
</div>
<h4 id="call_for_abstracts">Call for Abstracts</h4>
<div class="level4">
<p>
The abstract in Italian or English (fill in the <a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:allbio_italian_community-building_itb.doc" class="media mediafile mf_doc" title="public:allbio_italian_community-building_itb.doc (1.8 MB)">template</a>) should not exceed one page and should be divided into the following 4 parts:
</p>
<ul>
<li class="level1"><div class="li"> Biological background of the bioinformatics problem</div>
</li>
<li class="level1"><div class="li"> Nature of data to be analyzed</div>
</li>
<li class="level1"><div class="li"> Nature of bottleneck in the data analysis process</div>
</li>
<li class="level1"><div class="li"> Ideal workflow and final result of the analysis process</div>
</li>
</ul>
<p>
<strong>PLEASE send to: andreas.gisel(at)ba(dot)itb(dot)cnr(dot)it</strong>
</p>
<p>
<strong> Deadline of abstract submission will be 15 May 2012. </strong>
</p>
<p>
<strong> Notification of supported participants will be 21 May 2012. </strong>
</p>
<p>
<color red><strong><em class="u"> NEW Deadlines </em></strong></color>
</p>
<p>
<color red><strong> NEW Deadline of abstract submission will be 30 May 2012. </strong></color>
</p>
<p>
<strong> Notification of supported participants will be 6 June 2012. </strong>
</p>
</div>
<h4 id="participation">Participation</h4>
<div class="level4">
<p>
The participation to the workshop will be free, including coffee breaks and one dinner, and all providers of abstract are invited to participate in this event in Bari.
</p>
<p>
All abstracts, independently by the financial support, will be analyzed and forwarded to the AllBio community, and will be visible via the AllBio portal and subject to future selection for detailed processing within the AllBio consortium.
</p>
</div>
<h4 id="preliminary_programme">Preliminary Programme</h4>
<div class="level4">
<p>
First day (26 June):
</p>
<ul>
<li class="level1"><div class="li"> 13 – 15 Registration and lunch</div>
</li>
<li class="level1"><div class="li"> 15 – 18 Selected presentations</div>
</li>
</ul>
<p>
Second day (27 June):
</p>
<ul>
<li class="level1"><div class="li"> 09 – 13 Selected presentations</div>
</li>
<li class="level1"><div class="li"> 13 – 14 Lunch</div>
</li>
<li class="level1"><div class="li"> 14 – 17 Round table discussions of test cases</div>
</li>
</ul>
</div>
<h4 id="organization_committee">Organization Committee</h4>
<div class="level4">
<ul>
<li class="level1"><div class="li"> Andreas Gisel</div>
</li>
<li class="level1"><div class="li"> Domenica D'Elia</div>
</li>
<li class="level1"><div class="li"> Angelica Tulipano</div>
</li>
<li class="level1"><div class="li"> Sabino Liuni</div>
</li>
<li class="level1"><div class="li"> Flavio Licciulli</div>
</li>
<li class="level1"><div class="li"> Giorgio Grillo</div>
</li>
<li class="level1"><div class="li"> Arianna Consiglio</div>
</li>
<li class="level1"><div class="li"> Nicola Losito</div>
</li>
<li class="level1"><div class="li"> Domenico Catalano</div>
</li>
<li class="level1"><div class="li"> Giuseppe Cananzi </div>
</li>
</ul>
</div>
<!-- EDIT{"target":"section","name":"Bioinformatics Meets Biology","hid":"bioinformatics_meets_biology","codeblockOffset":0,"secid":1,"range":"131-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:localeventsrunmc
http://www.allbioinformatics.eu/doku.php?id=public:localeventsrunmc&rev=1549962287&do=diff
<h3 class="sectionedit1" id="allbio_community_bilding_event_in_the_netherlands">AllBio Community Bilding Event in the Netherlands</h3>
<div class="level3">
<p>
Purpose of the meeting was to bring together the Dutch metagenomics research community.
</p>
<p>
The meeting was organized <a href="http://www.nbic.nl/about-nbic/news-press/bioinformatics-news/detail/article/metagenomics-seminar-attracted-over-50-participants/" class="urlextern" title="http://www.nbic.nl/about-nbic/news-press/bioinformatics-news/detail/article/metagenomics-seminar-attracted-over-50-participants/" rel="ugc nofollow">together with NBIC</a> (special thanks to Leon Mei). There were about 60 participants from over 20 research institutes and / or companies and several research groups within the research institutes. <a href="https://wiki.nbic.nl/index.php/Metagenomics_seminar_on_10-4-2012" class="urlextern" title="https://wiki.nbic.nl/index.php/Metagenomics_seminar_on_10-4-2012" rel="ugc nofollow">Presentations</a> were given by various research groups on different topics. The plenary discussion in the afternoon was lively and resulted some test cases that will be formulated and uploaded onto the AllBio web portal.
</p>
<p>
<strong>Programme:</strong>
</p>
<div class="table sectionedit2"><table class="inline">
<tr class="row0">
<td class="col0">10:20-10:30</td><td class="col1">Rob Hooft, Sacha van Hijum</td><td class="col2">Welcome & Introduction</td>
</tr>
<tr class="row1">
<td class="col0">10:30-11:00</td><td class="col1">Victor de Jager (CMBI/NBIC)</td><td class="col2">The use of Grid and Cloud computing in functional metagenomics projects</td>
</tr>
<tr class="row2">
<td class="col0">11:00-11:30</td><td class="col1">Jos Boekhorst (NIZO/CMBI)</td><td class="col2">Analyzing microbial communities using 16S pyrosequencing</td>
</tr>
<tr class="row3">
<td class="col0">11:30-12:00</td><td class="col1">Jeroen Laros (LUMC)</td><td class="col2">Single molecule sequencing in bacterial metagenomics</td>
</tr>
<tr class="row4">
<td class="col0">12:00-13:00</td><td class="col1">lunch</td><td class="col2"></td>
</tr>
<tr class="row5">
<td class="col0">13:00-13:30</td><td class="col1">Robert Kraaij (ErasmusMC)</td><td class="col2">Microbiome sequencing in large human populations</td>
</tr>
<tr class="row6">
<td class="col0">13:30-14:00</td><td class="col1">Giske Biesbroek (UMC Utrecht)</td><td class="col2">The microbiome of the upper respiratory tract: key to respiratory disease?</td>
</tr>
<tr class="row7">
<td class="col0">14:00-14:30</td><td class="col1">József Geml (National Herbarium of the Netherlands)</td><td class="col2">Biodiversity assessment of soil fungal communities using 454 sequencing</td>
</tr>
<tr class="row8">
<td class="col0">14:30-14:40</td><td class="col1">tea break</td><td class="col2"></td>
</tr>
<tr class="row9">
<td class="col0">14:40-16:00</td><td class="col1">all</td><td class="col2">Plenary discussion</td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table","secid":2,"range":"808-1597"} -->
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:localeventssib
http://www.allbioinformatics.eu/doku.php?id=public:localeventssib&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="local_community_building_event_switzerland">Local community building event Switzerland</h2>
<div class="level2">
<p>
About 40 participants were following 11 presentations of the Swiss AllBio Commiunity Building event at the University of Lausanne. During the discussions several test case candidates were individuated. They will be developed further and uploaded onto the AllBio portal.
</p>
<p>
Programme of the meeting:
</p>
<ul>
<li class="level1"><div class="li"> 09:00 Welcome address by the director of Vital-IT, Prof. Ioannis Xenarios </div>
</li>
<li class="level1"><div class="li"> 09:15 Laurent Falquet: «Introduction to the ALLBIO European Action» </div>
</li>
<li class="level1"><div class="li"> 09.45 Adem Bilican: «Evolution of alternative splicing regulatory mechanisms in vertebrates» </div>
</li>
<li class="level1"><div class="li"> 10:15 Diego Cortez: «Finding mammalian Y chromosome transcripts using RNA sequencing data» </div>
</li>
<li class="level1"><div class="li"> 10:45 coffee break </div>
</li>
<li class="level1"><div class="li"> 11:15 Oksana Riba-Grognuz: «The making of a model: case study of the Red Fire Ant» </div>
</li>
<li class="level1"><div class="li"> 11:45 Yvan Wenger: «Orthologome computing reveals the dynamics underlying the emergence of eumetazoan traits» </div>
</li>
<li class="level1"><div class="li"> 12:15 lunch break </div>
</li>
<li class="level1"><div class="li"> 13:15 Gina Cannarozzi: «Genome and Transcriptome Sequencing of Eragrostis tef» </div>
</li>
<li class="level1"><div class="li"> 13:45 Luca Santuari: «Identification of EMS-induced mutations in Arabidopsis thaliana using ultra-high throughput sequencing» </div>
</li>
<li class="level1"><div class="li"> 14:15 Christian Fankhauser or Markus Kohnen: «A network of bHLH class transcription factors regulate growth in Arabidopsis» </div>
</li>
<li class="level1"><div class="li"> 14:45 coffee break </div>
</li>
<li class="level1"><div class="li"> 15.15 Vladimir Senchilo: «Metagenomic analysis of mobile DNA» </div>
</li>
<li class="level1"><div class="li"> 15:45 Anouk Necsulea: «Annotating long non-coding RNAs in non-model organisms» </div>
</li>
<li class="level1"><div class="li"> 16:15 Cédric Howald: «The ENCODE effort combining RNA-seq and RT-PCR-seq allows to catalog thousands of novel lncRNAs» </div>
</li>
<li class="level1"><div class="li"> 16:45 Final round table discussion </div>
</li>
</ul>
</div>
<h4 id="announcing_the_vital-it_user_day_2012">Announcing the Vital-IT User Day 2012</h4>
<div class="level4">
<p>
<br/>
</p>
<p>
Date: <strong>Friday March 30</strong>
</p>
<p>
Location: <strong>Auditorium A, Genopode UNIL, 1015 Lausanne Switzerland</strong>
</p>
<p>
Focus: <strong>Bioinformatics for large scale non-human projects</strong>
</p>
<p>
Bioinformatics tools for the effective exploitation of high throughput data are of increasing importance.
We would like to show that Vital-IT ensures a balanced approach between health and non-health related applications. For this purpose we focus our Vital-IT Users Day 2012 beyond the health dimension jointly with the ALLBIO european Coordinated and Support Action. We invite all Vital-IT users to participate to discuss their successes and difficulties together with Vital-IT experts.
</p>
<p>
Sponsor: ALLBIO project funded by the FP7 work programme KBBE-2011, “FOOD, AGRICULTURE AND FISHERIES, AND BIOTECHNOLOGY“
</p>
<p>
<a href="http://www.vital-it.ch/news.php?id=13" class="urlextern" title="http://www.vital-it.ch/news.php?id=13" rel="ugc nofollow">http://www.vital-it.ch/news.php?id=13</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"Local community building event Switzerland","hid":"local_community_building_event_switzerland","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:localeventsslu
http://www.allbioinformatics.eu/doku.php?id=public:localeventsslu&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_workshop_on_bioinformatics_community_building_in_uppsala">ALLBIO Workshop on "Bioinformatics Community Building" in Uppsala</h2>
<div class="level2">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsslu&media=public:dsc_1944_red.jpg" class="media" title="public:dsc_1944_red.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=638b60&media=public:dsc_1944_red.jpg" class="media" loading="lazy" alt="" width="300" /></a>
</p>
<p>
The AllBio community building workshop in Uppsala, Sweden was a successful and stimulating event.
</p>
<p>
SLU and SLU Global Bioinformatics Centre recently hosted the “AllBio Community Building Event” at Ultuna, Uppsala, Sweden.
</p>
<p>
30 participants attended the event, and 8 selected presentations were held by representatives of the animal, plant, and microbial research fields. The focus of the talks was on difficulties in *omics data analysis, and group discussions led to several test cases being collected for the development of bioinformatics tools in future efforts led by AllBio.
</p>
<p>
Below find the programme of the workshop:
</p>
<p>
10:00 Introduction to ALLBIO - Erik Bongcam-Rudloff
</p>
<p>
10:30 Coffee
</p>
<p>
10:45 Presentations:
</p>
<ul>
<li class="level1"><div class="li"> Ola Spjuth - UPPMAX</div>
</li>
<li class="level1"><div class="li"> Hans Ronne - Algal genome sequencing</div>
</li>
<li class="level1"><div class="li"> Robert Söderlund - Whole genome based SNP-typing of bacteria</div>
</li>
<li class="level1"><div class="li"> Ashfaq Ali - RNA-seq and proteomics in potato</div>
</li>
</ul>
<p>
12:00 Lunch
</p>
<p>
13:30 Presentations:
</p>
<ul>
<li class="level1"><div class="li"> Jacob Höglund, Biao Wang - Bioinformatics for a non model organism</div>
</li>
<li class="level1"><div class="li"> Erik Alexandersson - Annotation of potatogenome</div>
</li>
<li class="level1"><div class="li"> Eva Hellmén - Canine tumour analysis</div>
</li>
<li class="level1"><div class="li"> Magnus Alm Rosenblad - De novo-sequencing of marine organisms</div>
</li>
</ul>
<p>
14:30 Coffee
</p>
<p>
14:45 Group discussions aiming to identifying new test cases and important conferences/workshops i animal, plant and microbial research fields.
</p>
<p>
15:30 Discussion with short presentations from the group discussions
</p>
<p>
16:00 Closing of the event
<em>
</em>
<em>
</em>
</p>
</div>
<h4 id="call_for_the_allbio_community_building_event_in_sweden">Call for the AllBio Community building event in Sweden</h4>
<div class="level4">
<p>
AllBio is a concerted effort of 10 bioinformatics academic institutes and interfaces
between the agricultural sciences, microbiology, and bioinformatics. The goal of the
project is to identify and develop bioinformatics tools and databases to solve problems
for the scientific communities.
</p>
<p>
<strong>We would hereby like to invite you to attend the AllBio community building event in
Uppsala, which will take place on May 3 in Uppsala, Sweden.</strong> (<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:allbio-invitation_sweden.pdf" class="media mediafile mf_pdf" title="public:allbio-invitation_sweden.pdf (1.3 MB)">allbio-invitation_sweden.pdf</a>).
</p>
<p>
There are myriads of bioinformatics tools within each discipline that have been developed
by members in the respective areas, and although the tools within the !elds are known to
experts in the speci!c communities, there is a wealth of knowledge in the full
biological/bioinformatics spectrum that could be highly beneficial to other research areas.
</p>
<p>
As part of the bioinformatics community we would like to work on detecting gaps in
existing tools to handle biological data. We will identify your needs in a form which you
will help to fill out, describing the issue(s) that you want solved, which methods you have
tried before and how you would ideally see the results visualised. The test cases created
during the workshop will be forwarded to the AllBio consortium to define which challenges
should be met by bioinformatics tools from the perspective of the end user.
</p>
<p>
AllBio will be able to financially support a limited numbers of participants to this workshop.
To work efficiently during the day we would like to ask you to submit a short
abstract.
</p>
<p>
The abstract should be divided into 4 parts:
</p>
<ol>
<li class="level1"><div class="li"> Biological background of the bioinformatics problem</div>
</li>
<li class="level1"><div class="li"> Nature of data to be analysed</div>
</li>
<li class="level1"><div class="li"> Nature of bottleneck in the data analysis process</div>
</li>
<li class="level1"><div class="li"> Ideal workflow and end result of the analysis process</div>
</li>
</ol>
<p>
The abstract should not exceed one page!
</p>
<p>
Abstracts are submitted to <strong>henrik.lysell@slu.se</strong>
<strong>Deadline of abstract submission will be 30 April 2012.</strong>
</p>
<p>
Participation in the workshop will be free, including coffee breaks and dinner, and we
invite all abstract providers to participate in this event in Uppsala.
All abstracts will be analysed and forwarded to the AllBio community, shown on the AllBio portal and to be subject for future selection for detailed processing within the AllBio consortium.
