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Bioinformatics Workshop "Evaluation of Test Cases"
12 - 14 December 2012
Milan, Italy
Venue: BEST WESTERN PREMIER Cristoforo Colombo http://www.hotelcristoforocolombo.it/
The aim of the Bioinformatics Workshop “Evaluation of Test Cases” is to join the biologists who submitted the test cases with the (bio)informaticians who might be able to propose solutions for these bioinformatics challenges.
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 Horizon 2020 calls.
== Preliminary Programme == (see updates of the event) Hands-on
12 December 2012
- 13:00 - 14:00 Registration and Lunch
- 14:00 - 14:30 Welcome by the chair Erik Bongcom-Rudloff and the local organizer Andreas Gisel
- 14:30 - 18:00 Presentation of the 15 selected test cases - each 10 plus some questions
- FAIRE-seq data analyser - Amin Omidbakhshfard (University of Potsdam, Germany)
- Discovery of gene regulatory networks - Nooshin Omranian (Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany)
- Primer design for ChIP-PCR studies - Prashant Garapati (Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany)
- Integrative Omics analysis workflow Karl Göran Andersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)
- Bacterial Comparative Genomics - Laurent Falquet Swiss Institute of Bioinformatics, Lausanne, Switzerland)
- Pathway analysis of a poorly annotated but sequenced plant genome - Erik Alexandersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)
- Functional annotation of the potato genome - Erik Alexandersson (Swedish University for Agricultural Sciences, Uppsala, Sweden)
- Transcriptome and small RNA comparison of four phenotypically distinct cv “Primitivo” grapevine clones - Annalisa Giampetruzzi (Institute of Plant Virology CNR, Bari, Italy)
- Improved cell factories - Mikko Arvas (VTT Technical Research Centre of Finland, Espoo, Finland)
- Genetics, Genomics and Evolution of prolific breeds of domestic sheep (Ovis aries) - Juha Kantanen (MTT Agrifood Research Finland, Jokioinen, Finland)
- 16:20 Coffee Break
- 18:00 Coach
13 December 2012
- 09:00 - 11:30 Topic wise parallel sessions to discuss the test cases
| ⇒ We will divide the work in 4 parallel groups, one for each of the following topics: |
|---|
| - data formats / standardization and workflows |
| - scalability of tools (multi genome comparison/data compression) |
| - non model organisms and multiploidy |
| - visualization and training |
| ⇒ The 4 groups will analyze (according to the topic) each test case to identify |
|---|
| 1.) the difficulties or the current limitations affecting the test case |
| 2.) the existing tools required (with or without adaptation) |
| 3.) the missing tools required |
| 4.) keep minutes of discussion |
| 5.) prepare a summary for discussion |
- 10:30 Coffee Break
- 11:30 - 13:00 Reporting of the different sessions and general discussions
| ⇒ Each group will report in 15min the results of their session |
|---|
| a) is there a common trait in several test cases? |
| b) are there common tools required or missing? |
| c) can we split test cases according to operations? |
| d) can we group test cases? |
- 13:00 - 14:00 Lunch
- 14:00 - 15:30 Presentations of relevant data analysis tools - speaker to be defined
- Oren Tzfadia (Weizmann Institute of Science, Tel Aviv, Israel) - The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways
- Dimitris Vlachakis (Biomedical Research Foundation, Academy of Athens, Greece) - Recipes to make the most out of your wetlab data in less than 10 minutes.
- Jacques van Helden (Université Libre de Bruxelles, Bruxelles, Belgium) - A quick tour of Regulatory Sequence Analysis Tools (RSAT) and Network Analysis Tools (NeAT)
- Tatyana Goldberg (Technische Universität, München, Germany) - Loctree2 predicts localization for all domains of life
- 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
- Bruno Contreras Moreira (CSCI, Zaragoza, Spain) - Introducing get_homologues and footprintDB
- Petri Klemelä (IT Center for Science, Helsinki, Finland) - Chipster: user-friendly analysis software for high-throughput data
- Paul Kersey (European Bioinformatics Institute, Hinxton, GB) - Ensembl beyond humans: genomic resources for animals, plants and microbes
- 15:30 - 18:30 Parallell session for test cases specific discussions in light of the results of the topics-wise discussions
| ⇒ We will divide again the work in 3 parallel sessions. Each session will analyze 5 test cases (random distribution). |
|---|
| For each test case we need: |
| - identification of tools |
| - a SWOT analysis (Strength, Weaknesses, Opportunities and Threats) |
| - a preliminary work plan for a follow-up activity |
| - propose other collaborators for the follow-up activity |
| - keep minutes of discussion |
* 16:20 Coffee Break
14 December 2012
- 09:00 - 11:00 Cross-presentation of the results from the test case discussions
| ⇒ Selection of test cases (or operations) in 3 categories and discussion of the work plan |
|---|
| a) relatively easy, workflow exists or can be adapted within weeks |
| b) more difficult, some tools are missing, workflows are partial, need months to adapt |
| c) very difficult, scalability problem, tools completely missing, requires new developments (projects over years) |
- 10:30 Coffee Break
- 11:00 - 13:00 Organization of the follow-up events to approach the solutions of some test cases
| a) create work groups to prepare the hack-a-thon events |
| b) decide number of events and divide test cases or operations, plan a soon solution of one test case |
| c) collect emails and skype accounts |
| d) decide upon video meetings schedule and chairperson |
| e) keep minutes of discussion and decisions |
- 13:00 - 14:00 Lunch and end of the workshop
The topics were extracted as common problems from all proposed test cases are the following:
- multiploidy
- data formats / standardization
- workflows
- scalability of tools (multi genome comparison/data compression)
- non model organisms
- visualization
- best practice / guide line
- data to biology and biology to data
- training
Contact Us
If you are willing and able to help to work on one of the test cases and interested to create a working group capable to develop a proposal for future EU calls, please contact andreas.gisel[at]ba.itb.cnr[dot]it with the subject AllBio Bioinfo.
Organising committee and local organisers
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
Angelica Tulipano, Flavio Licciulli, Sabino Liuni, Domenica D'Elia
Trace: bioinf