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The 5th Workshop on Software Platforms for Systems Biology

University of Hertfordshire, UK
July 8–10, 2002

The fifth workshop was held at the Hatfield Campus of the University of Hertfordshire, UK. It was organized by Hamid Bolouri's group at the University. Attendance was overwhelming (more than would fit in the room!). This page contains the agenda and (where available) presentation materials from the two day workshop. It also contains links to the SBW Programmer's Manual documentation issued to all delegates attending the Forum, and used at the tutorial session on day 3.

Photo album

Photo album
(Elizabethan Dinner)

Day 1 (Monday, July 8)

Speaker(s) Time Title
Hiroaki Kitano 09:00–09:10 Welcome and introduction
Akira Funahashi 09:10–09:30 Diagram proposal: a proposal for SBEdit's extension of SBML Level 1
09:30–09:55 Discussion
Martin Ginkel 09:55–10:15 Modular SBML: Proposal for an extension of SBML towards Level 2
10:15–10:30 Discussion
Break 10:30–11:00
Daniel Lucio 11:00–11:20 Ion channel/membrane potential proposal
11:20–11:45 Discussion
Nicolas Le Novère 11:45–12:05 SBML Level 2 Proposal: Multistate Features
12:05–12:30 Discussion
Lunch 12:30–14:00
Andrew Finney 14:00–14:20 SBML Level 2 Proposal: Miscellaneous Features ("Other" functions and conditional expressions proposal)
14:20–14:45 Discussion
Andrew Finney 14:45–15:05 SBML Level 2 Proposal: Array Features
15:05–15:30 Discussion
Break 15:30–16:00
16:00–17:45 Parallel break-out groups

Additional material: A proposal for a minimal SBML Level 2 definition by Mike Hucka and Herbert Sauro. Additional materials included the SBML Level 1 specification document.

Day 2 (Tuesday, July 9)

Speaker(s) Time Title
Daniel Lucio 09:00–09:20 Experiences with SBML Level 1 in the Virtual Cell
09:20–09:25 Discussion
Pedro Mendes 09:25–09:45 Experiences with SBML Level 1 in Gepasi and elsewhere
09:45–09:50 Discussion
Mike Hucka 09:50–9:55 SBML Level 1 errata and clarifications
09:55–10:00 Discussion
10:00–10:30 Discussion about implementation issues with SBML Level 1
Break 10:30–11:00
Mike Hucka and David Morley 11:00–11:20 Overview of SBML Level 1.5
11:20–11:45 Discussion
11:45–12:30 Discussion: planning (1) the feature set of SBML Level 1.5, (2) documenting the SBML Level 1.5 standard, (3) deadline for comments on SBML Level 1.5, and (4) organizing Level 2 development.
Lunch 12:30–14:00
Andrew Finney 14:00–14:05 Overview of SBW developments
Mike Hucka 14:05–14:30 Distributed computing with SBW
14:30–14:40 Discussion
Andrew Finney 14:40–14:50 Perl and CORBA with SBW
14:50–15:00 Discussion
Herbert Sauro 15:00–15:20 New SBW-enabled modules (with demo)
15:20–15:30 Discussion
Break 15:30–16:00
Daniel Lucio 16:00–16:20 Recent developments in VCell
16:20–16:30 Discussion
Pedro Mendes 16:30–16:40 The latest version of Gepasi and Metabolite Neighbourhoods
16:40–16:45 Discussion
Claudine Chaouiya 16:45–16:55 Gene Interaction Network software
16:55–17:00 Discussion
Akira Funahashi 17:00–17:10 SBML and KEGG
17:10–17:15 Discussion
17:15–17:45 Organization of collaborations/Any Other Business
Break 17:45–19:30
19:30–22:45 Optional evening outing: Elizabethan Banquet at The Old Palace, Hatfield House, Old Hatfield, Hertfordshire

Day 3 (Wednesday, July 10)

Speaker(s) Time Title
09:00– SBW tutorials:
• Download and set up SBW installation
• Download and set up full range of available modules
• Run through a pre-worked example in which the user exercises the full range of SBW and its modules
• Implement a simple new module (in C, C++, Java, or Python), link it to SBW and "exercise" it.

Additional materials (SBW programmer's manuals and other documentation):

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