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Difference between revisions of "EU Codefest 2012"
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* ''Semantic Web for Bioinformatics'' by Toshiaki Katayama, Tokyo, Japan | * ''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 | * ''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 | * ''Software resources for Bioinformatics, including http://biogems.info/'' by Pjotr Prins, Wageningen University, The Netherlands | ||
Revision as of 10:51, 28 July 2012
Contents
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
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
- 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
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.
