Lisbon Training Event


Lisbon Training Event

When -

Knowledge Commons and Tools interoperability

Short description:

The Training Event will consist of lectures, brainstorming and practical exercises, aiming at producing data models corresponding to the needs defined during the workshop.

We want to bring together producers of gene regulation resources (databases of transcription factors, sites, motifs, ChIp-seq peaks, gene annotation) and (computational) users of such information: tool builders that access resourced information. The goal of the training workshop is to foster cross-understanding between the two involved communities (knowledge representation and gene regulation, resp.) and to initiate the creation of data models, exchange formats and procedures between the existing resources. We will exchange our understanding of current database content with respect to gene regulation and objects produced by regulatory analysis tools; how this information can currently be made available to software tools that work with this information, and to compare what is in place with what is ideally needed.

There are a limited number of seats available for this event, if you would like to participate please contact

Local organiser(s):
  • Pedro Monteiro

Wednesday, 25 October Lectures + Practicals

  • Concepts and representations of Gene Regulation entities and their relationships
  • Databases of gene regulation: demos and tutorials
  • Tools for gene regulation: demos and tutorials
  • Web services and the future of PSICQUIC
  • Exchange formats and conversions
  • Interoperability of resources and tools
  • Use cases and competency questions

Thursday, 26 October Practical work/ exercises

Hackathon-type exploration of:

  • Data format conversions
  • PSICQUIC web service setup for new resources
  •  PSICQUIC v2.0 for new entity and process concepts
  • Guideline development
  • Survey development

Friday, 27 October Practical work/ exercises

  • Presentation of results
  • Protocols
  • Guidelines, documents, other

Jacques van Helden – Gene Regulation: concepts, specialized tools, and databases
Benoit Ballester – Tools
Noemi Del Toro Ayllon – Databases and PSICQUIC
Anthony Mathelier – PWM