EU Codefest 2012

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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
  • RNA-seq project introduction by James Tojo, Karolinska University, Stockholm, Sweden
  • Software resources for Bioinformatics, including http://biogems.info/ by Pjotr Prins, Wageningen University, The Netherlands



We worked on developing bio-ngs to better handle pipelines

and reproducible workflows, plus semantic databases to manage and query NGS sec

ondary analysis data.

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.


In bioinformatics, and in general life sciences, there are plenty of web services built following the different web service paradigms and bioinformatic web service variants: REST , SOAP, BioMOBY[1], DAS[2], BioMart[3], etc... Although there are already web service repositories like BioMOBY and web service catalogues like BioCatalogue[4] or DASRegistry[5], we feel that many of the existing solutions are not extensible enough to be applied to new web service paradigms. Even worse, in some cases the source code of the registry is not available, so it cannot be reused, improved or extended.

So we (at INB) started the design and implementation of a new web service repository (in Ruby) that will allow us (and anyone using the codebase we are developing) to document and manage the web services developed by different groups, being open and extensible to the entire range of web service paradigms and variants used in bioinformatics. Due to the large web service portfolio the INB possesses, one of the main concerns when designing BioWSR was that web services from any paradigm should be describable at a certain level. As the new registry is strongly inspired by the BioMOBY repository, one requisite was that RDF triples should be a superset of the ones used in BioMOBY to make it backward compatible.

GFF3/GTF tools

During the codefest we collected info on what requirements are there for GFF3/GTF tools, and worked on Debian packages for the same tools

Debian packaging

RNA-seq visualisation

We were working on NGS, more specifically looking to our RNA sequencing project... Just wanted to check with you guys if everyone follows the same methods/pipeline for RNA sequencing. Also managed to set up Gbrowser with help of Paulo for our RNA seq project and also looked to other visualization tools. Meeting you guys and learning from the group was really helpful. Now I have a feeling to work on some of the open source projects but I guess I need to learn bit more to reach that level.