EU Codefest 2012

EU-codefest 2012 was 19 and 20 July in Lodi Italy

In coordination with the BOSC committee we are 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 would like it more free-flowing. There will be few invited speakers, and instead attendees will have a chance to give micro-presentations on their ongoing open source projects. In short, the focus of the EU-Codefest will be on coding, open source projects, and general fun. We also hope to show BOSC talks on video. You are invited to bring in your own open source software project, and to see how others can collaborate and involve it into general Open-Bio.

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

Location

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

Topics

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

Talks

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
• Software resources for Bioinformatics, including http://biogems.info/ by Pjotr Prins, Wageningen University, The Netherlands

Reports

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.