</p>
</div>
<h4 id="preliminary_programme">Preliminary programme:</h4>
<div class="level4">
<ul>
<li class="level1"><div class="li"> Registration and breakfast</div>
</li>
<li class="level1"><div class="li"> Selected presentations</div>
</li>
<li class="level1"><div class="li"> Lunch</div>
</li>
<li class="level1"><div class="li"> Round table discussions of test cases</div>
</li>
<li class="level1"><div class="li"> Dinner</div>
</li>
</ul>
<p>
Updates on this event: <a href="http://www.allbioinformatics.eu" class="urlextern" title="http://www.allbioinformatics.eu" rel="ugc nofollow">www.allbioinformatics.eu</a>
</p>
<p>
Find the venue (Ultuna, Undervisningshuset, Sal L):
<a href="http://www.slu.se/en/about-slu/locations/uppsala/find-your-way-to-campus-ultuna/" class="urlextern" title="http://www.slu.se/en/about-slu/locations/uppsala/find-your-way-to-campus-ultuna/" rel="ugc nofollow">www.slu.se/en/about-slu/locations/uppsala/find-your-way-to-campus-ultuna/</a>
</p>
<p>
Organised by SLU and SciLife lab.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Alocaleventsslu&media=public:scilifelab_slu.png" class="media" title="public:scilifelab_slu.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=be883d&media=public:scilifelab_slu.png" class="mediacenter" loading="lazy" alt="" width="200" /></a>
</p>
</div>
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http://www.allbioinformatics.eu/doku.php?id=public:max_planck_institute_for_molecular_genetics_berlin&rev=1549962287&do=diff
<h2 class="sectionedit1" id="max_planck_institute_for_molecular_genetics_berlin_germany">Max Planck Institute for Molecular Genetics, Berlin, Germany</h2>
<div class="level2">
<p>
<a href="http://www.molgen.mpg.de" class="urlextern" title="http://www.molgen.mpg.de" rel="ugc nofollow">www.molgen.mpg.de</a>
</p>
<p>
The Max Planck Institute for Molecular Genetics (MPIMG) is one of the key research institutes for molecular biology research and is perceived internationally as a stronghold of genome and genetics research. The overall research goal is to gain new insights into the development of diseases on a molecular level, thus contributing to the development of novel cause-related medical treatments. The MPIMG is one of the largest next generation sequencing centers in Europe and has outstanding expertise in the field of NGS technology development.
</p>
</div>
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<h3 class="sectionedit2" id="dr_babette_regierer">Dr. Babette Regierer</h3>
<div class="level3">
<p>
studied biology at the Free University Berlin and did her PhD on plant nutrition at the Max Planck Institute for Molecular Plant Physiology (<a href="http://www.mpimp-golm.mpg.de" class="urlextern" title="http://www.mpimp-golm.mpg.de" rel="ugc nofollow">www.mpimp-golm.mpg.de</a>). After her postdoc position in the frame of a European research consortium on phosphate efficiency in higher plants she specialized in scientific project coordination and management in the area of functional genomics and technology development. She broadened her skills working as a project manager for an agency in technology transfer and patent commercialization (<a href="http://www.iapl.de" class="urlextern" title="http://www.iapl.de" rel="ugc nofollow">www.iapl.de</a>) and established the Potsdam Research Network pearls (<a href="http://www.pearlsofscience.de" class="urlextern" title="http://www.pearlsofscience.de" rel="ugc nofollow">www.pearlsofscience.de</a>). Dr. Babette Regierer is currently working at the Max Planck Institute for Molecular Genetics and involved in the European initiative “IT Future of Medicine” to develop a ‘virtual patient’ model (<a href="http://www.itfom.eu" class="urlextern" title="http://www.itfom.eu" rel="ugc nofollow">www.itfom.eu</a>), but is also participating in the COST Action SeqAhead, a network for NGS data analysis (<a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">www.seqahead.eu</a>).
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Hoehenwarter W, van Dongen JT, Wienkoop S, Steinfath M, Hummel J, Erban A, Sulpice R, Regierer B, Kopka J, Geigenberger P, Weckwerth W (2008) A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics 8 (20): 4214-4225.
</p>
<p>
Geigenberger P, Regierer B, Nunes-Nesi A, Leisse A, Urbanczyk-Wochniak E, Springer F, van Dongen JT, Kossmann J, Fernie AR (2005) Inhibition of de novo pyrimidine synthesis in growing potato tubers leads to a compensatory stimulation of the pyrimidine salvage pathway and a subsequent increase in biosynthetic performance. Plant Cell. 17(7):2077-88. Epub 2005 Jun 10.
</p>
<p>
Zimmermann P, Regierer B, Kossmann J, Frossard E, Amrhein N, Bucher M (2004) Differential expression of three purple acid phosphatases from potato. Plant Biol (Stuttg) 6(5), 519-28
</p>
<p>
Geigenberger P, Regierer B, Lytovchenko A, Leisse A, Schauer N, Springer F, Kossmann J, Fernie AR (2004) Heterologous expression of a ketohexokinase in potato plants leads to inhibited rates of photosynthesis, severe growth retardation and abnormal leaf development. Planta 218(4), 569-78
</p>
<p>
Regierer B, Fernie AR, Springer F, Perez-Melis A, Leisse A, Koehl K, Willmitzer L, Geigenberger P, Kossmann J (2002) Starch content and yield increase as a result of altering adenylate pools in transgenic plants. Nat Biotechnol Dec, 20(12):1256-60
</p>
</div>
<!-- EDIT{"target":"section","name":"Dr. Babette Regierer","hid":"dr_babette_regierer","codeblockOffset":0,"secid":2,"range":"639-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:onto1
http://www.allbioinformatics.eu/doku.php?id=public:onto1&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h4 id="allbio_ontology_workshop">AllBio Ontology Workshop:</h4>
<div class="level4">
</div>
<h2 class="sectionedit1" id="using_web_services_for_improved_interoperability_in_bioinformatics">“Using web services for improved interoperability in bioinformatics”</h2>
<div class="level2">
<p>
<strong>October 3-5</strong><br/>
<strong>Garching, (Munich) Germany</strong>
</p>
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=23e432&media=public:allbio-ws-munich_small.jpg" class="media" loading="lazy" alt="" width="500" />
</p>
<p>
Over 3 days John Ison (<a href="http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=708" class="urlextern" title="http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=708" rel="ugc nofollow">EBI</a>), Matus Kalas (<a href="http://www.uib.no/persons/Matus.Kalas" class="urlextern" title="http://www.uib.no/persons/Matus.Kalas" rel="ugc nofollow">UIB</a>) and Steve Pettifer (<a href="http://aig.cs.man.ac.uk/people/srp/" class="urlextern" title="http://aig.cs.man.ac.uk/people/srp/" rel="ugc nofollow">UniMan</a>) gave 17 participants from biology and bioinformatics an introduction into web services, ontologies for bioinformatics.
The event was hosted by Guy Yachtav and Burkhard Rost at the Technische Universitaet Muenchen (<a href="http://www.rostlab.org/cms/" class="urlextern" title="http://www.rostlab.org/cms/" rel="ugc nofollow">TUM</a>).
</p>
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=46c9aa&media=public:allbio_ws_teachers.jpg" class="media" loading="lazy" alt="" width="500" />
</p>
<p>
The teachers in action.
</p>
<p>
<br/>
<br/>
<br/>
<br/>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aonto1&media=public:tum.png" class="media" title="public:tum.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=d8cd90&media=public:tum.png" class="media" loading="lazy" title=" " alt=" " width="500" /></a>
</p>
<p>
The Workshop will take place at the Institute for Advanced Studies (<a href="http://www.tum-ias.de/" class="urlextern" title="http://www.tum-ias.de/" rel="ugc nofollow">IAS</a>)
across he street form the <a href="https://maps.google.com/maps?q=Lichtenbergstra%C3%9Fe+2+a+85748+Garching&ie=UTF8&hnear=Lichtenbergstra%C3%9Fe+2,+85748+Garching,+Oberbayern,+Bayern,+Germany&gl=us&t=m&z=16" class="urlextern" title="https://maps.google.com/maps?q=Lichtenbergstra%C3%9Fe+2+a+85748+Garching&ie=UTF8&hnear=Lichtenbergstra%C3%9Fe+2,+85748+Garching,+Oberbayern,+Bayern,+Germany&gl=us&t=m&z=16" rel="ugc nofollow">TUM's Garching Campus</a>
</p>
<p>
This workshop is planned for biologists and bioinformaticians who are interested in the use of ontologies and web services for their data analysis pipelines.
</p>
<p>
<color red> <strong>Deadline for Registration prolonged to 5 September 2012 - SPACE IS LIMITED<br/>
THERE IS STILL SPACE - Late registration till 15 September 2012</strong></color>
</p>
</div>
<h5 id="please_register_by_sending_a_short_motivation_letter_to_andreas_gisel_andreasgisel_at_baitbcnrit_using_as_object_allbio_ontology">Please register by sending a short motivation letter to Andreas Gisel (andreas.gisel (at) ba.itb.cnr.it) using as object "AllBio Ontology.</h5>
<div class="level5">
</div>
<h4 id="programme">Programme</h4>
<div class="level4">
<p>
Day 1
</p>
<ul>
<li class="level1"><div class="li"> 12:00 - 12:45 Assembly</div>
</li>
<li class="level1"><div class="li"> 12:45 - 13:00 Welcome note and administrative</div>
</li>
<li class="level1"><div class="li"> 13:00 - 14:00 Welcome talk (Burkhard Rost)</div>
</li>
<li class="level1"><div class="li"> 14:00 - 14:45 Web services in the life sciences - best practices</div>
</li>
<li class="level1"><div class="li"> 14:45 - 15:30 RESTful services over JSON/BioSchema for JSON</div>
</li>
<li class="level1"><div class="li"> 15:30 - 15:45 Coffee break</div>
</li>
<li class="level1"><div class="li"> 15:45 - 17:00 Web services development for dummies</div>
</li>
</ul>
<p>
Day 2
</p>
<ul>
<li class="level1"><div class="li"> 09:00 - 09:15 Assembly</div>
</li>
<li class="level1"><div class="li"> 09:15 - 10:30 BioXSD tutorial part 1</div>
</li>
<li class="level1"><div class="li"> 10:30 - 10:45 Coffee break</div>
</li>
<li class="level1"><div class="li"> 10:45 - 12:00 BioXSD tutorial part 2 (hands on workshop)</div>
</li>
<li class="level1"><div class="li"> 12:00 - 13:30 Lunch</div>
</li>
<li class="level1"><div class="li"> 13:30 - 14:15 Web services demo</div>
</li>
<li class="level1"><div class="li"> 14:15 - 15:30 EDAM tutorial</div>
</li>
<li class="level1"><div class="li"> 15:30 - 15:45 Coffee break</div>
</li>
<li class="level1"><div class="li"> 15:35 - 17:00 EDAM hands on workshop</div>
</li>
</ul>
<p>
Day 3
</p>
<ul>
<li class="level1"><div class="li"> 09:00 - 09:15 Assembly</div>
</li>
<li class="level1"><div class="li"> 09:15 - 10:00 Web services demo</div>
</li>
<li class="level1"><div class="li"> 10:00 - 11:00 Data visualization on the web using jQuery </div>
</li>
<li class="level1"><div class="li"> 11:00 - 12:00 Closing remarks</div>
</li>
<li class="level1"><div class="li"> 12:00 - 15:00 Oktoberfest at the hippodrome tent In Munich. </div>
</li>
</ul>
<p>
<strong>Hotel</strong>
</p>
<p>
There are reserved 23 single rooms at hotel Hoyacker Hof from 03.10. to 05.10.2012. The Hotel is in Garching town's center a few minutes walk from the U-bahn stop (1 subway stop away from the IAS).
</p>
<p>
<strong>Organization Committee</strong>
</p>
<p>
Guy Yachdav<br/>
Burkhard Rost<br/>
Gert Vriend<br/>
Steve Pettifer<br/>
Andreas Gisel<br/>
Erik Bongcam-Rudloff<br/>
</p>
</div>
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<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:slu" class="wikilink1" title="public:slu" data-wiki-id="public:slu">SVERIGES LANTBRUKSUNIVERSITET</a></strong> Sweden
</p>
<ul>
<li class="level1"><div class="li"> Prof. Erik Bongcam-Rudloff</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:runmc" class="wikilink1" title="public:runmc" data-wiki-id="public:runmc">RADBOUD UNIVERSITY NIJMEGEN MEDICAL CENTRE</a></strong> Netherlands
</p>
<ul>
<li class="level1"><div class="li"> Prof. Gert Vriend</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:sib" class="wikilink1" title="public:sib" data-wiki-id="public:sib">SWISS INSTITUTE OF BIOINFORMATICS</a></strong> Switzerland
</p>
<ul>
<li class="level1"><div class="li"> Dr. Grégoire Rossier</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:uniman" class="wikilink1" title="public:uniman" data-wiki-id="public:uniman">THE UNIVERSITY OF MANCHESTER</a></strong> United Kingdom
</p>
<ul>
<li class="level1"><div class="li"> Prof. Teresa Attwood</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:cnr" class="wikilink1" title="public:cnr" data-wiki-id="public:cnr">CONSIGLIO NAZIONALE DELLE RICERCHE</a></strong> Italy
</p>
<ul>
<li class="level1"><div class="li"> Dr. Andreas Gisel</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:csc" class="wikilink1" title="public:csc" data-wiki-id="public:csc">CSC - IT CENTER FOR SCIENCE</a></strong> Finland
</p>
<ul>
<li class="level1"><div class="li"> Dr Eija Korpelainen</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:ulb" class="wikilink1" title="public:ulb" data-wiki-id="public:ulb">UNIVERSITÉ LIBRE DE BRUXELLES</a></strong> Belgium
</p>
<ul>
<li class="level1"><div class="li"> Prof. Jacques van Helden</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:ki" class="wikilink1" title="public:ki" data-wiki-id="public:ki">KAROLINSKA INSTITUTET</a></strong> Sweden
</p>
<ul>
<li class="level1"><div class="li"> Prof. Thomas Svensson</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:up" class="wikilink1" title="public:up" data-wiki-id="public:up">UNIVERSITÄT POTSDAM</a></strong> and <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:max_planck_institute_for_molecular_genetics_berlin" class="wikilink1" title="public:max_planck_institute_for_molecular_genetics_berlin" data-wiki-id="public:max_planck_institute_for_molecular_genetics_berlin">MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS BERLIN</a></strong> Germany
</p>
<ul>
<li class="level1"><div class="li"> Prof. Dr. Bernd Müller-Röber, Dr. Susanne Hollmann and Dr. Babette Regierer</div>
</li>
</ul>
<p>
<strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:ebi" class="wikilink1" title="public:ebi" data-wiki-id="public:ebi">EUROPEAN MOLECULAR BIOLOGY LABORATORY</a></strong> United Kingdom
</p>
<ul>
<li class="level1"><div class="li"> Prof. Paul Kersey</div>
</li>
</ul>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:plantomicsebi
http://www.allbioinformatics.eu/doku.php?id=public:plantomicsebi&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_sponsored_ebi_course_on_data_resources_and_tools_for_plant-omics">AllBio sponsored EBI course on data resources and tools for plant-omics</h2>
<div class="level2">
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=80&tok=39502c&media=public:plantomics.png" class="medialeft" align="left" loading="lazy" alt="" width="80" /><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=c44feb&media=public:ebi-tree.png" class="mediaright" align="right" loading="lazy" alt="" width="200" /> The European Bioinformatics will organize a practical course providing an overview of data resources and tools for plant scientists, with an emphasis on managing and analysing large-scale datasets from genomics, transcriptomics, proteomics and metagenomics projects. It will bring together lead researchers in the field of plant bioinformatics, experts in biological data resources, and a highly motivated group of experimental researchers through a common theme centred on plant-based research. The course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks. There will be computer-based practical sessions using plant-based use cases and public-domain data resources.
</p>
<p>
Full details (and a registration form) are available here: <a href="http://www.ebi.ac.uk/training/course/allbio-course-data-resources-and-tools-plant-omics-2013" class="urlextern" title="http://www.ebi.ac.uk/training/course/allbio-course-data-resources-and-tools-plant-omics-2013" rel="ugc nofollow">http://www.ebi.ac.uk/training/course/allbio-course-data-resources-and-tools-plant-omics-2013</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio sponsored EBI course on data resources and tools for plant-omics","hid":"allbio_sponsored_ebi_course_on_data_resources_and_tools_for_plant-omics","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:plantpathebi
http://www.allbioinformatics.eu/doku.php?id=public:plantpathebi&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_sponsored_ebi_phytopath_training_course">AllBio sponsored EBI PhytoPath Training Course</h2>
<div class="level2">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aplantpathebi&media=public:phytopath-logo2.png" class="media" title="public:phytopath-logo2.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=80&tok=1e37aa&media=public:phytopath-logo2.png" class="medialeft" align="left" loading="lazy" alt="" width="80" /></a><a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Aplantpathebi&media=public:ebi-tree.png" class="media" title="public:ebi-tree.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=c44feb&media=public:ebi-tree.png" class="mediaright" align="right" loading="lazy" alt="" width="200" /></a> The European Bioinformatics Institute is organising a workshop on 19th-20th September this year focused on the analysis of genome-scale data from plant pathogenic fungi (in the context of the PhytoPath project, which is developing a resource for fungal and oomycete genomes). The workshop will feature an opportunity to explore the use of the Ensembl Fungi, PHI-base resources, the Ondex network analysis tool, and the opportunity to share experiences of handling next generation sequencing data with the presenters and fellow participants. A number of bursuries, funded by AllBio, are available for applicants to this course, to cover travel, accomodation, and registration costs. Full details (and a registration form) are available here:
</p>
<p>
<a href="http://www.ebi.ac.uk/training/handson/course_120919_phytopath.html" class="urlextern" title="http://www.ebi.ac.uk/training/handson/course_120919_phytopath.html" rel="ugc nofollow">http://www.ebi.ac.uk/training/handson/course_120919_phytopath.html</a>
</p>
</div>
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http://www.allbioinformatics.eu/doku.php?id=public:project&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="allbio">AllBio</h1>
<div class="level1">
</div>
<h4 id="broadening_the_bioinformatics_infrastructure_to_unicellular_animal_and_plant_science">Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science</h4>
<div class="level4">
<p>
KBBE.2011.3.6-02: Supporting the development of Bioinformatics Infrastructures for the effective exploitation of genomic data: Beyond health applications.
