Second BioModels.net training camp - Manchester Conference Centre, 13-15 January 2007

The second BioModels.net training camp was held from January 13 2007 to monday 15 at the Manchester Conference Centre, Manchester, UK. The event followed the workshop BioSysBio2007.

Pictures!

• Pre-Meeting Background Material
• Travelling Directions
• Miscellaneous Information
• Accommodation
• Contact Information
• Local Information
• Participants

The meeting was divided in two parts. The first has been mainly devoted to presentations both about BioModels.net projects and related efforts. The second and third day were focussed on practical work, either curation or development.

The following Pre-Meeting Background Materials are available:

• MIRIAM
  MIRIAM is an effort to standardize "Minimal Information Requested In the Annotation of biochemical Models", so that different groups can collaborate on annotating and curating computational models in biology... More information in the following paper:
  Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005). Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nature Biotechnology, 23: 1509-1515. [PubMed][DOI]

  MIRIAM resources are now available. A database catalogues the data resources, their URIs and the corresponding physical URLs. We provide Web Services to interrogate the database and generate or resolve URIs.

• Systems Biology Ontology (SBO)
  The Systems Biology Ontologies project develops controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in systems biology, especially in the context of computational modeling. Some additional information on the use of SBO in conjunction with SBML can be found in the SBML Level 2 Version 2 specification.

• BioModels Database
  BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. More information in the following paper:
  Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006). BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Nucleic Acids Res., 34: D689-D691. [PubMed][DOI]

  The following tools have quite good SBML support, and are used to curate models for BioModels DB.

  • CellDesigner
  • COPASI
  • JDesigner and Jarnac
  • MathSBML
  • RoadRunner
  • SBMLodeSolveR

  Based on a correct SBML file and XSL transformations, we can also generate configuration files for:

  • XPP-Aut
  • SciLab

  Attendees are of course authorised to use any other SBML-aware software they would fancy!

More information to find the Manchester Conference Centre is available here.

Internet Connection

One week WIFI vouchers have been purchased for all participants and are available from Nicolas Le Novère.

Videoprojector

A videoprojector will be available in the Conference Room.

We already booked rooms for every attendees at the Premier Inn of Portland street. DO NOT contact the hotel yourself to book the rooms. Position of the hotel relative to the conference center

Workshop organizer:

Nicolas Le Novère
Computational Neurobiology, EMBL-EBI
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Tel: +44(0)1223 494 521
Mob: +33(0)689218676
email: lenov AT ebi.ac.uk

Workshop co-organizer:

Camille Laibe
Tel: +44(0)1223 494 403
email: laibe AT ebi.ac.uk

Administrative assistant:

Kathryn Hardwick
Tel: +44(0)1223 494 609
email: kathryn AT ebi.ac.uk

Contact Kathryn for issues related to accommodation.

Weather:

For a five day weather forecast for the Manchester area see Manchester weather.

Electrical Voltage:

UK electrical current is 50 Hz, 240 V. Adapters may be required to connect some equipment to the standard UK power outlets. Participants should equip themselves with the needed adapters. You will not be able to buy adapters on the campus. Get one before you leave, or at the airport.