EU Codefest 2012

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Revision as of 05:51, 28 July 2012 by Pjotrp (talk) (Talks)
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EU-codefest 2012 was 19 and 20 July in Lodi Italy

In coordination with the BOSC committee we organised the first EU-Codefest, a low-key event the week after BOSC 2012 in California.

The EU-Codefest took place on 19 and 20 July 2012, in Lodi, Italy, near the Bergamo and Milano airports (Bergamo is a hub for Ryanair).

The EU-Codefest is modeled on the successful biohackathons in Japan, though we like it more free-flowing.

The weekend after 21 and 22 July continued (unofficially) to have a good time, and organised some outings.

Organising committee: Francesco Strozzi, Raoul Bonnal and Pjotr Prins


Parco Tecnologico Padano vie Einstein - Loc. Cascina Codazza 26900, Lodi - ITALY


Three main topics were worked on during the CodeFest:

  • NGS and high performance parsers for OpenBio projects.
  • RDF and semantic web for bioinformatics.
  • Bioinformatics pipelines definition, execution and distribution.

During the conference we discussed current issues and added

  • Service discovery and integration (Debian, BioMoby, biogems.info, BioLinux)
  • Workflow (bio-ngs, Galaxy, Taverna)
  • PBS (bio-ngs)
  • Software
    • bio-ngs
    • bio-maf introducing into pipeline
    • gff3
    • biogems.info (Debian packages)
    • bio-table (RDF support)
    • biowsr


The following talks/introductons were given at the Codefest:

  • Semantic Web for Bioinformatics by Toshiaki Katayama, Tokyo, Japan
  • Writing the worlds fastest GFF3 parser by Marjan Povolni, Faculty of Technical Sciences Novi Sad, Serbia
  • BioWSR Bioinformatic Web Services Registry project update by José María Fernández González, Protein Design Group, CNB-CSIC Cantoblanco, Madrid, Spain
  • Software resources for Bioinformatics, including http://biogems.info/ by Pjotr Prins, Wageningen University, The Netherlands


Adding a list of BioLinux Software packages to biogems.info

We recognise is it often hard to find relevant information on current software packages. At the USA codefest, a week earlier, Brad Chapman and Hervé Ménager created a Manifest of bioinformatics packages installed on a running CloudBiolinux system (VM). At the EU codefest a web representation was created that parsed the manifest, pulled some more information from the Debian package information and generates the page http://www.biogems.info/biolinux.html.