</p>
<p>
Coordinator: Dr. Erik Bongcam-Rudloff
</p>
<p>
<strong>Introduction</strong>
</p>
<p>
The completion of the human genome sequence has triggered worldwide bioinformatics efforts to unravel its information content. Many projects have been successfully completed in areas such as gene hunting, functional annotation, post-translational modification prediction, protein-protein interactions, transcriptomics, or systems biology. These projects have produced large numbers of novel analytic and predictive computer programs. The majority of these developments, though, have focused on harvesting the human genome, transcriptome, proteome, epigenome, etcetera, and considerably less effort has been invested in the thousands of other genomes in life science research fields related to unicellular organisms, plants, or animals. The AllBio partners have selected these three fields as focus for their coordination actions because: 1) all AllBio partners already have extensive experience in collaborating with life scientists in at least one of these fields, and 2) these three fields cover a large number of the activities in the FP7 work programme KBBE-2011, “FOOD, AGRICULTURE AND FISHERIES, AND BIOTECHNOLOGY”.
</p>
<p>
<strong>Coordination through collaboration</strong>
</p>
<p>
All the partners in AllBio have a strong motivation to work on generic bioinformatics theory, technology, and application. They will now coordinate the generalisation and the broadening of the applicability of the many human-centric bioinformatics facilities that were originally designed for the purpose of analysing the human genome sequence and the subsequently collected post (human) genomic datasets. They will also coordinate the design of novel software and databases. This will primarily be research in projects they are actively involved in, but when possible also in third-party projects. These activities require that the partners start to structure and coordinate their collaborations with national researchers in life sciences such as biotechnology, cell biology, functional and comparative genomics, or biochemistry, and carry these collaborations to an international level.
</p>
<p>
<strong>European dimension</strong>
</p>
<p>
Non-human life science communities exist with different degrees of scientific coordination, and some areas have already agreed on ontologies and common procedures and standards. But only few efforts have gone into the wider task of harmonizing the research efforts of these communities. This coordination will require that the partners collaborate on a series of activities such as the design of ontologies for data and methods, and choosing common interoperability standards. These activities, by necessity require that the coordination efforts of this Coordination Action take place at a Europe-wide scale because databases, software, and human expertise have to come together that simply are not available at any national scale. The fact that the activities described in this project all are core-activities to AllBio consortium members will greatly enhance the overall success and the longevity of the results of this bioinformatics coordination project.
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio","hid":"allbio","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:runmc
http://www.allbioinformatics.eu/doku.php?id=public:runmc&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="radboud_university_nijmegen_medical_centre_netherlands">RADBOUD UNIVERSITY NIJMEGEN MEDICAL CENTRE Netherlands</h2>
<div class="level2">
<p>
<a href="http://www.cmbi.ru.nl/" class="urlextern" title="http://www.cmbi.ru.nl/" rel="ugc nofollow">http://www.cmbi.ru.nl/</a>
</p>
<p>
Partner CMBI is part of the Radboud University Nijmegen Medical Centre. The Radboud hospital is one of the eight national research hospitals, and it is a reference centre for a wide variety of diseases, which implies that medical facilities around the world send their difficult cases to the Radboud hospital where these problems can be investigated. This is a 'nice' situation for the bioinformaticians of the CMBI because they frequently are challenged with difficult bioinformatics questions that require research in a wide variety of directions.
The CMBI consists of five research groups that work on the topics: Systems Biology, Drug Design; Bacterial Genomics; Comparative Genomics; and Protein Structure Bioinformatics. Gert Vriend heads the protein structure bioinformatics group, and he is the director of the CMBI.
</p>
</div>
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<h3 class="sectionedit2" id="prof_gert_vriend">Prof. Gert Vriend</h3>
<div class="level3">
<p>
<a href="http://swift.cmbi.ru.nl/gv/" class="urlextern" title="http://swift.cmbi.ru.nl/gv/" rel="ugc nofollow">http://swift.cmbi.ru.nl/gv/</a>
</p>
<p>
G Vriend studied biochemistry at the university of Utrecht, The Netherlands and got his PhD in 1983 at the agricultural university of Wageningen, The Netherlands. His PhD project was the study of the assembly process of plant viruses using NMR, EPR, and computational methods. He post-doc-ed in Purdue, Indiana, USA on the X-ray structure of the common cold virus, and in Groningen, The Netherlands where he helped solve several structures by X-ray crystallography, and where he started the WHAT IF project. From 1989-1999 he worked at the EMBL in Heidelberg, Germany, where he continued working on (and with) the WHAT IF program. His main research topics in the EMBL period were protein structure validation and protein engineering. In the summer of 1999 he took up a position at the Radboud University Nijmegen, The Netherlands where he built-up the Centre for Molecular and Biomolecular Informatics (CMBI). At the CMBI he continued working on fundamental and applied aspects of protein structure (homology modelling, structure quality, visualization, molecular dynamics, ligand interactions) and of information technology (data-mining, information systems, interoperability issues). The move of the CMBI from the science faculty to the Medical Centre of the Radboud University in 2007 allowed him to put greater emphasis on the application of protein structure bioinformatics in biomedical research, thereby broadening the applied aspects of his protein structure research.
</p>
<p>
Databases <a href="http://swift.cmbi.ru.nl/gv/facilities/" class="urlextern" title="http://swift.cmbi.ru.nl/gv/facilities/" rel="ugc nofollow">http://swift.cmbi.ru.nl/gv/facilities/</a>
</p>
<p>
Bacterial genomics <a href="http://www2.cmbi.ru.nl/groups/bacterial-genomics/research/" class="urlextern" title="http://www2.cmbi.ru.nl/groups/bacterial-genomics/research/" rel="ugc nofollow">http://www2.cmbi.ru.nl/groups/bacterial-genomics/research/</a>
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
<br/>
Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis. IMBH van de Laar, et al. Nature Genetics (2011) 43,2 121-126.
</p>
<p>
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. H Venselaar et al BMC Bioinformatics (2010) 11 548-557.
</p>
<p>
Human Dectin-1 Deficiency and Mucocutaneous Fungal Infections. B Ferwerda et al New England J Medicine (2009) 361,18 1760-1767.
</p>
<p>
Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35. RWJ Collin, et al. American J Human Genetics (2008) 82,1 125-138.
</p>
<p>
PDB improvement starts with data deposition. RP Joosten, G Vriend. Science (2007) 317,5835 195-196.
</p>
</div>
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http://www.allbioinformatics.eu/doku.php?id=public:sib&rev=1549962287&do=diff
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<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="swiss_institute_of_bioinformatics_switzerland">SWISS INSTITUTE OF BIOINFORMATICS Switzerland</h1>
<div class="level1">
<p>
<strong><a href="http://www.isb-sib.ch" class="urlextern" title="http://www.isb-sib.ch" rel="ugc nofollow">www.isb-sib.ch</a></strong>
</p>
<p>
The SIB Swiss Institute of Bioinformatics is an academic, non-profit foundation recognised of public utility and established in 1998. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community.
</p>
</div>
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<h3 class="sectionedit2" id="dr_laurent_falquet_senior_scientist">Dr. Laurent Falquet (Senior Scientist)</h3>
<div class="level3">
<p>
studied biochemistry at the University of Geneva and obtained his PhD in 1997. He joined the newly created Swiss Institute of Bioinformatics in 1998 as member of the EMBnet team where he was responsible for organizing undergraduate and post-graduate courses, and was involved in teaching activities as well. In addition, he was responsible of the help desk support to the life sciences community, which led to a number of collaborations, and was in charge of several web sites.
In 2002 he became manager of the Swiss EMBnet node. Within the <a href="http://www.embnet.org" class="urlextern" title="http://www.embnet.org" rel="ugc nofollow">EMBnet</a> organisation he was chief editor of the EMBnet.news newsletter from 2003 to 2005 and was secretary of the EMBnet Executive Board from 2007 to 2009. From 2008 to 2010 he was president of the sub-committee for biochemistry and fundamental medicine of the 3eme cycle romand in Biological Sciences. He is member of the StarOmics PhD program and of the SIB PhD network committee. He joined the <a href="http://www.vital-it.ch" class="urlextern" title="http://www.vital-it.ch" rel="ugc nofollow">Vital-IT</a> group in 2009, with responsibility for the genome assembly, annotation and comparative genomics.
He is MC member, representative of Switzerland, in the COST Action <a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">SeqAhead</a>, a network for NGS data analysis.
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Andrés-Barrao C, <strong>Falquet L</strong>, Calderon-Copete SP, Descombes P, Ortega Perez R, Barja F.<br/>
Genome sequence of high acetic acid resistant bacteria: <em>Gluconacetobacter europaeus</em> LMG 18890T, <em>Gluconacetobacter europaeus</em> LMG 18494 (references strains), <em>Gluconacetobacter europaeus</em> 5P3 and <em>Gluconacetobacter oboediens</em> 174Bp2 (isolates from vinegar). <br/>
J. Bacteriology. 2011;193(10):2670-2671.
</p>
<p>
Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, <strong>Falquet L</strong>, Nipitwattanaphon M, Gotzek D, Dijkstra <abbr title="Megabyte">MB</abbr>, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MA, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D, Keller L. <br/>
The Genome of the fire ant, <em>Solenopsis invicta</em>.<br/>
Proc Natl Acad Sci U S A. 2011;108(14):5679-5684.
</p>
<p>
Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, <strong>Falquet L</strong><br/>
The <em>Mycoplasma conjunctivae</em> genome sequencing, annotation and analysis. <br/>
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S7.
</p>
<p>
Beckmann J S, Maurer F, Delorenzi M, <strong>Falquet L.</strong> <br/>
On ubiquitin ligases and cancer<br/>
Hum Mutat. 2005, 25(6):507-12.
</p>
<p>
<strong>Falquet L</strong>, Bordoli L, Ioannidis V, Pagni M, Jongeneel CV.<br/>
Swiss EMBnet node web server.<br/>
Nucleic Acids Res. 2003 Jul 1;31(13):3782-3.
</p>
</div>
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http://www.allbioinformatics.eu/doku.php?id=public:slu&rev=1549962287&do=diff
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<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="sveriges_lantbruksuniversitet_sweden">SVERIGES LANTBRUKSUNIVERSITET Sweden</h2>
<div class="level2">
<p>
SLU (Sveriges lantbruksuniversitet – Swedish University of Agricultural Sciences) is a university with a clearly defined role in society: to take responsibility for the development of learning and expertise in areas concerning biological resources and biological production. This responsibility stretches over the wide-ranging fields of agriculture, forestry and food industry to environmental questions, veterinary medicine and biotechnology. A comprehensive viewpoint, inter-disciplinary approach and applicability are keywords in SLU's research and teaching and in the contacts with industry and society.
</p>
<p>
University activities are spread between several departments in four faculties: the Faculty of Landscape Planning, Horticulture and Agricultural Science, the Faculty of Natural Resources and Agriculture Sciences, the Faculty of Veterinary Medicine and Animal Science and the Faculty of Forest Sciences. A total of 3 200 people are employed at the University.
</p>
<p>
SLU offers a broad spectrum of educational programmes and single subjects courses. About 3 300 undergraduates and 800 postgraduate students are enrolled at SLU.
</p>
<p>
Main campuses are located at Alnarp, Skara, Ultuna and Umeå. Research and teaching activities are carried out throughout the country.
</p>
<p>
<a href="http://www.slu.se/en/" class="urlextern" title="http://www.slu.se/en/" rel="ugc nofollow">http://www.slu.se/en/</a>
</p>
</div>
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<h3 class="sectionedit2" id="prof_erik_bongcam_‐rudloff">Prof. Erik Bongcam‐Rudloff</h3>
<div class="level3">
<p>
Associate Professor Erik Bongcam-Rudloff, is a doctor in medical sciences and a computer scientist.
<a href="http://www.rudloff.se" class="urlextern" title="http://www.rudloff.se" rel="ugc nofollow">http://www.rudloff.se</a>
</p>
<p>
COMMISSIONS:
ONGOING
</p>
<ul>
<li class="level1"><div class="li"> Coordinator of the FP7 project ALLBIO: “Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant sciences” (<a href="http://www.allbioinformatics.eu" class="urlextern" title="http://www.allbioinformatics.eu" rel="ugc nofollow">http://www.allbioinformatics.eu</a> ). 2011-2014.</div>
</li>
<li class="level1"><div class="li"> Coordinator COST Action: Next Generation Sequencing Data Analysis Network” SeqAhead, <a href="http://www.nextgensequencing.org" class="urlextern" title="http://www.nextgensequencing.org" rel="ugc nofollow">www.nextgensequencing.org</a> 2011-2015</div>
</li>
<li class="level1"><div class="li"> Board Member of the International Society for computational Biology (ISCB <a href="http://www.iscb.org" class="urlextern" title="http://www.iscb.org" rel="ugc nofollow">www.iscb.org</a> ), 2012-2015.</div>
</li>
<li class="level1"><div class="li"> Executive board member of EMBnet, 2010-2013.</div>
</li>
<li class="level1"><div class="li"> Coordinator WP7 in the EU FP7 Affinomics project, <a href="http://www.affinomics.org" class="urlextern" title="http://www.affinomics.org" rel="ugc nofollow">www.affinomics.org</a>, 2010-2014</div>
</li>
<li class="level1"><div class="li"> Board member of UPPMAX, Uppsala Multidisciplinary Center for Advanced Computational Sciences <a href="http://www.uppmax.uu.se" class="urlextern" title="http://www.uppmax.uu.se" rel="ugc nofollow">www.uppmax.uu.se</a>. </div>
</li>
<li class="level1"><div class="li"> Board member of the National Supercomputer Centre in Sweden (NSC). Linköping, Sweden. <a href="http://www.nsc.liu.se" class="urlextern" title="http://www.nsc.liu.se" rel="ugc nofollow">www.nsc.liu.se</a></div>
</li>
<li class="level1"><div class="li"> Editor in Chief for EMBnet.Journal since 2000. <a href="http://journal.embnet.org/" class="urlextern" title="http://journal.embnet.org/" rel="ugc nofollow">http://journal.embnet.org/</a> </div>
</li>
<li class="level1"><div class="li"> Director of eBioinformatics.org creators of eBiotools and BioX. <a href="http://www.ebioinformatics.org" class="urlextern" title="http://www.ebioinformatics.org" rel="ugc nofollow">www.ebioinformatics.org</a>. </div>
</li>
</ul>
<p>
PAST
</p>
<ul>
<li class="level1"><div class="li"> Chairman of EMBnet, a science-based group of collaborating bioinformatics nodes</div>
</li>
<li class="level1"><div class="li"> throughout Europe and a number of nodes outside Europe. <a href="http://www.embnet.org" class="urlextern" title="http://www.embnet.org" rel="ugc nofollow">www.embnet.org</a>. 2003-2009.</div>
</li>
<li class="level1"><div class="li"> Executive board member of EMBRACE, a FP6 funded Network of Excellence, which encompasses computational biologists from 17 institutes in 11 European countries. <a href="http://www.embracegrid.info" class="urlextern" title="http://www.embracegrid.info" rel="ugc nofollow">www.embracegrid.info</a>. 2005-2010. WP4 Coordinator.</div>
</li>
<li class="level1"><div class="li"> Member of the WP4 in the ESFRI BBMRI project. <a href="http://www.bbmri.org" class="urlextern" title="http://www.bbmri.org" rel="ugc nofollow">www.bbmri.org</a></div>
</li>
<li class="level1"><div class="li"> Member of the WP10 in the ESFRI ELIXIR project <a href="http://www.elixir-europe.org/" class="urlextern" title="http://www.elixir-europe.org/" rel="ugc nofollow">http://www.elixir-europe.org/</a> </div>
</li>
<li class="level1"><div class="li"> Coordinator WP4 Eurokup, EU COST action. <a href="http://www.eurokup.org" class="urlextern" title="http://www.eurokup.org" rel="ugc nofollow">www.eurokup.org</a> </div>
</li>
</ul>
<p>
<strong>SOFTWARE DEVELOPMENT:</strong>
The Bongcam-Rudloff group has developed web-based bioinformatics analysis systems and desktop applications.
