Please visit the new BioModels platform to access the latest content. This website is no longer updated and will be retired on 31 May 2019.
BioModels Database logo

BioModels Database


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

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



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

Saturday January 13th
  (Conference Room 1)
  Nicolas Le Novère - BioModels projects. The EBI side. PDF
  Michael Hucka - SBML, a summary of current happenings and plans PDF
  Herbert Sauro - Human readable model definition language PDF
  Lena Strömbäck Standards, exchange and databases PowerPoint
  Dagmar Koehn Working with different pathway standards PDF
  Coffee break  
  Interoperability of standards:, BioPAX, SBGN  
  • Usability: What would the user need to improve usage of projects
  • What additional projects should be undertaken by initiative
Sunday January 14th
  BioModels Database (Conference Room 1)  
  Chen Li - BioModels DB internals. Insights in BioModels DB v3 PDF
  Nicolas Le Novère - BioModels DB in action: for users and curators  
  Lu Li - Graphical exports for BioModels DB PDF
  Coffee break  
  Harish Dharuri - Curation of models: painstaking effort or rewarding activity? PowerPoint
  Akira Funahashi - CellDesigner 4, towards CellDesigner 5 PDF
  Christian Knuepfer - Formal Semantics of Bio-Models PDF
  Adrián López - Calibration of model parameters. Benchmarking ByoDyn with BioModels Database PDF
  Emanuele Raineri - A data-driven quantitative (SBML) model of Mycoplasma pneumoniae PDF
  Coffee break  
  Discussion and practical work  
Monday January 15th
  SBO and Miriam (Conference Room 1)
  Mélanie Courtot - SBO resources, formats and Web Services PDF
  Camille Laibe - MIRIAM Resources and Web Services  
  Sarah Keating - LibSBML interface to MIRIAM and SBO PDF
  Coffee break  
  Nicolas Rodriguez - MIRIAM and SBO annotation in SBMLeditor  
  Martin Golebiewski - Annotating SABIO-RK: Integration of MIRIAM and SBO PowerPoint
  Andy Jones - FUGE PowerPoint
  Allyson Lister - OBI PDF
  Rainer Machne - SOSLib, past, present and future PDF
  Matthew Pocock - ComparaGRID Ontology Mapping PowerPoint
  Discussion and practical work  
  Coffee break  
  Discussion and practical work  
18:00 End of the second Training Camp.  
  Pre-meeting Background Information

The following Pre-Meeting Background Materials are available:

    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.

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

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

  Travelling Directions

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

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

  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

Workshop co-organizer:

Camille Laibe
Tel: +44(0)1223 494 403
email: laibe AT

Administrative assistant:

Kathryn Hardwick
Tel: +44(0)1223 494 609
email: kathryn AT

Contact Kathryn for issues related to accommodation.

  Local Information
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.
Manuel Corpas Manchester Interdisciplinary Biocentre, UK
Mélanie Courtot EMBL-EBI, UK SBO
Harish Dharuri California Institute of Technology, USA BioModels DB
John Easton Biomedical Informatics, Signals and Systems Research Laboratory, University of Birmingham, UK
Segun Fatumo German Cancer Research Center, Heidelberg, DE
Akira Funahashi Systems Biology Institute, JP CellDesigner
Martin Golebiewski EML Research, DE SABIO-RK
Alex Gómez Research Group on Biomedical Informatics, ES ByoDyn
Enuo He EMBL-EBI, UK BioModels DB
Michael Hucka California Institute of Technology, USA SBML,
Sarah Keating University of Hertfordshire, UK SBMLtoolbox, libSBML
Christian Knuepfer Friedrich-Schiller-Universitaet Jena, DE Sembiotics
Dagmar Koehn University of Rostock, DE
Nicolas Le Novère EMBL-EBI, UK SBML,
Chen Li EMBL-EBI, UK BioModels DB
Allyson Lister Centre for Integrated Systems Biology for Ageing and Nutrition, Newcastle, UK
Adrián López Research Group on Biomedical Informatics, ES ByoDyn
Rainer Machne University of Vienna, AT BioModels DB, SOSlib
Yukiko Matsuoka Systems Biology Institute, JP CellDesigner
Matthew Pocock University of Newcastle upon Tyne, UK
Emanuele Raineri CRG-Barcelona, ES Centre for Genomic Regulation
Nicolas Rodriguez EMBL-EBI, UK SBMLeditor
Evangelos Simeonidis Manchester Centre for Integrative Systems Biology, UK
Lena Strömbäck IDA (Department of Computer and Information Science), Linköpings universitet, Sewden
Neil Swainston Manchester Centre for Integrative Systems Biology, UK
Katja Wegner University of Hertfordshire, UK
Top Last modification: Fri Jan 12 13:10:07 GMT 2007 Contact