AllBio public:bioinfo

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            <title>public:bioinfo:update</title>
            <link>http://www.allbioinformatics.eu/doku.php?id=public:bioinfo:update&amp;rev=1549962286&amp;do=diff</link>
            <description>
&lt;p&gt;
&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=650&amp;amp;tok=ee71b7&amp;amp;media=public:header4.jpg&quot; class=&quot;mediacenter&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;650&quot; /&gt;
&lt;/p&gt;

&lt;h2 class=&quot;sectionedit1&quot; id=&quot;bioinformatics_workshop_evaluation_of_test_cases&quot;&gt;Bioinformatics Workshop &amp;quot;Evaluation of Test Cases&amp;quot;&lt;/h2&gt;
&lt;div class=&quot;level2&quot;&gt;

&lt;p&gt;
&lt;strong&gt;12 - 14 December 2012&lt;/strong&gt;
&lt;/p&gt;

&lt;p&gt;
&lt;strong&gt;Milan, Italy&lt;/strong&gt;
&lt;/p&gt;

&lt;p&gt;
THANKS FOR THESE NICE WORDS:
&lt;/p&gt;

&lt;/div&gt;

&lt;h5 id=&quot;december_2012&quot;&gt;12 December 2012&lt;/h5&gt;
&lt;div class=&quot;level5&quot;&gt;

&lt;p&gt;
All the participants (43) from all over Europe gathered for lunch in time in the hotel lounge.
&lt;/p&gt;

&lt;p&gt;
Shortly after 14:00 Andreas Gisel, the local organiser, opened the event with a welcome to all &lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=725b48&amp;amp;media=public:p1070101_small.jpg&quot; class=&quot;medialeft&quot; align=&quot;left&quot; loading=&quot;lazy&quot; title=&quot;Greetings of the AllBio chair via Skype&quot; alt=&quot;Greetings of the AllBio chair via Skype&quot; width=&quot;300&quot; /&gt;participants and the information that the chair Erik Boncgam-Rudloff because of illness was not able to join. However, via Skpe he was able to greet all and wished the workshop community a successful event.
&lt;/p&gt;

&lt;p&gt;
After this virtual greeting of the chair, Andreas Gisel was introducing in a few words the concept, idea and goal of the AllBio Project.
&lt;/p&gt;

&lt;p&gt;
&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=137835&amp;amp;media=public:p1070103_small.jpg&quot; class=&quot;mediaright&quot; align=&quot;right&quot; loading=&quot;lazy&quot; title=&quot;Laurent Falquet guiding the test case presentations&quot; alt=&quot;Laurent Falquet guiding the test case presentations&quot; width=&quot;300&quot; /&gt;Laurent Falquet then guided the presentations of the 15 selected test cases which already stimulated the participants for interesting discussions. &lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=93a90d&amp;amp;media=public:p1070104_small.jpg&quot; class=&quot;media&quot; loading=&quot;lazy&quot; title=&quot;Discussion during the test case presentations&quot; alt=&quot;Discussion during the test case presentations&quot; width=&quot;300&quot; /&gt;Tomorrow the community will be ready for the &amp;#039;work&amp;#039; to thoroughly analyse and disect the presented test cases to discuss the further processes for the solution of some of these test cases.
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&lt;/p&gt;

&lt;/div&gt;

&lt;h5 id=&quot;december_20121&quot;&gt;13 December 2012&lt;/h5&gt;
&lt;div class=&quot;level5&quot;&gt;

&lt;p&gt;
The big discussion day started with the splitting of the participants into 4 moderated groups analysing &lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=191c5d&amp;amp;media=public:p1070133_small.jpg&quot; class=&quot;medialeft&quot; align=&quot;left&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;the selected test cases according to the following brought topics:
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; data formats / standardization and workflows - (Jacques)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; scalability of tools (multi genome comparison/data compression) - (Laurent)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; non model organisms and multiploidy - (Paul)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; visualization and training – (Andreas)&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
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Each group was then reporting to the whole group there results of the discussions. These information will then be reported in an extended document including the upstream and downstream discussions and conclutions drawn at the end of the workshop.
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&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=23e511&amp;amp;media=public:p1070138-small.jpg&quot; class=&quot;media&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;
&lt;/p&gt;

&lt;p&gt;
After lunch we had 10 very interesting presentations of bioinformatics tools or bio databases which &lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=a35545&amp;amp;media=public:p1070162_small.jpg&quot; class=&quot;medialeft&quot; align=&quot;left&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;
could be helpfull in the solution of some of the selected test cases.
&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=4dc4db&amp;amp;media=public:p1070176_small.jpg&quot; class=&quot;mediacenter&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;
&lt;/p&gt;