</p>
<p>
<em>Desktop applications:</em>
</p>
<ul>
<li class="level1"><div class="li"> eBioTools: is a collection of more than 300 open source bioinformatics programs, <a href="http://www.ebioinformatics.org" class="urlextern" title="http://www.ebioinformatics.org" rel="ugc nofollow">www.ebioinformatics.org</a>. </div>
</li>
<li class="level1"><div class="li"> eBioX: A highly popular graphic user interface for the eBiotools programmes. eBioX brings easy-to-use sequence analysis to Mac-using biologists. <a href="http://www.ebioinformatics.org" class="urlextern" title="http://www.ebioinformatics.org" rel="ugc nofollow">www.ebioinformatics.org</a></div>
</li>
<li class="level1"><div class="li"> </div>
</li>
</ul>
<p>
<em>WEB-BASED ANALYSIS SYSTEMS:</em>
</p>
<ul>
<li class="level1"><div class="li"> Evaller: In collaboration with Livsmedelsverket: <a href="http://www.slv.se/en-gb/Group1/Food-Safety/e-Testing-of-protein-allergenicity/e-Test-allergenicity/" class="urlextern" title="http://www.slv.se/en-gb/Group1/Food-Safety/e-Testing-of-protein-allergenicity/e-Test-allergenicity/" rel="ugc nofollow">http://www.slv.se/en-gb/Group1/Food-Safety/e-Testing-of-protein-allergenicity/e-Test-allergenicity/</a> </div>
</li>
<li class="level1"><div class="li"> eBioKit: eBioKit is a compilation of online open source databases and software hosted on the same server and connected to educational resources. Test site: <a href="http://ebiokit.hgen.slu.se" class="urlextern" title="http://ebiokit.hgen.slu.se" rel="ugc nofollow">http://ebiokit.hgen.slu.se</a>. </div>
</li>
<li class="level1"><div class="li"> MolMeth: MolMeth is a structured database that provides free access to methods used in molecular biology and molecular medicine: <a href="http://www.molmeth.org" class="urlextern" title="http://www.molmeth.org" rel="ugc nofollow">www.molmeth.org</a>. </div>
</li>
<li class="level1"><div class="li"> SeqScoring: Use the information to score mutations found by large re-sequencing projects. Finds positions for conserved elements among different species and present the results on a graphical way: <a href="http://www.seqscoring.net" class="urlextern" title="http://www.seqscoring.net" rel="ugc nofollow">www.seqscoring.net</a>. </div>
</li>
</ul>
</div>
<h4 id="publications_2012">Publications 2012</h4>
<div class="level4">
<p>
1. Klingström T, Soldatova L, Stevens R, et. al. - “Workshop on laboratory protocol standards for the molecular methods database” N Biotechnol. 2012 Jun 2. [Epub ahead of print]
</p>
<p>
2. Biao Wang, Robert Ekblom, Todd A. Castoe, et. al. - “Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development” 10.1098/rsob.120054 Open Biol April 2012
</p>
<p>
3. Anne Fischer, Beth Shapiro, Cecilia Muriuki, et. al. - “The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants” 2012. PLoS ONE 7(4): e36150. doi:10.1371/journal.pone.0036150
</p>
<p>
4. Harald Mischak, John P.A., Ioannidis Angel Argiles, et. al. - “Implementation of proteomic biomarkers: making it work. European Journal of Clinical Investigation” Article first published online: 21 APR 2012. DOI: 10.1111/j.1365-2362.2012.02674.x
</p>
</div>
<h4 id="publications_2011">Publications 2011</h4>
<div class="level4">
<p>
1. SEQscoring: a tool to facilitate the interpretation of data generated with next generation sequencing technologies. Katarina Truvé, Oscar Eriksson, Martin Norling, Maria Wilbe, Evan Mauceli, Kerstin Lindblad-Toh, Erik Bongcam-Rudloff. EMBnet.journal. 2011, Vol 17, no 1, pp 38-45
</p>
<p>
2. SEQAHEAD - COST Action BM1006: Next Generation Sequencing Data Analysis Network , EMBnet.journal, 2011, Vol 17, no1, pp 7-9
</p>
<p>
3. The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. Martínez Barrio A, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff E, Blomberg J, Andersson G. PLoS One. 2011 May 12;6(5):e19832.
</p>
<p>
4. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.
Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K.
PLoS Genet. 2011 Mar;7(3):e1001332. Epub 2011 Mar 17.
</p>
<p>
5. Contributions of the EMERALD project to assessing and improving microarray data quality. Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M. Biotechniques. 2011 Jan;50(1):27-31.
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Erik Bongcam\u00ad\u2010Rudloff","hid":"prof_erik_bongcam_\u2010rudloff","codeblockOffset":0,"secid":2,"range":"1395-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:sluplant
http://www.allbioinformatics.eu/doku.php?id=public:sluplant&rev=1549962287&do=diff
<h3 class="sectionedit1" id="the_future_of_plant_biotechnology_in_europe">The Future of Plant Biotechnology in Europe</h3>
<div class="level3">
</div>
<h4 id="emerging_technologies_and_policy_making">- Emerging Technologies and Policy Making</h4>
<div class="level4">
<p>
A SEMINAR DAY ORGANIZED BY PLANT LINK, MISTRA BIOTECH AND PARTNERSHIP ALNARP
</p>
<p>
Europe has adopted restrictive policies on genetically modified crops. This restrictiveness has partly been dictated by a prevailing skepticism among the general public and NGOs. As a consequence the cultivation of genetically modified crops has remained limited in Europe. Still, several research groups continue to develop crops with new traits, refine breeding technologies, and develop new ways to improve crop properties with the help of biotechnology. But what are the future prospects for these projects and which is the way forward?
This seminar day will give insight on current plant biotech research in Europe, legislative processes, new technologies and farmer and public acceptance. The day will provide good possibilities to discuss the future for plant biotechnology in the EU.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:future_plant_biotech_7_nov.pdf" class="media mediafile mf_pdf" title="public:future_plant_biotech_7_nov.pdf (546.8 KB)">Programme</a>
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:start
http://www.allbioinformatics.eu/doku.php?id=public:start&rev=1549962287&do=diff
<h2 class="sectionedit1" id="hackathon2_test_cases_9_and_12">HACKATHON2 Test Cases #9 and #12</h2>
<div class="level2">
<p>
Promising results from the first hack-a-thon session in September (Amsterdam) encouraged us to organize a second session for for these 2 Test Cases #9 and #12. It will take place from 27 to 29 November in the Department of Plant Protection Biology of Sveriges lantbruksuniversitet (SLU), Alnarp, Sweden.
</p>
<p>
More details about working room and hotel will follow…
</p>
<p>
TC Leaders: Oren Tzfadia and Erik Alexandersson
</p>
<p>
<strong>Participants:</strong><br/>
Agnieszka Danek (Silesian University of Technology, Gliwice, Poland)<br/>
Estelle Wera (SLU)<br/>
Itziar Frades (SLU)<br/>
Didi Amar (Weizmann Institute)<br/>
Erik Alexandersson (SLU)<br/>
Oren Tzfadia (Weizmann Institute)<br/>
</p>
<p>
<strong>Software</strong>: Use of already set-up VM (surfSara, Amsterdam)
</p>
<p>
<strong>To-do list before the hack-a-thon:</strong><br/>
Finish outstanding workflows for comparison during hack-a-thon and visualization of outcome (Didi, Estelle, Itziar and Tanya).<br/>
Maintenance of VM (Agnieszka).
</p>
<p>
<strong>To-do list during the hack-a-thon:</strong><br/>
More details will follow soon…
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:tc5-15
http://www.allbioinformatics.eu/doku.php?id=public:tc5-15&rev=1549962287&do=diff
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atc5-15&media=public:dsc_2592.jpg" class="media" title="public:dsc_2592.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=079bb7&media=public:dsc_2592.jpg" class="media" loading="lazy" alt="" width="500" /></a>
</p>
<p>
<strong>HACKATON for Test Cases 5 and 15</strong>
</p>
<p>
This meeting was the start-up for two submitted test cases:
</p>
<ul>
<li class="level1"><div class="li"> TC 5, CattleOmics- Integrative Omics analysis workflow</div>
</li>
<li class="level1"><div class="li"> TC 15, SOMICS- Genetics, Genomics and Evolution of prolific breeds of domestic sheep (Ovis aries).</div>
</li>
</ul>
<p>
The meeting hosted 17 participants representing; Life Glimmer GmbH, Germany, Swiss Institute of Bioinformatics, Switzerland, MTT Agrifood Research, Finland, Centro de Investigación Príncipe Felipe (CIPF), Spain, CSC-IT Centre for Science, Finland, Biomedical Research Foundation of the Academy of Athens, Greece, and the Swedish University of Agricultural Sciences.
</p>
<p>
Researchers from SLU submitted TC 5 and researchers from MTT Agrifood Research submitted TC 15. Both TCs involve the study of reproduction ability in domesticated animals under different feeding conditions, which made it possible to merge this start-up session. Both TCs will also use high-throughput methods such as RNA-sequencing to reach their goals.
</p>
<p>
One common problem for both TCs is that integration of results from different datasets is needed to reach the expected goals. TC 5 represents parts of the EU-project PROLIFIC where several researchers from Hgen are involved and SGBC carries the main responsibility for solving the bioinformatics needed for the project.
</p>
<p>
<strong>Schedule</strong>
</p>
<p>
The time set for presentations should also include questions and discussion.
</p>
<p>
<em><strong>Day 1, Monday 7th of October:</strong></em><br/>
9.30- Event starts at Park Inn Uppsala, Erik will have a small welcome talk.<br/>
9.40- Grégoire presents the role of the hack-a-thon days in the project.<br/>
10.00- Break for coffee.<br/>
10.30- Presentation of test case 5, CattleOmics, Patrice Humblot.<br/>
11.15- Presentation of test case 15, SOMICS, Juha Kantanen.<br/>
12.00- Lunch<br/>
13.00- Solution provider presentation, STATegra, Ana Conesa.<br/>
14.00- Solution provider presentation, Chipster, Eija Korpelainen.<br/>
15.00- Break for coffee.<br/>
15.30- 17.00 Discussion about how to divide the work to provide solutions for each TC. Coordinate groups for discussion and problem solving Day 2.<br/>
19.00- Go out for dinner.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atc5-15&media=public:dsc_2583.jpg" class="media" title="public:dsc_2583.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=1378f8&media=public:dsc_2583.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
</p>
<p>
<em><strong>Day 2, Tuesday 8th of October:</strong></em><br/>
06.30-8.30 Breakfast<br/>
8.30- Group discussions, problem solving.<br/>
10.00- Break for coffee.<br/>
10.30- Continue group discussions and problem solving.<br/>
12.00- Lunch<br/>
13.00- Continue group discussions and problem solving.<br/>
14.00- Make summary and evaluation of event. Make plans for second hack-a- thon. Who will do what to keep the work moving forward?<br/>
15.00- Coffee. Continue with summary and evaluation.<br/>
16.00- Event ends.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atc5-15&media=public:dsc_2538.jpg" class="media" title="public:dsc_2538.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=e655fb&media=public:dsc_2538.jpg" class="media" loading="lazy" title=" " alt=" " width="300" /></a>
</p>
<p>
<em><strong>How to get to Uppsala from Stockholm Arlanda</strong></em><br/>
The easiest way to get from the airport to Uppsala central station is to go by train. This is both faster and cheaper than taking a cab. There is one train every 30 min leaving from Arlanda central station, the trip to Uppsala C will take approximately 20 min. You can buy tickets for the train at Arlanda central station. For more information follow the link and scroll down to commuter trains.
<a href="http://www.swedavia.com/arlanda/to-from/train/" class="urlextern" title="http://www.swedavia.com/arlanda/to-from/train/" rel="ugc nofollow">http://www.swedavia.com/arlanda/to-from/train/</a>
Note that these trains also are used for people travelling to Stockholm, so make sure that you catch the train going in the right direction, i.e. to Uppsala and NOT to Stockholm.
</p>
<p>
<em><strong>How to find the hotel and meeting location?</strong></em><br/>
All participants will be accommodated at hotel Park Inn, Uppsala. This is also the location for our meetings. The hotel will provide lunch and coffee during the event. The hotel is located only a 5 min walk from Uppsala central station. For more information, please see the links below.<br/>
<a href="http://www.parkinn.com/hotel-uppsala" class="urlextern" title="http://www.parkinn.com/hotel-uppsala" rel="ugc nofollow">http://www.parkinn.com/hotel-uppsala</a><br/>
<a href="http://www.parkinn.com/hotel-uppsala/location" class="urlextern" title="http://www.parkinn.com/hotel-uppsala/location" rel="ugc nofollow">http://www.parkinn.com/hotel-uppsala/location</a><br/>
</p>
<p>
<em><strong>General information</strong></em><br/>
Since Swedish stores are not obligated to take euros you will need Swedish kronor or a payment card to buy train tickets (and for shopping).<br/>
Some of you asked about the Swedish electrical outlet, the link below provide a guide with all European standards.<br/>
<a href="http://www.worldstandards.eu/electricity.htm" class="urlextern" title="http://www.worldstandards.eu/electricity.htm" rel="ugc nofollow">http://www.worldstandards.eu/electricity.htm</a>
</p>
<p>
If you need to contact me (Monika Brandt) when you have arrived to Sweden, call me on 004673-669 53 27.
</p>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:testcaseanalysis
http://www.allbioinformatics.eu/doku.php?id=public:testcaseanalysis&rev=1549962287&do=diff
<h3 class="sectionedit1" id="allbio_consortium_meeting">AllBio Consortium Meeting</h3>
<div class="level3">
</div>
<h4 id="test_case_analysis_and_ontology_meeting">Test Case Analysis and Ontology meeting</h4>
<div class="level4">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atestcaseanalysis&media=public:dsc_3457.jpg" class="media" title="public:dsc_3457.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=4d940c&media=public:dsc_3457.jpg" class="media" loading="lazy" title="dsc_3457.jpg" alt="dsc_3457.jpg" width="500" /></a>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atestcaseanalysis&media=public:dsc_3465.jpg" class="media" title="public:dsc_3465.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=5ee912&media=public:dsc_3465.jpg" class="media" loading="lazy" title="dsc_3465.jpg" alt="dsc_3465.jpg" width="500" /></a>
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Atestcaseanalysis&media=public:dsc_3469.jpg" class="media" title="public:dsc_3469.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=f0dcd3&media=public:dsc_3469.jpg" class="media" loading="lazy" title="dsc_3469.jpg" alt="dsc_3469.jpg" width="500" /></a>
</p>
<p>
3 June 2012 - Uppsala, Sweden
</p>
<p>
09:00 Welcome by Erik Bongcam-Rudloff
</p>
<p>
09:00 - 10:30 Test Case presentations collected (shortly present each test case)
</p>
<p>
10:30 - 10:45 Coffee Break
</p>
<p>
10:45 - 12:30 Test Case discussion (discuss feasibility and challenges)
</p>
<p>
12:30 - 14:00 Lunch
</p>
<p>
14:00 - 15:30 Meeting: Ontology, Webservices and technology recommendation - responsible UNIMAN & RUNMC
</p>
<p>
15:30 - 16:00 Coffee Break
</p>
<p>
16:00 - 17:00 Strategic meeting
</p>
<ul>
<li class="level1"><div class="li"> preparation “Bioinformatics Workshop: Evaluation of Test Cases” for November/December - responsible CNR</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> preparation AGM in September, place and time - responsible SLU</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Inventory of tools - responsible UP</div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Inventory design - responsible UNIMAN</div>
</li>
</ul>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:testcasetempl
http://www.allbioinformatics.eu/doku.php?id=public:testcasetempl&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="allbio_test_case_form">AllBio Test Case Form</h2>
<div class="level2">
<form class="bureaucracy__plugin" id="bureaucracy__plugin2" enctype="multipart/form-data" method="post" action="" accept-charset="utf-8"><div class="no">
<input type="hidden" name="sectok" value="" /><input type="hidden" name="bureaucracy[$$id]" value="2" /><fieldset ><legend>Basic information</legend>
<label><span>Test Case Title <sup>*</sup></span> <input type="text" name="bureaucracy[1]" class="edit required" required="required" /></label>
<p> A short title</p><label><span>Test Case Acronyme <sup>*</sup></span> <input type="text" name="bureaucracy[3]" class="edit required" required="required" /></label>
<label><span>Select a Test Case Class <sup>*</sup></span> <select name="bureaucracy[5]">
<option value="Microbial" selected="selected">Microbial</option><option value="Livestock">Livestock</option><option value="Plants">Plants</option><option value="Microbial-Livestock">Microbial-Livestock</option><option value="Microbial-Plants">Microbial-Plants</option><option value="Livestock-Plants">Livestock-Plants</option><option value="Microbial-Livestock-Plants">Microbial-Livestock-Plants</option>
</select></label>
<label><span>Name of contact person <sup>*</sup></span> <input type="text" name="bureaucracy[7]" class="edit required" required="required" /></label>
<label><span>E-mail of the contact person <sup>*</sup></span> <input type="text" name="bureaucracy[8]" class="edit required" required="required" /></label>
</fieldset>
<fieldset ><legend>Test Case Description</legend>
<label class=" textareafield">
<span>Short introduction to the Test Case <sup>*</sup></span>
<textarea name="bureaucracy[10]" id="" rows="10" cols="10" class="edit required" required="required">Which is the biological question that needs to be answered? Which organism(s) will the test case address?</textarea>
</label><p>Try to write this such that someone not from the field can read it.</p><label class=" textareafield">
<span>Background knowledge (optional!)</span>
<textarea name="bureaucracy[12]" id="" rows="10" cols="10" class="edit 1"></textarea>
</label><p>Provide additional information to the introduction to place the problem in a 'real-world' context; supplies conceptual relevance that is not part of the problem.</p><label class=" textareafield">
<span>Actors <sup>*</sup></span>
<textarea name="bureaucracy[14]" id="" rows="10" cols="10" class="edit required" required="required"></textarea>
</label><p>List here all major actors. Actors can be groups or individuals. If a research group participates, don't list all members. Write a few words about the roles of the actors, Separate out whom you are locally/nationally going to start with (use the top box for the initial, mostly local actors, and the bottom box in case you later get more actors involved. It will often be useful to distinguish between biologists, bioinformaticians, and service providers as the end-user. </p><label class=" textareafield">
<span>Initial state of the Test case <sup>*</sup></span>
<textarea name="bureaucracy[16]" id="" rows="10" cols="10" class="edit required" required="required">Which type of data is available? (sequencing - which technology? data from other -omics technologies/other data resources? Which state of processing/intermediate software tools are used and how are they used?</textarea>
</label><p>Briefly describe where the project is standing now (i.e. give some kind of zero-state description). Please write this in the light of the next box.</p><label class=" textareafield">
<span>Desired final state of the Test Case <sup>*</sup></span>
<textarea name="bureaucracy[18]" id="" rows="10" cols="10" class="edit required" required="required">What will be the result of the development? Or if known which tool(s) and/or database(s) should be included?</textarea>
</label><p>Briefly describe where the project should be standing at the end of ALLBIO support. Please write this in the light of the previous box.</p><label class=" textareafield">
<span>Test Case Work Plan (optional!)</span>
<textarea name="bureaucracy[20]" id="" rows="10" cols="10" class="edit 1"></textarea>
</label><p>Briefly describe what you are going to do. Describe which problems you believe should be solved to get from the initial state to the desired final state. Feel free to think out of the box. Use the top box for the technical things. Use the bottom box for the meetings you plan (nationally and internationally).
