spacer
spacer

First BioModels.net training camp - EBI, Hinxton, 10-12 April 2006

Pictures!


  Programme

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.

Monday April 10th
  The Rosalind Franklin Pavilion
08:45  
  Welcome  
  Michael Hucka - BioModels.net: toward semantics  
  Nicolas Le Novère - BioModels Database, a curate database of quantitative models in biology PDF
  Michael Hucka - The Systems Biology Ontology, aims and structure  
  Andrew Finney - MIRIAM standard of model curation PowerPoint
10:30  
  Coffee  
11:00  
  Andrew Finney - SBML Level 2 Version 2 and beyond PowerPoint
  Midori Harris - Introduction to the Gene Ontology  
  Bernard de Bono - Structure and function in the Reactome data model PowerPoint
12:30  
  Lunch  
 
 
14:00  
  Marvin Schulz - SBMLmerge and MIRIAM support PDF
  Jim Schaff - The Virtual Cell  
  Martin Golebiewski - SABIO-RK: Making Reaction Kinetics Data Accessible PowerPoint
15:30  
  Coffee  
16:00  
  BioModels hands-on: model search; simulation tests; analysis of annotation.  
 
17:00  
  Discussion.  
 
18:00 IT room closes  
18:30 Bus to The Chequers, Fowlmere  
Tuesday April 11th
  EBI room A2/301 EBI room A233
09:00  
  Nicolas Le Novère - model curation for BioModels Database Curation guidelines Chen Li - BioModels Database structure, search and annotation; MIRIAM webservices  
  Harish Dharuri and Lu Li - BioModels Database curation experience OpenOffice Lu Mélanie Courtot - SBO edition and export  
  Nicolas Le Novère - curation of SBO terms   Ben Borstein and/or Sarah keating - libSBML and MIRIAM support PDF
10:30  
  Coffee  
11:00  
  Nicolas Rodriguez - SBML editor and MIRIAM support   Practical work: Everyone minds his own BioModels DB, MIRIAM or SBO business  
Everyone pick one or several models; Discussion and beginning of curation.    
   
12:30  
  Lunch  
 
 
14:00  
  Curation   Development  
   
   
15:30  
  Coffee  
16:00  
  Curation   Development  
   
   
  report of curation results    
18:00 Let's call it a day  
18:30 Bus to Jesus College in Cambridge, to have dinner in the Prioress room  
Wednesday April 12th
  The Rosalind Franklin Pavilion
09:00  
  Nicolas Le Novère - Introduction to model annotation annotation guidelines Development  
  Annotation  
 
10:30  
  Coffee  
11:00  
  Annotation   Development  
 
   
12:30  
  Lunch  
 
 
14:00  
  Annotation   Development  
   
  Report on annotation   Report on development  
15:30  
  Coffee  
16:00  
  Debriefing on the training camp; criticisms, suggestions  
  Next steps for BioModels.net; next camp  
17:00 Bar opens  
  Next steps for BioModels.net  
18:00 IT room closes  
top
  Pre-meeting Background Information

The following Pre-Meeting Background Materials were 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. Our goal is to produce a set of guidelines suitable for use with any structured format for computational models (not just SBML).. 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]

  • 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 the database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. BioModels Database is developed in collaboration by the teams of Nicolas Le Novère (EMBL-EBI, United-Kingdom), Michael Hucka (SBML Team, Caltech, USA), Herbert Sauro (Keck Graduate Institute, USA), as part of the BioModels.net initiative. BioModels Database development is funded by the European Molecular Biology Laboratory and the National Institute of General Medical Sciences. 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]

  • Systems Biology Ontology (SBO)
    SBO is the Systems Biology Ontologies project, another cornerstone of the BioModels.net effort. The goal of SBO is to develop 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 following document:
    Michael Hucka, Chris D. Cox and James Michael McCollum. A Simple Proposal for Indicating Modeling Framework Assumptions Underlying an SBML Model

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

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

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

top
  Travelling Directions

The European Bioinformatics Institute is situated In the United-Kingdom, south of Cambridge, near the villages of Hinxton and Ickleton. Directions for getting to the Wellcome Trust Genome Campus and the EBI by car, bus, train and plane.

top
  Accommodation

Reservations for the Workshop were made at the Wellcome Trust Conference Centre for the nights of 9th, 10th, 11th and 12th. Tell us if you want extra nights. Be aware that we will not support those.

The Conference Centre is open Monday to Friday, 8am until 6pm. Outside of these hours, arrivals should check-in with the Campus security staff as indicated on the Site Map. Upon arrival participants will be asked by the Conference Center staff to fill out registration cards with personal details when they collect their keys.

All residential rooms have their own telephone lines. Payphones are available in the Conference Centre. All rooms also have ethernet ports with free high-speed access to the internet. Ethernet cables are available for purchase from the Conference Centre reception, which also has a small shop selling commonly forgotten items such as toothpastes and deodorant etc.

The conference centre contact numbers
tel: +44 (0)1223 495000
Fax: +44 (0)1223 495023
Email: info@wtconference.org.uk
URL: www.wtconference.org.

top
  Contact Information

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

Contact Nicolas for anything related to the programme, and if you cannot be helped by the other contacts.

Workshop co-organizers:

Mélanie Courtot
Tel: +44(0)1223 494 418
email: courtot AT ebi.ac.uk

Chen Li
Tel: +44(0)1223 494 403
email: chenli AT ebi.ac.uk

Contact Mélanie or Chen for issue related to computing (wireless, shared resources etc.)

Administrative assistant:

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

Contact Kathryn for issues related to ground transportation and accommodation.

top
  Local Information
Weather:
For a five day weather forecast for the Cambridge area see Cambridge 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.
Around the campus:
Two villages are very close to the EBI, Hinxton and Ickleton, and you will find a pub serving food in each of them:

About Cambridge:
For more information about Cambridge, see the following websites:

About the Genome Campus:

The Genome Campus is undergoing a large expansion plan, some images of the Campus can be seen below.

top
spacer
spacer