Marseille Training Event
Marseille Training Event
The Marseille Training School is designed as a BioHackathon. Participants contribute to the design of various use cases for the Gene Regulation Knowledge Commons; engage in coding efforts to improve various data exchange mechanisms (PSICQUIC 1.0 (for fetching causal PPIs) and REST (ReMAP, UniBind, RSAT)) and test workflows with various data types (rSNPs, ChIP data, RNAseq and HI-C) to address specific questions about gene regulatory mechanisms.
- Jacques Van Helden
- Martin Kuiper
The GREEKC COST Action organises together with the French Institute of Bioinformatics (IFB) a 3-days training session / hackathon in Marseille, that will aim at developing and using interoperable workflows invoking remote bioinformatics resources (knowledge bases, databases, analysis tools) to gather information about regulatory networks and enable an integrative analysis of gene regulation processes.
Bioinformatics resources
The workflows will mobilise and combine a variety of bioinformatics and Knowledge Commons resources:
- Specialized resources for gene regulation (Ensembl Regulation, JASPAR, Regulatory Sequence Analysis Tools, ReMap, ArrayExpress, …);
- Core data resources about gene and protein functions (EnsemblGenomes, Uniprot, …);
- ELIXIR interoperability resources and catalogues (bio.tools, BioSchemas, …);
- Literature knowledge (Europe PMC / SciLite; extracted by text mining ExTRI corpus / Transcription Factor / Target Gene information generated by NTNU/BSC (www.BioGateway.eu; www.ExTRI.org); IMEX resources / IntAct, Signor):
- Any other relevant resource that would answer specific needs emerging from the hacking sessions.
Audience
This hackathon will bring together bioinformaticians and biologists who are developing and interlinking these resources and use them for their research purposes. The workflows will be made tested and made available to enable a series of study cases conceived during previous GREEKC workshops.
Expected outcome
The expected results of the workshop are multiple
- Improvement of the interoperability between the main European resources on gene regulation.
- Foster collaborations between developers and users of these resources.
- New programmatic interface for some resources that would be mobilized in the workflows.
- A set of up-and-running workflows addressing illustrative biological questions, by mobilizing remote data and computing resources on gene regulation.
- Training material for the user of these workflows, and their adaptation/customization for user-specific purposes;
Promote the adoption of interoperability standards.
Contact and registration
For further questions or registration to the event, send an e-mail to Martin Kuiper (martin.kuiper@ntnu.no) and Rafel Riudavets Puig (rafael.riudavets@ntnu.no).