In the technical box, list whether you intend to use exsiting things, whether you intend to write new software (and which actors will do that), etc. Please do not forget the ALLBIO mission.</p><label class=" textareafield">
<span>Discussion (optional!)</span>
<textarea name="bureaucracy[22]" id="" rows="10" cols="10" class="edit 1"></textarea>
</label><p>This is the free for all box. You can list here things like the importance of this test case for certain fields, groups, or actors. References to projects or articles that relate to the problem, etc.</p><label class=" textareafield">
<span>Related Test Cases (optional!)</span>
<textarea name="bureaucracy[24]" id="" rows="10" cols="10" class="edit 1"></textarea>
</label><p>If you accidentally know about related test cases (i.e. test cases with which you can share software or actors), then please list them here; if not, leave this box here for the board or other ALLBIO members to write notes on inter test case relations.</p></fieldset>
<fieldset ><legend>Agreement</legend>
<p>Agree that the Test Case will be published on this site as soon as selected. The authors will be informed before the publication.</p><label><span>You need to write 'agree' here <sup>*</sup></span> <input type="text" name="bureaucracy[28]" class="edit required" required="required" /></label>
<p> ☞ </p><div id="plugin__captcha_wrapper"><input type="hidden" name="fc9c95b2ae45ddb7a95b798f3a76edcf" value="OeDCYwheA0GmwxvMwSOJrqR48YjbfLmtBuF31pwjrCs=" /><label for="plugin__captcha">Please fill all the letters into the box to prove you're human.</label> <img src="http://www.allbioinformatics.eu/lib/plugins/captcha/img.php?secret=OeDCYwheA0GmwxvMwSOJrqR48YjbfLmtBuF31pwjrCs%3D&id=public:testcasetempl" width="125" height="30" alt="" /> <input type="text" size="5" name="2f0ef0b391e33e23c30a7336932f5524" class="edit" /> <label class="no">Please keep this field empty: <input type="text" name="944d9678cc153d98bd080b6c3e8bea12" /></label></div><button type="submit">Submit Form</button>
</fieldset>
</div></form>
</div>
<!-- EDIT{"target":"section","name":"AllBio Test Case Form","hid":"allbio_test_case_form","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:test_cases
http://www.allbioinformatics.eu/doku.php?id=public:test_cases&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="test_cases">Test Cases</h2>
<div class="level2">
<p>
AllBio will work with Test Cases the partners will define with help of external groups. Test cases will come from livestock, microbiology and plant research and will describe complex bionformatics problems. AllBio will coordinate the solution of some Test Cases and present the solutions during dedicated events.
</p>
<p>
In July 2012 AllBio will publish a list of test cases and will search for collaboration to solve them.
In January 2013 during the “Open Bioinformatics Workshop: Evaluation of Test Cases” concrete approaches for there solution will be developed and interest groups will be formed to work them out.
</p>
<p>
Submit online a <a href="http://www.allbioinformatics.eu/doku.php?id=public:testcasetempl" class="wikilink1" title="public:testcasetempl" data-wiki-id="public:testcasetempl">Test Case</a> describing your data analysis approach or download the <a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:allbio_test_case_template.doc" class="media mediafile mf_doc" title="public:allbio_test_case_template.doc (1.7 MB)"> Test Case Template</a> and submit it to <strong>andreas.gisel AT ba.itb.cnr DOT it</strong> adding “Allbio Test Case” as subject.
<br/>
<br/>
</p>
</div>
<!-- EDIT{"target":"section","name":"Test Cases","hid":"test_cases","codeblockOffset":0,"secid":1,"range":"39-945"} -->
<h2 class="sectionedit2" id="selected_test_cases">Selected Test Cases</h2>
<div class="level2">
<ol>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc1" class="wikilink1" title="public:loadedtestcases:tc1" data-wiki-id="public:loadedtestcases:tc1">FAIRE-seq data analyser</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc2" class="wikilink1" title="public:loadedtestcases:tc2" data-wiki-id="public:loadedtestcases:tc2">Identification of large structural variations</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc3" class="wikilink1" title="public:loadedtestcases:tc3" data-wiki-id="public:loadedtestcases:tc3">Discovery of gene regulatory networks</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc4" class="wikilink1" title="public:loadedtestcases:tc4" data-wiki-id="public:loadedtestcases:tc4">Primer design for ChIP-PCR studies</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc5" class="wikilink1" title="public:loadedtestcases:tc5" data-wiki-id="public:loadedtestcases:tc5">Integrative Omics analysis workflow</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc6" class="wikilink1" title="public:loadedtestcases:tc6" data-wiki-id="public:loadedtestcases:tc6">Bacterial Comparative Genomics</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc7" class="wikilink1" title="public:loadedtestcases:tc7" data-wiki-id="public:loadedtestcases:tc7">Processing an un-annotated genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc8" class="wikilink1" title="public:loadedtestcases:tc8" data-wiki-id="public:loadedtestcases:tc8">Discover non-coding RNA in yeast</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9" class="wikilink1" title="public:loadedtestcases:tc9" data-wiki-id="public:loadedtestcases:tc9">Pathway analysis of a poorly annotated but sequenced plant genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc10" class="wikilink1" title="public:loadedtestcases:tc10" data-wiki-id="public:loadedtestcases:tc10">Gene prediction modelling for plants</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc11" class="wikilink1" title="public:loadedtestcases:tc11" data-wiki-id="public:loadedtestcases:tc11">Genome assembly of heterozygous diploid data</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12" class="wikilink1" title="public:loadedtestcases:tc12" data-wiki-id="public:loadedtestcases:tc12">Functional annotation of the potato genome</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc13" class="wikilink1" title="public:loadedtestcases:tc13" data-wiki-id="public:loadedtestcases:tc13">Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc14" class="wikilink1" title="public:loadedtestcases:tc14" data-wiki-id="public:loadedtestcases:tc14">Improved cell factories</a></strong></div>
</li>
<li class="level1"><div class="li"> <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc15" class="wikilink1" title="public:loadedtestcases:tc15" data-wiki-id="public:loadedtestcases:tc15">Genetics, Genomics and Evolution of prolific breeds of domestic
sheep (Ovis aries)</a></strong></div>
</li>
</ol>
</div>
<!-- EDIT{"target":"section","name":"Selected Test Cases","hid":"selected_test_cases","codeblockOffset":0,"secid":2,"range":"946-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:tools_and_services
http://www.allbioinformatics.eu/doku.php?id=public:tools_and_services&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="inventory_of_available_tools_and_services_across_the_areas">Inventory of available tools and services across the areas</h2>
<div class="level2">
<p>
A comprehensive search for bioinformatics tools, databases and services was conducted throughout the project, focusing in particular on those relevant to animals, unicellular animals and plants,
and to those required for the completion of the test cases outlined in Working Package 1
</p>
<p>
The extensive list including the liks to the tools are available on the following site:
</p>
<p>
<a href="http://bioinformatics.hgen.slu.se/ALLBIO-TOOLS/" class="urlextern" title="http://bioinformatics.hgen.slu.se/ALLBIO-TOOLS/" rel="ugc nofollow">http://bioinformatics.hgen.slu.se/ALLBIO-TOOLS/</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"Inventory of available tools and services across the areas","hid":"inventory_of_available_tools_and_services_across_the_areas","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:ulb
http://www.allbioinformatics.eu/doku.php?id=public:ulb&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="universite_libre_de_bruxelles_belgium">UNIVERSITÉ LIBRE DE BRUXELLES Belgium</h2>
<div class="level2">
</div>
<!-- EDIT{"target":"section","name":"UNIVERSIT\u00c9 LIBRE DE BRUXELLES\tBelgium","hid":"universite_libre_de_bruxelles_belgium","codeblockOffset":0,"secid":1,"range":"39-90"} -->
<h3 class="sectionedit2" id="prof_jacques_van_helden">Prof. Jacques van Helden</h3>
<div class="level3">
<p>
Since 15 years, my research activities consist in conceiving, developing, assessing and applying original bioinformatics approaches to analyze regulatory sequences, metabolic pathways and biomolecular networks. The current project is in direct continuation with the results of this research and development activity.
</p>
</div>
<h4 id="bioinformatics_approaches_and_tools">Bioinformatics approaches and tools</h4>
<div class="level4">
</div>
<h5 id="regulatory_sequence_analysis_tools_rsat">Regulatory Sequence Analysis Tools (RSAT)</h5>
<div class="level5">
<p>
Web site: <a href="http://rsat.ulb.ac.be/rsat/" class="urlextern" title="http://rsat.ulb.ac.be/rsat/" rel="ugc nofollow">http://rsat.ulb.ac.be/rsat/</a>
</p>
<p>
A software suite dedicated to the analysis of motifs in cis-regulatory sequences. RSAT combines several original algorithms for detecting cis-regulatory motifs in promoters of co-expressed genes (transcriptome data), detection of phylogenetic footprints (conserved elements in promoters of orthologous genes), analysis of high-throughput sequencing data (ChIP-seq) or full genomes. To my best knowledge, RSAT is currently the most complete Web resource worldwide for the analysis of regulatory sequences.
</p>
</div>
<h5 id="network-based_approaches_to_analyze_metabolic_pathways">Network-based approaches to analyze metabolic pathways</h5>
<div class="level5">
<p>
Since 1999, I developed bioinformatics approaches applying graph theory methods (path finding, subgraph extraction) to discover metabolic pathways in reaction networks (built by compiling all known reactions, their substrates and products). Typical applications are the analysis of metabolic regulation by inferring pathways from groups of co-expressed enzymes, or the reconstruction of bacterial metabolism by building pathways from operons, regulons or groups of genes co-occurring across genomes (phylogenetic profiles).
</p>
</div>
<h5 id="network_analysis_tools_neat">Network analysis tools (NeAT)</h5>
<div class="level5">
<p>
Web site: <a href="http://rsat.ulb.ac.be/neat/" class="urlextern" title="http://rsat.ulb.ac.be/neat/" rel="ugc nofollow">http://rsat.ulb.ac.be/neat/</a>
</p>
<p>
Since 2005, the RSAT suite has been complemented by a series of specialized tools for the analysis of biomolecular networks. The software suite Network Analysis Tools (NeAT) supoprts the analysis of various types of biomolecular networks: protein interactions, gene regulation, horizontal transfer between bacterial genomes, etc. The metabolic pathway discovery tools have also been integrated in the NeAT suite.
</p>
</div>
<h5 id="assessment_of_bioinformatics_approaches">Assessment of bioinformatics approaches</h5>
<div class="level5">
<p>
A specificity of my work is the permanent effort to assess bioinformatics approaches. Irrespective of the domain of application (cis-regulatory motifs, metabolic pathways, network analysis), bioinformatics is essentially predictive and relies, implicitly or explicitly, on theoretical models. An important part of my scientific research has been dedicated to the assessment of the reliability of predictions, by establishing positive controls (correspondence between predictions and previous knowledge) and negative controls (capacity of the programs to return a negative response when the input data contains no significant signal). Beyond the evaluations accompanying the development of each novel algorithm, several of my publications are explicitly dedicated to methodological evaluations.
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Jacques van Helden","hid":"prof_jacques_van_helden","codeblockOffset":0,"secid":2,"range":"91-3072"} -->
<h3 class="sectionedit3" id="publications">Publications</h3>
<div class="level3">
</div>
<h4 id="recent_publications">Recent publications</h4>
<div class="level4">
<ul>
<li class="level1"><div class="li"> Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568 <a href="http://www.ncbi.nlm.nih.gov/pubmed/22836136" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/22836136" rel="ugc nofollow">PMID
22836136</a></div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Jacques van Helden, Ariane Toussaint and Denis Thieffry (2012). Bacterial Molecular Networks. Methods in Molecular Biology, Volume 804 (28 chapters) <a href="http://www.springer.com/life+science/microbiology/book/978-1-61779-360-8" class="urlextern" title="http://www.springer.com/life+science/microbiology/book/978-1-61779-360-8" rel="ugc nofollow">Publisher's site</a></div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> van Helden, J., Toussaint, A. and Thieffry, D. (2012). Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling. Methods Mol Biol 804, 1-11 <a href="http://www.ncbi.nlm.nih.gov/pubmed/22144145" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/22144145" rel="ugc nofollow">PMID 22144145</a></div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Faust, K. and van Helden, J. (2012). Predicting Metabolic Pathways by Sub-network Extraction. Methods Mol Biol 804, 107-30.<a href="http://www.ncbi.nlm.nih.gov/pubmed/22144151" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/22144151" rel="ugc nofollow">PMID 22144151</a></div>
</li>
</ul>
<ul>
<li class="level1"><div class="li"> Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31. <a href="http://www.ncbi.nlm.nih.gov/pubmed/22156162" class="urlextern" title="http://www.ncbi.nlm.nih.gov/pubmed/22156162" rel="ugc nofollow">PMID 22156162</a> <a href="http://nar.oxfordjournals.org/content/early/2011/12/08/nar.gkr1104.full?keytype=ref&ijkey=zOvloLjtKzL73F8" class="urlextern" title="http://nar.oxfordjournals.org/content/early/2011/12/08/nar.gkr1104.full?keytype=ref&ijkey=zOvloLjtKzL73F8" rel="ugc nofollow">Open access</a></div>
</li>
</ul>
</div>
<h5 id="full_list_of_publications">Full list of publications</h5>
<div class="level5">
<p>
<a href="http://www.bigre.ulb.ac.be/Users/jvanheld/publications_JvH.html" class="urlextern" title="http://www.bigre.ulb.ac.be/Users/jvanheld/publications_JvH.html" rel="ugc nofollow">http://www.bigre.ulb.ac.be/Users/jvanheld/publications_JvH.html</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"Publications","hid":"publications","codeblockOffset":0,"secid":3,"range":"3073-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:uniman
http://www.allbioinformatics.eu/doku.php?id=public:uniman&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="the_university_of_manchester_united_kingdom">THE UNIVERSITY OF MANCHESTER United Kingdom</h2>
<div class="level2">
<p>
<a href="http://www.manchester.ac.uk/" class="urlextern" title="http://www.manchester.ac.uk/" rel="ugc nofollow">www.manchester.ac.uk/</a>
</p>
<p>
The University of Manchester was created by bringing together The Victoria University of Manchester and UMIST, two of Britain's most distinguished universities, in 2004. Around 4,300 academic and research staff teach more than 28,000 undergraduate and more than 11,000 postgraduate students across 400 degree programmes. The University hosts arguably the largest bioinformatics research group outside the EBI, with strong research programmes in molecular and genome evolution, comparative and organismal biology, computational biology, and structural and functional systems.