&lt;p&gt;
The participants then split in a second round in 4 groups, different than before, to discuss the bioinformatic solutions, bottlenecks and possible collaborations specific to the selected test cases.
the groups were formed according to the general topic these test case could be categorized:
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; Genome comparison (TCs 2 6 8 11 - Laurent)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; Gene regulation (TCs 1 3 4 13 -Jacques)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; Gene annotation (TCs 7 9 10 12 14 - Paul)&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; Data integration (TCs 5 15 - Andreas)&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
Each group then was selecting 2 test cases according there criteria to propose tomorrow morning for being part for the AllBio Roadmap and subject of the future AllBio activities.
&lt;/p&gt;

&lt;p&gt;
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After a hard working but very successful day demonstrating the willingness of collaborative efforts to solve hand-in-hand biological data processing problems/challenges the participants enjoyed the social dinner at the hotel.
&lt;/p&gt;

&lt;p&gt;
&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=8a46a0&amp;amp;media=public:p1070187_small.jpg&quot; class=&quot;medialeft&quot; align=&quot;left&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;
&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=300&amp;amp;tok=362948&amp;amp;media=public:p1070181_small.jpg&quot; class=&quot;mediaright&quot; align=&quot;right&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;300&quot; /&gt;
&lt;/p&gt;

&lt;p&gt;
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&lt;h5 id=&quot;december_20122&quot;&gt;14 December 2012&lt;/h5&gt;
&lt;div class=&quot;level5&quot;&gt;

&lt;p&gt;
This last session of the workshop was the time to take decisions and shape the roadmap for the future activities of AllBio.
&lt;/p&gt;

&lt;p&gt;
Each group from the separate sessions yesterday afternoon was reporting there analysis of the selected test cases and 10 of the 15 test cases were placed into one event AllBio will organice with interested workshop participants.
AllBio will support five physical events where the groups around the 10 test cases will meet and terminate the total or partial solutions of these test cases and apply data challenges to verify the functionality.
&lt;/p&gt;

&lt;p&gt;
&lt;strong&gt;Preliminary schedule:&lt;/strong&gt;
&lt;/p&gt;

&lt;p&gt;
Bari, Italy (March 2013)
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc8&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc8&quot; data-wiki-id=&quot;public:loadedtestcases:tc8&quot;&gt;Discover non-coding RNA in yeast&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc13&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc13&quot; data-wiki-id=&quot;public:loadedtestcases:tc13&quot;&gt;Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
Amsterdam, Netherlands (March 2013)
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc1&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc1&quot; data-wiki-id=&quot;public:loadedtestcases:tc1&quot;&gt;FAIRE-seq data analyser&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc2&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc2&quot; data-wiki-id=&quot;public:loadedtestcases:tc2&quot;&gt;Identification of large structural variations&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
Helsinki, Finland (TBD)
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc5&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc5&quot; data-wiki-id=&quot;public:loadedtestcases:tc5&quot;&gt;Integrative Omics analysis workflow&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc15&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc15&quot; data-wiki-id=&quot;public:loadedtestcases:tc15&quot;&gt;Genetics, Genomics and Evolution of prolific breeds of domestic
sheep (Ovis aries)&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
Amsterdam, Netherlands (September 2013)
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc9&quot; data-wiki-id=&quot;public:loadedtestcases:tc9&quot;&gt;Pathway analysis of a poorly annotated but sequenced plant genome&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc10&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc10&quot; data-wiki-id=&quot;public:loadedtestcases:tc10&quot;&gt;Gene prediction modelling for plants&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc12&quot; data-wiki-id=&quot;public:loadedtestcases:tc12&quot;&gt;Functional annotation of the potato genome&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
Marseille, France (September 2013)
&lt;/p&gt;
&lt;ul&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc3&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc3&quot; data-wiki-id=&quot;public:loadedtestcases:tc3&quot;&gt;Discovery of gene regulatory networks&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;li class=&quot;level1&quot;&gt;&lt;div class=&quot;li&quot;&gt; &lt;strong&gt;&lt;a href=&quot;http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc4&quot; class=&quot;wikilink1&quot; title=&quot;public:loadedtestcases:tc4&quot; data-wiki-id=&quot;public:loadedtestcases:tc4&quot;&gt;Primer design for ChIP-qPCR studies&lt;/a&gt;&lt;/strong&gt;&lt;/div&gt;
&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;
AllBio and the local organisers would like to thank all participants for their time and effort to turn this event so successful. We are looking forward to continue this fruitful collaborations.
&lt;/p&gt;

&lt;p&gt;
After the work we have fun!!!!
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&lt;img src=&quot;http://www.allbioinformatics.eu/lib/exe/fetch.php?w=600&amp;amp;tok=4d8e5b&amp;amp;media=public:allbiomilanoworkshop_small.jpg&quot; class=&quot;mediacenter&quot; loading=&quot;lazy&quot; alt=&quot;&quot; width=&quot;600&quot; /&gt;
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            <author>anonymous@undisclosed.example.com (Anonymous)</author>
        <category>public:bioinfo</category>
            <pubDate>Tue, 12 Feb 2019 09:04:46 +0000</pubDate>
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