Hackathon Bioinformatique
L'IFB organise en partenariat avec ELIXIR bio.tools un hackathon à destination de la communauté bioinformatique française.
Du 24-03-2016 au 25-03-2016 à IFB-Core, Gif sur Yvette
Date limite d'inscription: Aucune information
Why

The first hackathons included exemplar content from various ELIXIR nodes and other key partners beyond ELIXIR.  In follow-up, IFB (ELIXIR-FR) and ELIXIR-DK are organising a new hackathon to organize the registration of the resources provided by the IFB members to the community.

Who

We hope representatives of all the IFB platforms and the french bioinformatics community (at large) will attend.  Please decide on who should attend from your organisation.  You should be prepared to “roll up your sleeves”; help steer the workshop and engage directly in practical activities in an informal atmosphere.

http://tinyurl.com/frhackathonparticipants

 

Outcomes

During the workshop we will:

  • Agree upon a representative set of resources (tools and data services) from each partner to import into the registry
  • Annotate the resources with (at least) all mandatory information fields, including terms from the EDAM vocabulary for types of primary I/O data, function and topic
  • Prepare the resource descriptions for registration by whatever mutually convenient mechanism, and register the resources

Transport to venue - how to get to IFB-core?

http://www.france-bioinformatique.fr/en/access-map

 

Hotel

The simplest way to be hosted near IFB core is the CNRS hosting complex:

http://www.dr4.cnrs.fr/delegation/delegation_service/complexe_accueil.htm

 

Mailing lists

Please subscribe to the “ELIXIR Registry mailing list”:

http://elixirmail.cbs.dtu.dk/mailman/listinfo/registry

Please use the mailing list as the main channel for all discussions around the event.  Send mail to:

registry@elixir-dk.org

Several other relevant mailing lists are available.  Please consider subscribing to any which are relevant:

They are summarised here:

http://elixirmail.cbs.dtu.dk/mailman/listinfo

 


Day 1

12:00-14:00    Lunch

14:00-15:00    Session 1 : Introduction, presentations

  • Welcome, introduction and practical information (H.Ménager, Institut Pasteur - 5mn)
  • Introduction to bio.tools including biotoolsXSD and EDAM (J.Ison, DTU - 20mn) pdf
  • ReGaTE : automatic registration of Galaxy Tools in the ELIXIR registry (F.Mareuil, Institut Pasteur, 5mn) pdf
  • BioShadock : a curated BioInformatics container registry (O.Collin, GenOuest - 10 mins) pdf

16:00-16:30    Coffee break

16:30-18:00    Session 2 : bio.tools & EDAM : first look, tool registration

18:30        “Meet the IFB-Core” (beers and soft drinks)

19:30        Dinner (for participants who registered) at Le Canapé

 

Day 2

09:00-12:00    Session 3 : Presentations & Open Discussion on bio.tools requirements

  • Presentations
  • A RainBio over the Life Science Cloud (Bryan Brancotte, 15mn)
  • Snakemake is great (J. Van Helden, 15mn)
  • Open Discussion on bio.tools requirements
  • API
  • Data model
  • Content owner / permissions model

12:00-14:00    Lunch

14:00-16:00    Session 4: Towards a French national registry

  • Discussion around a registry or view for IFB:
    • technical options (hosting, software)
    • organisation: how can IFB members organize the maintenance of this registry

What can I register ?

All types of computational resource from the bioinformatics and biomedical domains can be registered, including “tools” (for query and retrieval, analysis, deposition, visualisation, and utilities), databases, services, platforms and so on. All sorts of resource interface types are acceptable, including command line, Web UI, desktop GUI etc.

 

What information must I supply ?