</p>
</div>
<!-- EDIT{"target":"section","name":"THE UNIVERSITY OF MANCHESTER\tUnited Kingdom","hid":"the_university_of_manchester_united_kingdom","codeblockOffset":0,"secid":1,"range":"50-703"} -->
<h3 class="sectionedit2" id="prof_teresa_attwood">Prof. Teresa Attwood</h3>
<div class="level3">
<p>
<a href="http://www.bioinf.manchester.ac.uk/dbbrowser" class="urlextern" title="http://www.bioinf.manchester.ac.uk/dbbrowser" rel="ugc nofollow">www.bioinf.manchester.ac.uk/dbbrowser</a>
</p>
<p>
Terri Attwood is a biophysicist by training, having received her BSc and PhD from Leeds University in 1982 and 1984. As a postdoc, she became interested in protein sequence and structure analysis and, in 1993, was awarded a prestigious Royal Society University Research Fellowship to develop tools for computational analysis of protein families: the first 5 years of the fellowship were held at University College London, and the last 4 at the University of Manchester, where she became Professor of Bioinformatics in 2001.
</p>
<p>
Her work on protein sequence analysis (especially of G protein-coupled receptors) led to the development of various databases: e.g., PRINTS (<a href="http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS" class="urlextern" title="http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS" rel="ugc nofollow">www.bioinf.manchester.ac.uk/dbbrowser/PRINTS</a>), InterPro (<a href="http://www.ebi.ac.uk/interpro" class="urlextern" title="http://www.ebi.ac.uk/interpro" rel="ugc nofollow">www.ebi.ac.uk/interpro</a>), CADRE (<a href="http://www.cadre-genomes.org.uk" class="urlextern" title="http://www.cadre-genomes.org.uk" rel="ugc nofollow">www.cadre-genomes.org.uk</a>). She has also pioneered and co-developed a range of software tools: e.g., CINEMA/Utopia (utopia.cs.man.ac.uk/utopia), MINOTAUR (<a href="http://www.bioinf.manchester.ac.uk/dbbrowser/minotaur/about.html" class="urlextern" title="http://www.bioinf.manchester.ac.uk/dbbrowser/minotaur/about.html" rel="ugc nofollow">www.bioinf.manchester.ac.uk/dbbrowser/minotaur/about.html</a>), EMBER (<a href="http://www.ember.man.ac.uk" class="urlextern" title="http://www.ember.man.ac.uk" rel="ugc nofollow">www.ember.man.ac.uk</a>).
</p>
<p>
More recently, her interests have extended to semantic integration of research data with scholarly publications, in order to bring static documents to ‘life’. In particular, with Steve Pettifer, she ran a pilot project with Portland Press Ltd. to create the <em>Semantic Biochemical Journal</em> by embedding Utopia functionality directly into static PDF articles. The <em>Semantic BJ</em> was launched in 2009, powered by Utopia Documents (<a href="http://www.biochemj.org/bj/semantic_faq.htm" class="urlextern" title="http://www.biochemj.org/bj/semantic_faq.htm" rel="ugc nofollow">www.biochemj.org/bj/semantic_faq.htm</a>).
</p>
<p>
In her spare time, she Chairs EMBnet, the Global Bioinformatics Network (<a href="http://www.embnet.org" class="urlextern" title="http://www.embnet.org" rel="ugc nofollow">www.embnet.org</a>), and sits on the Executive Board of the International Society for Biocuration (<a href="http://biocurator.org" class="urlextern" title="http://biocurator.org" rel="ugc nofollow">http://biocurator.org</a>). She is currently Co-Chair of the Bioinformatics Training Network (<a href="http://www.biotnet.org" class="urlextern" title="http://www.biotnet.org" rel="ugc nofollow">www.biotnet.org</a>), Vice Chair of the COST Action NGS Data Analysis Network, SeqAhead (<a href="http://www.seqahead.eu" class="urlextern" title="http://www.seqahead.eu" rel="ugc nofollow">www.seqahead.eu</a>) and co-Chair of Working Group 4 of COST Action EuroKUP (<a href="http://www.eurokup.org" class="urlextern" title="http://www.eurokup.org" rel="ugc nofollow">www.eurokup.org</a>).
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Attwood, T.K., Gisel, A., Eriksson, N-E. & Bongcam-Rudloff, E. (2011) Concepts, historical milestones and the central place of bioinformatics in modern biology: a European perspective. <em>Intech Online Publishers</em>, ISBN 978-953-307-282-1.
</p>
<p>
Schneider, M.V., Walter, P., Blatter, M.C., Watson, J., Brazas, M.D., Rother, K., Budd, A., Via, A., van Gelder, C.W.G., Jacob, J., Fernandes, P., Nyronen, T., De Las Rivas, J., Blicher, T., Loveland, J., McDowall, J., Jones, P., Vaughan, B., Lopez, R., Attwood, T.K. & Brooksbank, C. (2011) Bioinformatics Training Network (BTN): A community resource for bioinformatics trainers. <em>Briefings in Bioinformatics</em>, PMID: 22110242.
</p>
<p>
Vroling, B., Thorne, D., McDermott, P., Attwood, T.K. & Pettifer, S.R. (2011) Integrating GPCR-specific information with full text articles. <em>BMC Bioinformatics</em>, <strong>12(1)</strong>, 362.
</p>
<p>
Attwood, T.K., Kell, D.B., McDermott, P., Marsh, J., Pettifer, S.R. & Thorne, D. (2010) Utopia Documents: linking scholarly literature with research data. <em>Bioinformatics</em>, <strong>26</strong>, i568-i574.
</p>
<p>
Attwood, T.K., Kell, D.B., McDermott, P., Marsh, J., Pettifer, S.R. & Thorne, D. (2009) Calling International Rescue - knowledge lost in literature and data landslide! <em>Biochemical Journal</em>, <strong>424(3)</strong>, 317-333.
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Teresa Attwood","hid":"prof_teresa_attwood","codeblockOffset":0,"secid":2,"range":"704-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:up
http://www.allbioinformatics.eu/doku.php?id=public:up&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h2 class="sectionedit1" id="universitaet_potsdam_germany">UNIVERSITÄT POTSDAM Germany</h2>
<div class="level2">
<p>
<a href="http://www.uni-potsdam.de/" class="urlextern" title="http://www.uni-potsdam.de/" rel="ugc nofollow">http://www.uni-potsdam.de/</a>
</p>
<p>
The University of Potsdam was established in 1991 and since its foundation has developed into an institution with modern infrastructure and a forward-looking scientific orientation. More than 20,000 students are currently enrolled in more than 100 degree programs hosted by its five faculties, of which the Faculty of Science is the largest.
The University has developed Life Sciences as a major focus area with an emphasis on plant sciences, biochemistry and systems biology. It closely cooperates with a number of internationally renowned research institutes such as the Potsdam Institute for Climate Impact Research, the German Institute for Human Nutrition, the Helmholtz Centre Potsdam - German Research Centre for Geosciences, the Max Planck Institutes of Molecular Plant Physiology, of Colloids and Interfaces, and of Gravitational Physics, and with institutes of the Fraunhofer Society.
The University of Potsdam is located at the Science Park Potsdam-Golm, a rapidly growing research campus gaining significance far beyond Germany's borders.
</p>
</div>
<!-- EDIT{"target":"section","name":"UNIVERSIT\u00c4T POTSDAM\tGermany","hid":"universitaet_potsdam_germany","codeblockOffset":0,"secid":1,"range":"39-1163"} -->
<h3 class="sectionedit2" id="prof_dr_bernd_mueller-roeber">Prof. Dr. Bernd Müller-Röber</h3>
<div class="level3">
<p>
<a href="http://www.uni-potsdam.de/ibb/molbiol" class="urlextern" title="http://www.uni-potsdam.de/ibb/molbiol" rel="ugc nofollow">http://www.uni-potsdam.de/ibb/molbiol</a>
</p>
<p>
Bernd Mueller-Roeber heads the Department of Molecular Biology at the University of Potsdam and the Plant Signalling Group at the Max Planck Institute of Molecular Plant Physiology. After studying biology and philosophy in Tübingen, Marburg and Berlin he was awarded a PhD degree in biology in 1992. He completed his postdoctoral research with a habilitation in molecular plant physiology in 1998. In 2000, he became C4 Professor of Molecular Biology at the University of Potsdam. He is member of the Berlin-Brandenburg Academy of Sciences and the German Academy of Science and Engineering (acatech).
His group studies the functions of transcription factors and the gene regulatory networks they control, employing a combination of molecular, genomics and systems biology approaches. The focus is on regulators that control leaf growth, aging and senescence, and the response to abiotic stress. The group also uses synthetic biology approaches to construct artificial regulatory networks with the aim of building synthetic bio-systems.
Within Allbio he collaborates with Dr. Babette Regierer from the Max-Planck Institute of Genetics in Berlin.
</p>
</div>
<h4 id="publications">Publications</h4>
<div class="level4">
<p>
Wu A, Allu AD, Garapati P, Siddiqui H, Dortay H, Zanor M-I, Asensi-Fabado MA, Munné-Bosch S, Antonio C, Tohge T, Fernie AR, Kaufmann K, Xue G-P, Mueller-Roeber B, Balazadeh S (2012) JUNGBRUNNEN1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in Arabidopsis. Plant Cell, in press. PMID:22345491
</p>
<p>
Omranian N, Mueller-Roeber B, Nikoloski Z (2012) PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana. Molecular BioSystems, 8(4):1121-7. PMID: 22327945
</p>
<p>
Winck FV, Riaño-Pachón DM, Sommer F, Rupprecht J, Mueller-Roeber B. (2012) The nuclear proteome of the green alga Chlamydomonas reinhardtii. Proteomics.12(1):95-100. PMID: 22065562
</p>
<p>
Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, Mehrnia M, Zanor MI, Köhler B, Mueller-Roeber B. (2010) A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 62(2):250-64. PMID: 20113437
</p>
<p>
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38(Database issue): D822-7. PMID: 19858103
</p>
</div>
<!-- EDIT{"target":"section","name":"Prof. Dr. Bernd M\u00fcller-R\u00f6ber","hid":"prof_dr_bernd_mueller-roeber","codeblockOffset":0,"secid":2,"range":"1164-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:val
http://www.allbioinformatics.eu/doku.php?id=public:val&rev=1549962287&do=diff
<h2 class="sectionedit1" id="validation_and_training_workshops">Validation and Training Workshops</h2>
<div class="level2">
<p>
10 Validation workshops (see below ‘Workshop topics’) took place during the last year of the project.
</p>
<p>
These workshops consisted of a data hack-a-thon session and a training session. During the data hack-a-thon session bioinformaticians and but mainly life scientists worked together to challenge some solutions AllBio worked out together with external scientists.
</p>
</div>
<h5 id="embl-ebi">EMBL-EBI</h5>
<div class="level5">
<p>
Titel: <strong><a href="http://www.ebi.ac.uk/training/course/Agri-Omics" class="urlextern" title="http://www.ebi.ac.uk/training/course/Agri-Omics" rel="ugc nofollow">AllBio Plant and Pathogen Bioinformatics</a></strong> training course - 8 - 11 July 2014
</p>
</div>
<h5 id="cnr">CNR</h5>
<div class="level5">
<p>
Title: <strong><a href="http://allbioinformatics.eu/bari2014/" class="urlextern" title="http://allbioinformatics.eu/bari2014/" rel="ugc nofollow">Epigenetics, coding and non-coding RNAs- Challenging NGS data</a></strong> - 25 - 26 June 2014
</p>
</div>
<h5 id="uniman">UNIMAN</h5>
<div class="level5">
<p>
Title: <strong>Metagenomics Interoperability and Web Services Workshop</strong> - 10-12 April 2014, Amsterdam, The Netherlands
</p>
</div>
<h5 id="slu">SLU</h5>
<div class="level5">
<p>
Title: <strong><a href="http://teacher.bmc.uu.se/ALLBIO2014/" class="urlextern" title="http://teacher.bmc.uu.se/ALLBIO2014/" rel="ugc nofollow">Bioinformatics approaches to Identify causative sequence variants in farm animals</a></strong> Training course, Uppsala Sweden, 12 - 16. May 2014
</p>
</div>
<h5 id="sib">SIB</h5>
<div class="level5">
<p>
Title: <strong><a href="http://edu.isb-sib.ch/course/view.php?id=104" class="urlextern" title="http://edu.isb-sib.ch/course/view.php?id=104" rel="ugc nofollow">NGS methods for identification of mutations and large structural variants</a></strong> 11th -12th March 2014, Lausanne, Switzerland
</p>
</div>
<h5 id="csc">CSC</h5>
<div class="level5">
<p>
Title: <strong><a href="http://www.allbioinformatics.eu/doku.php?id=public:valid-csc" class="wikilink1" title="public:valid-csc" data-wiki-id="public:valid-csc">RNA-seq data analysis workshop</a></strong> 8th - 10th January 2014, Espoo, Finland
</p>
<p>
Title: <strong><a href="http://www.csc.fi/english/csc/courses/archive/chipseq2014" class="urlextern" title="http://www.csc.fi/english/csc/courses/archive/chipseq2014" rel="ugc nofollow">ChIP- and DNase-seq data analysis workshop, 16 - 19 September 2014, CSC, Helsinki, Finland</a></strong>
</p>
</div>
<h5 id="up">UP</h5>
<div class="level5">
<p>
Title: <strong><a href="http://teacher.bmc.uu.se/BIGDATA/Managing_Big_Data.pdf" class="urlextern" title="http://teacher.bmc.uu.se/BIGDATA/Managing_Big_Data.pdf" rel="ugc nofollow">
Tutorial: Comparative genome annotation methods
</a></strong> 29-30 April 2014, University of Potsdam, Campus Golm Karl-Liebknecht-Str. 24-25 House 25 Room D 002. Germany
</p>
<p>
Title: <strong>Comparative genome annotation methods</strong>
</p>
</div>
<h5 id="runmc">RUNMC</h5>
<div class="level5">
<p>
Title: <strong><a href="http://biosb.nl/education/course-portfolio/course-metagenomics-approaches-and-data-analysis/" class="urlextern" title="http://biosb.nl/education/course-portfolio/course-metagenomics-approaches-and-data-analysis/" rel="ugc nofollow">Bioinformatics of bacteriology</a></strong> Course: Metagenomics Approaches and Data Analysis, March 31, 2014 / April 2, 2014, Nijmegen, The Netherlands.
</p>
</div>
<h5 id="ki">KI</h5>
<div class="level5">
<p>
Title: <strong><a href="https://docs.google.com/forms/d/1gfUvWYW12pmnJ-wYKdDNi2coGbrn2vL0UpVQgN9h5WU/ viewform?usp=send_form" class="urlextern" title="https://docs.google.com/forms/d/1gfUvWYW12pmnJ-wYKdDNi2coGbrn2vL0UpVQgN9h5WU/ viewform?usp=send_form" rel="ugc nofollow">AllBio Metagenome data analysis! - 21. - 23. May 2014 - Science for Life Laboratory, Stockholm, Sweden</a></strong>
</p>
</div>
<h5 id="ulb">ULB</h5>
<div class="level5">
<p>
Title: <strong>AllBio Workshop: <a href="http://www.allbioinformatics.eu/doku.php?id=public:valid-ulb" class="wikilink1" title="public:valid-ulb" data-wiki-id="public:valid-ulb">Analyzing thousands of bacterial genomes:
gene annotation, metabolism, regulation</a></strong> - 23 - 25 June 2014, Marseille, France
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:valid-csc
http://www.allbioinformatics.eu/doku.php?id=public:valid-csc&rev=1549962287&do=diff
<h2 class="sectionedit1" id="csc_-_it_center_for_science_finland">CSC - IT CENTER FOR SCIENCE Finland</h2>
<div class="level2">
</div>
<h4 id="rna-seq_data_analysis_workshop">RNA-seq data analysis workshop</h4>
<div class="level4">
<p>
8th - 10th January 2014
</p>
<p>
<strong>Helsinki, Finland</strong>
</p>
<p>
<a href="http://www.csc.fi/english/csc/courses/archive/rnaseq2014" class="urlextern" title="http://www.csc.fi/english/csc/courses/archive/rnaseq2014" rel="ugc nofollow">http://www.csc.fi/english/csc/courses/archive/rnaseq2014</a>
</p>
<p>
<strong>Program</strong>
</p>
<p>
Thursday 9.1.2014
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-csc&media=public:dsc_0434_part.jpg" class="media" title="public:dsc_0434_part.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=ed86aa&media=public:dsc_0434_part.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
Session III: Transcriptome assembly
</p>
<p>
10:00-10:30 Introduction to transcriptome assembly (Panu Somervuo, University of Helsinki, Finland)
10:30-11:00 Assessment of transcript reconstruction methods for RNA-seq (Pär Engström, SciLifelab, Sweden)
11:00-11:30 Targeted assembly of RNA-seq data using phylogenetic information (Ari Löytynoja, University of Helsinki, Finland)
Session IV: miRNA-seq data analysis
11:30-12:20 Introduction to small RNA sequence analysis with applications in nematodes (Garry Wong, UEF, Finland)
Lunch
</p>
<p>
13:20-14:00 Small RNA data analysis and miRNA discovery in plants and mammalians (Andreas Gisel, ITB, Italy)
14:00-14:50 Joint analysis of miRNA and mRNA expression data (Angel Rubio, CEIT, Spain)
</p>
<p>
Coffee
</p>
<p>
BOOKED OUT! 15:00-18:00 <strong>Hands-on tutorial 2: Small RNA data analysis</strong> (Andreas Gisel CNR-ITB)
This tutorial covers a command line based workflow to find known and novel miRNAs using tools like BWA and mirDeep2, so participants should be familiar with Unix. The workflow is developed at ITB, Italy, and it reports the results in a graphical form allowing an easy way to extract the required information.
