Bioinformatics Workshop "Evaluation of Test Cases"

12 - 14 December 2012

Milan, Italy

Venue: BEST WESTERN PREMIER Cristoforo Colombo

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.


(see updates of the event)

12 December 2012

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
  1. Oren Tzfadia (Weizmann Institute of Science, Tel Aviv, Israel) - The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways
  2. Dimitris Vlachakis (Biomedical Research Foundation, Academy of Athens, Greece) - Recipes to make the most out of your wetlab data in less than 10 minutes.
  3. Jacques van Helden (Université Libre de Bruxelles, Bruxelles, Belgium) - A quick tour of Regulatory Sequence Analysis Tools (RSAT) and Network Analysis Tools (NeAT)
  4. Tatyana Goldberg (Technische Universität, München, Germany) - Loctree2 predicts localization for all domains of life
  5. 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
  6. Bruno Contreras Moreira (CSCI, Zaragoza, Spain) - Introducing get_homologues and footprintDB
  7. Petri Klemelä (IT Center for Science, Helsinki, Finland) - Chipster: user-friendly analysis software for high-throughput data
  8. Paul Kersey (European Bioinformatics Institute, Hinxton, GB) - Ensembl beyond humans: genomic resources for animals, plants and microbes
  9. Mikko Arvas (VTT Technical Research Centre of Finland) - Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species
  10. Marco Masseroli (Politecnico di Milano, Milan, Italy) - Genomic and Proteomic Knowledge Base (GPKB) & Bio Search Computing (Bio-SeCo)
  • 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

public/bioinf.txt · Last modified: 2012/12/18 09:10 by andreas
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