You will need to supply at least the following information for each resource:

Attribute Description Format
name (1 only) Canonical resource name Text
homepage (1 only) Resource homepage URL
description (1 only) Short textual description of the resource Text
resourceType (1 or more) Basic resource type enum (see below)
interfaceType (1 or more) Resource interface type enum (see below)
topic (1 or more) General scientific domain(s) the resource serves, e.g. "Proteomics" URI of EDAM Topic concept(s)
functionName (1 or more) The basic resource function(s), e.g. "Multiple sequence alignment" URI of EDAM Operation concept(s)
input->dataType (0 or more) Type(s) of data: primary inputs (if any), e.g. "Protein sequences" URI of EDAM Data concept(s)
output->dataType (0 or more) Type(s) of data: primary outputs (if any), e.g. "Protein sequence alignment" URI of EDAM Data concept(s)
contact (1 or more) Primary contact, e.g. a person, helpdesk or mailing list Email address or URL of contact

 

Resource types (valid values of resourceType)

 

type Description
Database A collection of data, datasets, a registry etc.
Tool Software which you can download, install, configure and run yourself.
Service Software provided as a service and available for immediate use, e.g. on the Web.
Workflow A definition of a collection of tools, services etc. for running in a workflow system.
Platform An integrated environment, including suites, workbenches, workflow systems, frameworks etc.
Container A collection of data, tools, services etc. in a portable environment, e.g. VMs, Docker.
Library A package of code for building/extending tools, including widgets, plug-ins, toolkits etc.
Other Other type of resource not listed above.

 

 

Interface types (valid values of interfaceType)

 

type Description
Command line Text-based interface to a tool or service.
Web UI Graphical user interface available on the Web.
Desktop GUI Graphical user interface that runs on your own machine.
SOAP WS Programmatic access provided via SOAP and WSDL file.
HTTP WS Access provided via HTTP, including simple URLs, RESTful APIs etc.
API Application Programming Interface to a library.
QL Query language interface to a database, e.g. SQL, SPARQL etc.

 

 

What’s EDAM - how do I use it ?

EDAM is the ontology underpinning the registry.  It provides the controlled vocabulary - a set of terms - that you must use to annotate your resources, as per the table above. You can browse EDAM here:

http://bioportal.bioontology.org/ontologies/EDAM?p=classes

http://www.ebi.ac.uk/ols/beta/ontologies/edam

 

We encourage you to take a look at EDAM and to try to find the right terms.  We do not expect you to learn all about it before annotating though - and will provide you with direct assistance in making the annotations.  To request terms, and for help, please use:

https://github.com/edamontology/edamontology/issues/new

 

You can download EDAM, and read more about it, here:

https://github.com/edamontology/edamontology

 

How should I maintain the information?

For registration purposes, you can use the interactive registration interface (bio.tools) or post a biotoolsXSD-compliant XML to the API.  In both cases you will need a Registry account: either a personal account (which you can get by going to bio.tools and clicking “Log in”) or (probably better) an institutional account (which you can get by mailing  registry@elixir-dk.org).

 

Resource description schema (biotoolsXSD)

biotoolsXSD is a formal XML schema (XSD) that describes completely the information that may be specified; including the 10 mandatory fields above, from 50 fields in total.  Please see the schema documentation, where you can download the XML Schema and sample XML file.  You can read more about biotoolsXSD here:

https://github.com/bio-tools/biotoolsxsd


 

Topic Work done at the hackathon Next steps
     

 


New data model (reference set of tools)

Please build on the existing plans

 

New content management model (Google docs style)

Please build on the existing plans

 

New fully featured API (persistent IDs for tools)

Please build on the existing plans

 


May need to acknowledge “regions” - as well as Nations, RIs, institutes, projects etc … we need simply to enumerate all of the types of “entities” to which a tool can be affiliated.

Bio.tools should provide a way for tools to be declared as issuing from some Research Unit (e..g CNRS, Insern).  But the definition of these units is not the problem of biu.tools per se.  

Each FR developer would specify the ID of their Unit, upon registration of a tool

Affiliations are propagated up the “collaborators network” e.g. something affiliated with IFB is also affiliated with France (but not vica versa)

But every Nation will probably require a specific solution, e.g. DE likely will have a very specific requirement to FR.

 

Bio.tools must be concerned with Nations (certainly) and also RIs such as ELIXIR, BBMRI etc.

 

It must be possible to affiliate a tool to such RIs, in addition to everything else (i..e multiple affiliations) are needed.

 


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