</p>
<p>
<br/>
</p>
<p>
Wednesday 8.1.2014
Registration and coffee
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-csc&media=public:dsc_0427_red.jpg" class="media" title="public:dsc_0427_red.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=350&tok=43b1c9&media=public:dsc_0427_red.jpg" class="mediaright" align="right" loading="lazy" alt="" width="350" /></a>
</p>
<ol>
<li class="level1"><div class="li"> 10:00 Welcome (Eija Korpelainen, CSC)</div>
</li>
</ol>
<p>
Session I: Quality control and alignment
</p>
<ol>
<li class="level1"><div class="li"> 10:15-11:05 Quality checking and pre-processing your RNA-seq data (Mikael Huss, SciLifelab, Sweden)</div>
</li>
<li class="level1"><div class="li"> 11:05-12:00 Systematic evaluation of spliced aligners for RNA-seq (Pär Engström, SciLifelab, Sweden)</div>
</li>
</ol>
<p>
Lunch
</p>
<p>
Session II: Reliability of RNA-seq, differential expression analysis
</p>
<ol>
<li class="level1"><div class="li"> 13:00-13:45 Reliability and interpretation of RNA-Seq expression profiles (Pawel Labaj, BOKU, Austria)</div>
</li>
<li class="level1"><div class="li"> 13:45-14:20 Transcript isoform expression and differential expression estimation with BitSeq (Antti Honkela, University of Helsinki, Finland)</div>
</li>
<li class="level1"><div class="li"> 14:20-15:00 Comparison of differential expression analysis tools (Laura Elo, University of Turku, Finland)</div>
</li>
<li class="level1"><div class="li"> Coffee</div>
</li>
</ol>
<p>
BOOKED OUT! 15:00-18:00 <strong>Hands-on tutorial 1: Differential expression analysis using R/Bioconductor and Unix</strong> (Mikael Huss, Pär Engström)
This hands-on session covers quantification and differential expression analysis of RNA-seq data. The analysis tools used in the exercises include command line applications and Bioconductor packages such as Cuffdiff and DESeq2, so participants need to be familiar with Unix and R.
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-csc&media=public:dsc_0429_red.jpg" class="media" title="public:dsc_0429_red.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=500&tok=d2429b&media=public:dsc_0429_red.jpg" class="mediacenter" loading="lazy" title=" Instructions by the trainers" alt=" Instructions by the trainers" width="500" /></a>
<br/>
Tuesday 7.1.2014
</p>
<p>
Coffee
</p>
<p>
BOOKED OUT! 12:00-15:00 <strong>Additional hands-on tutorial 3: RNA-seq data analysis using Chipster</strong> (Eija Korpelainen)
This tutorial covers quality control (FastQC and PRINSEQ), alignment (TopHat) and quantification (HTSeq) as well as differential expression analysis (edgeR and DESeq) and genome browser visualization. The user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required and the tutorial is thus suitable for everybody.
</p>
<p>
This workshop consists of two lecture days and four hands-on sessions. More information and registration can be found <a href="http://www.csc.fi/english/csc/courses/archive/rnaseq2014" class="urlextern" title="http://www.csc.fi/english/csc/courses/archive/rnaseq2014" rel="ugc nofollow">here</a>.
</p>
<p>
<strong>Speakers</strong>
</p>
<ul>
<li class="level1"><div class="li"> Mikael Huss (SciLifelab, Sweden): Quality checking and pre-processing your RNA-seq data</div>
</li>
<li class="level1"><div class="li"> Pawel Labaj (BOKU, Austria): Reliability and interpretation of RNA-Seq expression profiles</div>
</li>
<li class="level1"><div class="li"> Pär Engström (SciLifelab, Sweden): Systematic evaluation of spliced aligners for RNA-seq</div>
</li>
<li class="level1"><div class="li"> Panu Somervuo (University of Helsinki, Finland): Introduction to transcriptome assembly</div>
</li>
<li class="level1"><div class="li"> Ari Löytynoja (University of Helsinki, Finland): Targeted assembly of RNA-seq data using phylogenetic information</div>
</li>
<li class="level1"><div class="li"> Laura Elo (University of Turku, Finland): Comparison of differential expression analysis tools</div>
</li>
<li class="level1"><div class="li"> Antti Honkela (University of Helsinki, Finland): BitSeq - transcript isoform expression and differential expression estimation from RNA-seq data</div>
</li>
<li class="level1"><div class="li"> Garry Wong (UEF, Finland): An introduction to small RNA sequence analysis with applications in nematodes</div>
</li>
<li class="level1"><div class="li"> Andreas Gisel (ITB, Italy): smallRNA data analysis and miRNA discovery in plants and mammalians</div>
</li>
<li class="level1"><div class="li"> Angel Rubio / Ander Muniategui (CEIT, Spain): Joint analysis of miRNA and mRNA expression data</div>
</li>
</ul>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:valid-ki
http://www.allbioinformatics.eu/doku.php?id=public:valid-ki&rev=1549962287&do=diff
<h1 class="sectionedit1" id="metagenome_data_analysis_workshop">Metagenome data analysis Workshop</h1>
<div class="level1">
</div>
<h4 id="may_21-23_solna_sweden">May 21-23, Solna, Sweden</h4>
<div class="level4">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-ki&media=public:bild.jpg" class="media" title="public:bild.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=600&tok=f9bb08&media=public:bild.jpg" class="media" loading="lazy" alt="" width="600" /></a>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-ki&media=public:bild_1.jpg" class="media" title="public:bild_1.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=f7fab5&media=public:bild_1.jpg" class="media" loading="lazy" alt="" width="300" /></a>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-ki&media=public:bild_2.jpg" class="media" title="public:bild_2.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=293e18&media=public:bild_2.jpg" class="media" loading="lazy" alt="" width="300" /></a>
</p>
<p>
<br/>
With technological advances we face an increasing number projects dealing with the size and
complexity of metagenomics datasets and therefore SciLifelab and AllBio are arranging a
workshop on the analysis and interpretation of metagenomics data.
</p>
<p>
In this workshop we will combine talks by experts in the field with practical tutorials guiding the participants in the analysis of representative datasets.
</p>
<p>
<strong>Confirmed speakers:</strong>
</p>
<ul>
<li class="level1"><div class="li"> Lex Nederbragt, Oslo University, Norway</div>
</li>
<li class="level1"><div class="li"> Saskia Smits, Erasmus University Rotterdam, Netherlands</div>
</li>
<li class="level1"><div class="li"> Joakim Larsson, Göteborg University, Sweden</div>
</li>
<li class="level1"><div class="li"> Paul Wilmes, University of Luxembourg, Luxembourg</div>
</li>
<li class="level1"><div class="li"> Anders Andersson, SciLifeLab, Sweden</div>
</li>
<li class="level1"><div class="li"> Noan Le Bescot, UPMC (Tara expedition), France</div>
</li>
</ul>
<p>
<strong>Confirmed tutorial supervisors:</strong>
</p>
<ul>
<li class="level1"><div class="li"> Ino de Bruijn, SciLifeLab, Sweden</div>
</li>
<li class="level1"><div class="li"> Johannes Alneberg, SciLifeLab, Sweden</div>
</li>
<li class="level1"><div class="li"> Luisa Hugerth, SciLifeLab, Sweden</div>
</li>
<li class="level1"><div class="li"> Johan Bengtsson, Göteborg University, Sweden</div>
</li>
<li class="level1"><div class="li"> Mikael Huss, SciLifeLab, Sweden</div>
</li>
<li class="level1"><div class="li"> </div>
</li>
</ul>
<p>
<strong>Venue:</strong>
</p>
<p>
Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
Conference room Air/Fire, Gamma building
</p>
<p>
<strong>Schedule:</strong>
The presentations will be given between 9-12 in the morning, followed by practical tutorials after lunch. Detailed schedule will soon be published.
</p>
<p>
<strong>Organisers:</strong>
</p>
<p>
Mikael Huss (mikael.huss at scilifelab.se)
Thomas Svensson (thomas.svensson at scilifelab.se)
</p>
<p>
<strong>Mandatory registration:</strong>
</p>
<p>
<a href="https://docs.google.com/forms/d/1gfUvWYW12pmnJ-wYKdDNi2coGbrn2vL0UpVQgN9h5WU/" class="urlextern" title="https://docs.google.com/forms/d/1gfUvWYW12pmnJ-wYKdDNi2coGbrn2vL0UpVQgN9h5WU/" rel="ugc nofollow">https://docs.google.com/forms/d/1gfUvWYW12pmnJ-wYKdDNi2coGbrn2vL0UpVQgN9h5WU/</a>
</p>
<p>
<strong>Flyer:</strong>
<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:flyer_metagenomics_workshop.pdf" class="media mediafile mf_pdf" title="public:flyer_metagenomics_workshop.pdf (71.5 KB)">flyer_metagenomics_workshop.pdf</a>
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:valid-slu
http://www.allbioinformatics.eu/doku.php?id=public:valid-slu&rev=1549962287&do=diff
<h3 class="sectionedit1" id="bioinformatics_approaches_to_identify_causative_sequence_variants_in_farm_animals_training_course">Bioinformatics approaches to Identify causative sequence variants in farm animals Training course</h3>
<div class="level3">
<p>
Students from eight different EU countries are attending the ALLBIO course “Bioinformatics approaches to Identify causative sequence variants in farm animals”.
</p>
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-slu&media=public:dsc_4555.jpg" class="media" title="public:dsc_4555.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=b71181&media=public:dsc_4555.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-slu&media=public:dsc_4570.jpg" class="media" title="public:dsc_4570.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=bba950&media=public:dsc_4570.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-slu&media=public:dsc_4589.jpg" class="media" title="public:dsc_4589.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=6f1be1&media=public:dsc_4589.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-slu&media=public:dsc_4594.jpg" class="media" title="public:dsc_4594.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&tok=b5240b&media=public:dsc_4594.jpg" class="mediaright" align="right" loading="lazy" alt="" width="300" /></a>
</p>
<p>
On the picture students visiting the Supercomputer facilities at UPPMAX. The cluster in the background is the one used for the Hands-On tutorials.
</p>
</div>
anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:valid-ulb
http://www.allbioinformatics.eu/doku.php?id=public:valid-ulb&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h5 id="allbio_training_workshop_marseille_june_23-25_2014">ALLBIO training workshop – Marseille, June 23-25, 2014</h5>
<div class="level5">
</div>
<h3 class="sectionedit1" id="analyzing_thousands_of_bacterial_genomesgene_annotation_metabolism_regulation">Analyzing thousands of bacterial genomes: gene annotation, metabolism, regulation</h3>
<div class="level3">
</div>
<h5 id="practical_info">Practical info</h5>
<div class="level5">
<div class="table sectionedit2"><table class="inline">
<tr class="row0">
<td class="col0 leftalign"> Date </td><td class="col1 leftalign">June 23-25, 2014 </td><td class="col2" rowspan="5"><a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-ulb&media=public:sugiton_1538x1024.jpg" class="media" title="public:sugiton_1538x1024.jpg"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=350&tok=52c13d&media=public:sugiton_1538x1024.jpg" class="medialeft" align="left" loading="lazy" alt="" width="350" /></a> </td>
</tr>
<tr class="row1">
<td class="col0 leftalign"> Location </td><td class="col1 leftalign"><a href="http://www.novotel.com/gb/hotel-0911-novotel-marseille-vieux-port/" class="urlextern" title="http://www.novotel.com/gb/hotel-0911-novotel-marseille-vieux-port/" rel="ugc nofollow">Hotel Novotel Marseille Vieux Port</a> </td>
</tr>
<tr class="row2">
<td class="col0 leftalign"> Organizer </td><td class="col1"><a href="mailto:Jacques.van-Helden@univ-amu.fr" class="mail" title="Jacques.van-Helden@univ-amu.fr">Jacques.van-Helden@univ-amu.fr</a> </td>
</tr>
<tr class="row3">
<td class="col0"> Participants </td><td class="col1 leftalign">~20 </td>
</tr>
<tr class="row4">
<td class="col0"> Cost</td><td class="col1 leftalign">0€ </td>
</tr>
<tr class="row5">
<td class="col0"> Registration </td><td class="col1"></td><td class="col2"></td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table","secid":2,"range":"212-650"} -->
<p>
<br/>
<strong>THE REGISTRATION IS CLOSED</strong></color>| ::: |
</p>
</div>
<h5 id="funding">Funding</h5>
<div class="level5">
<p>
This training workshop is funded by the ALLBIO project (<a href="http://www.allbioinformatics.eu/" class="urlextern" title="http://www.allbioinformatics.eu/" rel="ugc nofollow">http://www.allbioinformatics.eu/</a>), whose goal is to establish the link between bioinformatics and biologist communities who express uncovered needs for other fields than human genomics (microbial, plant, livestock).
</p>
</div>
<h5 id="motivation">Motivation</h5>
<div class="level5">
<p>
Description: sequencing technologies allow microbiologists to sequence, for a moderate cost, not only the genome of their favourite species, but a few dozens of related species, a collection of strains, and even to characterize inter-individual variations. The Ensembl Genomes resource contains over 10,000 completely sequenced genomes. The availability of such data requires new bioinformatics resources suited for annotating, querying and analysing multitudes of sequenced bacterial genomes in parallel.
</p>
<p>
This training workshop will show how to combine several specialized bioinformatics resources to extract information about bacterial genes and their annotations (Ensembl Genomes), metabolism (MICROSCOPE), and regulation (RSAT). The course will be oriented towards comparative genomics, and give a perspective about advances that can be expected from the massive reduction of sequencing costs resulting from Next Generation Sequencing.
The course will mainly be based on user-friendly Web interfaces. It will also include a basic introduction about the programmatic access to bioinformatics resources, showing by simple and well-documented examples how to automatize the collection of data, and extract information from multiple data sets.
</p>
</div>
<h5 id="target_audience">Target audience</h5>
<div class="level5">
<p>
This course is addressed to microbiologists confronted to the need to use bioinformatics resources to analyse multiple genomes.
</p>
</div>
<h5 id="prerequisites">Prerequisites</h5>
<div class="level5">
<p>
The course does not require any computing skills. A basic knowledge of the Linux environment is welcome, but not required.
</p>
</div>
<h5 id="contents">Contents</h5>
<div class="level5">
<p>
This training course will include
</p>
<ol>
<li class="level1"><div class="li"> Short talks illustrating the functionalities offered by bioinformatics resources suited for the analysis of multiple bacterial genomes. </div>
</li>
<li class="level1 node"><div class="li"> Practicals based on concrete study cases:</div>
<ul>
<li class="level2"><div class="li"> collecting multiple genomes from bacteria;</div>
</li>
<li class="level2"><div class="li"> comparing annotations between different species;</div>
</li>
<li class="level2"><div class="li"> extracting metabolic information for selected genomes;</div>
</li>
<li class="level2"><div class="li"> metabolic projection: coverage of reference pathways by the enzymes found in a genome;</div>
</li>
<li class="level2"><div class="li"> phylogenetic profiling: detecting genes co-occurrences across genomes;</div>
</li>
<li class="level2"><div class="li"> phylogenetic footprints: detection of conserved cis-regulatory elements.</div>
</li>
</ul>
</li>
<li class="level1 node"><div class="li"> Practicals on programmatic use of the tools:</div>
<ul>
<li class="level2"><div class="li"> extracting data for multiple genomes;</div>
</li>
<li class="level2"><div class="li"> combining data from diverse sources.</div>
</li>
</ul>
</li>
</ol>
</div>
<h5 id="computer_environment">Computer environment</h5>
<div class="level5">
<p>
If possible, participants are invited to bring their own laptop if they wish to work in their familiar environment. We will rent additional computers for participants who do not dispose of a laptop.
</p>
</div>
<h5 id="schedule">Schedule</h5>
<div class="level5">
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/detail.php?id=public%3Avalid-ulb&media=public:screen_shot_2014-05-18_at_11.41.37.png" class="media" title="public:screen_shot_2014-05-18_at_11.41.37.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=600&tok=58e445&media=public:screen_shot_2014-05-18_at_11.41.37.png" class="media" loading="lazy" alt="" width="600" /></a>
</p>
</div>
<h5 id="teachers">Teachers</h5>
<div class="level5">
<div class="table sectionedit3"><table class="inline">
<tr class="row0">
<td class="col0">Dan Staines</td><td class="col1">European Bioinformatics Institute (EBI), UK</td><td class="col2">Ensembl Genomes <a href="http://ensemblgenomes.org/" class="urlextern" title="http://ensemblgenomes.org/" rel="ugc nofollow">http://ensemblgenomes.org/</a></td>
</tr>
<tr class="row1">
<td class="col0">François LeFevre, Eugeni Belda, Claudine Médigue</td><td class="col1">Genoscope (CEA), France</td><td class="col2">MICROSCOPE <a href="http://www.genoscope.cns.fr/agc/microscope/" class="urlextern" title="http://www.genoscope.cns.fr/agc/microscope/" rel="ugc nofollow">http://www.genoscope.cns.fr/agc/microscope/</a></td>
</tr>
<tr class="row2">
<td class="col0">Jacques van Helden, Denis Puthier</td><td class="col1">Aix-Marseille Université (AMU), France</td><td class="col2">Regulatory Sequence Analysis Tools (RSAT) <a href="http://www.rsat.eu/" class="urlextern" title="http://www.rsat.eu/" rel="ugc nofollow">http://www.rsat.eu/</a></td>
</tr>
</table></div>
<!-- EDIT{"target":"table","name":"","hid":"table1","secid":3,"range":"3650-4020"} -->
</div>
<!-- EDIT{"target":"section","name":"Analyzing thousands of bacterial genomes: gene annotation, metabolism, regulation","hid":"analyzing_thousands_of_bacterial_genomesgene_annotation_metabolism_regulation","codeblockOffset":0,"secid":1,"range":"101-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:workiscb
http://www.allbioinformatics.eu/doku.php?id=public:workiscb&rev=1549962287&do=diff
<p>
<a href="http://www.allbioinformatics.eu/lib/exe/fetch.php?media=public:screen_shot_2013-08-20_at_10.45.58.png" class="media" title="public:screen_shot_2013-08-20_at_10.45.58.png"><img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=200&tok=b95525&media=public:screen_shot_2013-08-20_at_10.45.58.png" class="media" loading="lazy" alt="" width="200" /></a>
</p>
<h2 class="sectionedit1" id="allbio_at_icsb_2013_copenhagen">AllBio at ICSB 2013 Copenhagen</h2>
<div class="level2">
</div>
<h4 id="allbio_workshop_on_standardisation_operation_procedures_sop">AllBio workshop on Standardisation Operation Procedures (SOP)</h4>
<div class="level4">
<p>
Susanne Hollmann, Babette Regierer, Joachim Lonien, Martin Golebiewski
</p>
<p>
<a href="http://www.icsb2013.dk" class="urlextern" title="http://www.icsb2013.dk" rel="ugc nofollow">www.icsb2013.dk</a>
</p>
<p>
<a href="http://www.icsb2013.dk/images/Media/pdf/icsb2013_workshop.pdf" class="urlextern" title="http://www.icsb2013.dk/images/Media/pdf/icsb2013_workshop.pdf" rel="ugc nofollow">http://www.icsb2013.dk/images/Media/pdf/icsb2013_workshop.pdf</a>
</p>
<p>
The integration of data for modelling is a critical step where intelligent rules play an essential role
for the success. As systems biology needs to integrate heterologous and complex data to build
models, the need for data standards in the life sciences becomes an urgent topic. Therefore, systems
biology could play a major role in the development of new and helpful standards for the production
of high quality data. Systems biology could therefore be a driver for standardisation processes in the
life sciences in general.
The systems biology community needs the close cooperation with data generation groups and the
bioinformatics world to define a strategy how to generate the high quality data in the life sciences
needed for model generation.
The workshop will address questions on standardization activities and processes in the life sciences
with specific emphasis on systems biology needs. It also offers fundamental information about the
creation of economically reasonable conditions for future industrial application.
Standard operating procedures (SOPs) for the generation and processing of data are highly
important for data integration and model creation in particular in respect to because only the use of
standards lead to
</p>
<ul>
<li class="level1"><div class="li"> high quality and comparable data, regardless of the sample origin and environment, and</div>
</li>
<li class="level1"><div class="li"> for the use and application of results for industrial exploitation (e.g. in Synthetic biology).</div>
</li>
</ul>
<p>
The development of SOPs can also feedback and thus have impact to the creation of new standards.
During the workshop 'Standardizing Data and Metadata in Systems Biology' experts will provide an
inside view on the processes around standardisation on the national (e.g. German) and international
(CEN, ISO) level, followed by an overview on ongoing initiatives on standardisation (e.g.
COMBINE, ISBE, AllBIO) in different life science areas. In a final discussion with the participants
it is expected to define challenges and needs for standardisation activities in the systems biology
and – if possible – also in the whole life science area. As a consequence, strategic considerations
will be developed addressing key stakeholders on the European level. Thus, the systems biology
community could benefit from the prominent role and be a driver in this area influencing the way
how data are generated in the life sciences in general.
</p>
</div>
<!-- EDIT{"target":"section","name":"AllBio at ICSB 2013 Copenhagen","hid":"allbio_at_icsb_2013_copenhagen","codeblockOffset":0,"secid":1,"range":"63-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:work_packages
http://www.allbioinformatics.eu/doku.php?id=public:work_packages&rev=1549962287&do=diff
<h2 class="sectionedit1" id="wp1_community_building">WP1 Community building</h2>
<div class="level2">
<p>
The main objective of <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp1" class="wikilink1" title="public:wp1" data-wiki-id="public:wp1">WP1</a> is to build a joint platform/community of life science bioinformatics developers and users to identify demands and needs for the future. Test cases defined by interviews with the user community will serve as a basis to identify the main challenges in life science bioinformatics.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP1\tCommunity building","hid":"wp1_community_building","codeblockOffset":0,"secid":1,"range":"12-361"} -->
<h2 class="sectionedit2" id="wp2_inventory_and_roadmap">WP2 Inventory and Roadmap</h2>
<div class="level2">
<p>
The objective of <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp2" class="wikilink1" title="public:wp2" data-wiki-id="public:wp2">WP2</a> is to generate a catalogue of bioinformatics tools and services that are available in the different fields of the life sciences (AllBioCatalogue). Based on this inventory, tools missing in the life science fields that are necessary to solve the test cases will be identified and form the basis for a roadmap defining needs in bioinformatics tools and services.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP2\tInventory and Roadmap","hid":"wp2_inventory_and_roadmap","codeblockOffset":0,"secid":2,"range":"362-790"} -->
<h2 class="sectionedit3" id="wp3_life_science_bioinformatics_projects">WP3 Life Science Bioinformatics Projects</h2>
<div class="level2">
<p>
The objective of the <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp3" class="wikilink1" title="public:wp3" data-wiki-id="public:wp3">WP3</a> is to introduce the selected “test cases” from WP1 to the bioinformatics community and find together with them solution for these test cases.
The bioinformatics community will contribute to the solution of each selected test case. These solutions will be validated under the coordination of WP5.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP3\tLife Science Bioinformatics Projects","hid":"wp3_life_science_bioinformatics_projects","codeblockOffset":0,"secid":3,"range":"791-1179"} -->
<h2 class="sectionedit4" id="wp4_interoperability">WP4 Interoperability</h2>
<div class="level2">
<p>
The main aim of the <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp4" class="wikilink1" title="public:wp4" data-wiki-id="public:wp4">WP4</a> is to coordinate the process of making life science-related software packages, services and data resources work together, in a similar way as has been done over the last decade for many human health-related packages. Additionally, the modification of human genome and human health-related software packages for application in other life science fields will be coordinated.
Specific objectives are: to identify and harmonise existing ontologies that are necessary for interoperability in this field; to establish minimum standards for web service deployment; to provide an on-line, searchable catalogue of resources; and to co-ordinate these activities whilst staying up-to-date with complementary initiatives in other projects.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP4\tInteroperability","hid":"wp4_interoperability","codeblockOffset":0,"secid":4,"range":"1180-1974"} -->
<h2 class="sectionedit5" id="wp5_validation_and_training">WP5 Validation and Training</h2>
<div class="level2">
<p>
The objective of <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp5" class="wikilink1" title="public:wp5" data-wiki-id="public:wp5">WP5</a> is the validation of the proposed solutions for the “test cases” generated in WP3 for different areas of the life sciences. The validation tests will also encompass the agreements from WP4 on standards for interoperability of systems. Instruments for the extended validation processes with the target community employed for WP5 are experts’ workshops and training courses. Results from WP5 will feed back to WP3 and WP4 for further optimisation of their coordination activities.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP5\tValidation and Training","hid":"wp5_validation_and_training","codeblockOffset":0,"secid":5,"range":"1975-2529"} -->
<h2 class="sectionedit6" id="wp6_management">WP6 Management</h2>
<div class="level2">
<p>
Main objective of <a href="http://www.allbioinformatics.eu/doku.php?id=public:wp6" class="wikilink1" title="public:wp6" data-wiki-id="public:wp6">WP6</a> is the management of the AllBio project including the responsibility for contractual, financial, legal, and administrative issues. The management will also oversee the execution of the milestones in the timeframe of the project and the reporting.
The second objective is the establishment and continuous communication between the AllBio participants and the officers of the EC.
Third objective is the organization of the kick-off and the final meeting of the AllBio participants.
Fourth objective is the support of the partners in the communication with the broader public and stakeholders for general issues of the project.
</p>
</div>
<!-- EDIT{"target":"section","name":"WP6\tManagement","hid":"wp6_management","codeblockOffset":0,"secid":6,"range":"2530-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:wp1
http://www.allbioinformatics.eu/doku.php?id=public:wp1&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp1_community_building">WP1 Community building</h1>
<div class="level1">
<p>
The main objective of WP1 is to build a joint platform/community of life science bioinformatics developers and users to identify demands and needs for the future. Test cases defined by interviews with the user community will serve as a basis to identify the main challenges in life science bioinformatics.
</p>
<p>
Responsabile: <strong>Gert Vriend</strong> - STICHTING KATHOLIEKE UNIVERSITEIT (RUNMC), Nijmegen, Netherlands
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D1.1 Web portal is available with different services</div>
</li>
<li class="level1"><div class="li"> D1.2 Representative “test cases” available</div>
</li>
<li class="level1"><div class="li"> D1.3 Community building</div>
</li>
<li class="level1"><div class="li"> D1.4 Description of test case community</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP1\tCommunity building","hid":"wp1_community_building","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:wp2
http://www.allbioinformatics.eu/doku.php?id=public:wp2&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp2_inventory_and_roadmap">WP2 Inventory and Roadmap</h1>
<div class="level1">
<p>
The objective of WP2 is to generate a catalogue of bioinformatics tools and services that are available in the different fields of the life sciences (AllBioCatalogue). Based on this inventory, tools missing in the life science fields that are necessary to solve the test cases will be identified and form the basis for a roadmap defining needs in bioinformatics tools and services.
</p>
<p>
Responsabile: <strong>Erik Bongcam-Rudloff</strong>, SVERIGES LANTBRUKSUNIVERSITET (SLU), Uppsala, Sweden
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D2.1 AllBioCatalogue available</div>
</li>
<li class="level1"><div class="li"> D2.2 Roadmap for adaptation and further development of tools and services needed for the communities</div>
</li>
<li class="level1"><div class="li"> D2.3 Inventory of available tools and services across the areas</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP2\tInventory and Roadmap","hid":"wp2_inventory_and_roadmap","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:wp3
http://www.allbioinformatics.eu/doku.php?id=public:wp3&rev=1549962287&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp3_life_science_bioinformatics_projects">WP3 Life Science Bioinformatics Projects</h1>
<div class="level1">
<p>
The objective of the WP3 is to introduce the selected “test cases” from WP1 to the bioinformatics community and find together with them solution for these test cases. The bioinformatics community will contribute to the solution of each selected test case. These solutions will be validated under the coordination of WP5.
</p>
<p>
Responsable: <strong>Grégoire Rossier</strong>, SWISS INSTITUTE OF BIOINFORMATICS (SIB), Lausanne, Switzerland
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D3.1 Workflow description of the selected test cases</div>
</li>
<li class="level1"><div class="li"> D3.2 Guideline for collaborative activities for test cases solutions</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP3\tLife Science Bioinformatics Projects","hid":"wp3_life_science_bioinformatics_projects","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:47 +0000public:wp4
http://www.allbioinformatics.eu/doku.php?id=public:wp4&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp4_interoperability">WP4 Interoperability</h1>
<div class="level1">
<p>
The main aim of the WP4 is to coordinate the process of making life science-related software packages, services and data resources work together, in a similar way as has been done over the last decade for many human health-related packages. Additionally, the modification of human genome and human health-related software packages for application in other life science fields will be coordinated. Specific objectives are: to identify and harmonise existing ontologies that are necessary for interoperability in this field; to establish minimum standards for web service deployment; to provide an on-line, searchable catalogue of resources; and to co-ordinate these activities whilst staying up-to-date with complementary initiatives in other projects.
</p>
<p>
Reasponsable: <strong>Teresa Attwood</strong>, THE UNIVERSITY OF MANCHESTER (UNIMAN), Manchester, United Kingdom
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D4.1 Technology recommendation report</div>
</li>
<li class="level1"><div class="li"> D4.2 AllBio Web Service Catalogue (First Version}</div>
</li>
<li class="level1"><div class="li"> D4.3 Extended ontologies and exchange schema</div>
</li>
<li class="level1"><div class="li"> D4.4 AllBio Web Service Catalogue (Final version)</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP4\tInteroperability","hid":"wp4_interoperability","codeblockOffset":0,"secid":1,"range":"40-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:wp5
http://www.allbioinformatics.eu/doku.php?id=public:wp5&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp5_validation_and_training">WP5 Validation and Training</h1>
<div class="level1">
<p>
The objective of WP5 is the validation of the proposed solutions for the “test cases” generated in WP3 for different areas of the life sciences. The validation tests will also encompass the agreements from WP4 on standards for interoperability of systems. Instruments for the extended validation processes with the target community employed for WP5 are experts’ workshops and training courses. Results from WP5 will feed back to WP3 and WP4 for further optimisation of their coordination activities.
</p>
<p>
Responsable: <strong>Andreas Gisel</strong>, CONSIGLIO NAZIONALE DELLE RICERCHE (CNR), Bari, Italy
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D5.1 Report on the first solved test cases</div>
</li>
<li class="level1"><div class="li"> D5.2 Report on AllBio Conference</div>
</li>
<li class="level1"><div class="li"> D5.3 Final summary report on solved test cases</div>
</li>
<li class="level1"><div class="li"> D5.4 Training package from partner specific topics</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP5\tValidation and Training","hid":"wp5_validation_and_training","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000public:wp6
http://www.allbioinformatics.eu/doku.php?id=public:wp6&rev=1549962286&do=diff
<p>
<img src="http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&tok=ee71b7&media=public:header4.jpg" class="mediacenter" loading="lazy" alt="" width="650" />
</p>
<h1 class="sectionedit1" id="wp6_management">WP6 Management</h1>
<div class="level1">
<p>
Main objective of WP6 is the management of the AllBio project including the responsibility for contractual, financial, legal, and administrative issues. The management will also oversee the execution of the milestones in the timeframe of the project and the reporting. The second objective is the establishment and continuous communication between the AllBio participants and the officers of the EC. Third objective is the organization of the kick-off and the final meeting of the AllBio participants. Fourth objective is the support of the partners in the communication with the broader public and stakeholders for general issues of the project.
</p>
<p>
Responsable: <strong>Erik Bongcam-Rudloff</strong>, SVERIGES LANTBRUKSUNIVERSITET (SLU), Uppsala, Sweden
</p>
<p>
Deliverables:
</p>
<ol>
<li class="level1"><div class="li"> D6.1 First annual report finalised</div>
</li>
<li class="level1"><div class="li"> D6.2 Second annual report finalised</div>
</li>
<li class="level1"><div class="li"> D6.3 Final project report finalised</div>
</li>
<li class="level1"><div class="li"> <a href="http://www.allbioinformatics.eu/doku.php?id=public:kick-off" class="wikilink1" title="public:kick-off" data-wiki-id="public:kick-off">D6.4 Kick-off</a> meeting organised</div>
</li>
<li class="level1"><div class="li"> D6.5 First annual meeting organised</div>
</li>
<li class="level1"><div class="li"> D6.6 Second annual meeting organised</div>
</li>
<li class="level1"><div class="li"> D6.7 Final project meeting organised</div>
</li>
</ol>
<p>
<a href="http://www.allbioinformatics.eu/doku.php?id=public:work_packages" class="wikilink1" title="public:work_packages" data-wiki-id="public:work_packages">all workpackages</a>
</p>
</div>
<!-- EDIT{"target":"section","name":"WP6\tManagement","hid":"wp6_management","codeblockOffset":0,"secid":1,"range":"39-"} -->anonymous@undisclosed.example.com (Anonymous)publicTue, 12 Feb 2019 09:04:46 +0000