RBM Agenda: Difference between revisions
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3:00-3:30 '''Coffee Break Sponsored by SFI''' | 3:00-3:30 '''Coffee Break Sponsored by SFI''' | ||
=== | ===Representational Issues in Rule-Based Modeling=== | ||
'' | |||
3:30-4:00 ''Sohyoung Kim (NIH/NCI)'' '''Depicting combinatorial complexity with the molecular interaction map notation''' | |||
4:00-4:30 '' | 4:00-4:30 ''Stephen Racunas (Penn State)'' '''Representation and Evaluation of Biochemical Hypotheses''' | ||
4:30-5:00 '' | 4:30-5:00 ''Ty Thomson (MIT)'' '''A Collaborative Process for Building and Documenting Biological Models''' | ||
5:00-5:30 '' | 5:00-5:30 ''Jean Krivine (École Polytechnique)'' '''TBA''' | ||
5:30-5:45 '''Day 1 Summary and Thoughts About Day 2''' (Hucka) | 5:30-5:45 '''Day 1 Summary and Thoughts About Day 2''' (Hucka) | ||
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==Friday, June 15== | ==Friday, June 15== | ||
=== | ===Applications and Computational Aspects === | ||
8:30-9:00 '' | 8:30-9:00 ''Vincent Danos (CNRS)'' '''What is so special about biological signalling?''' | ||
9:00-9:30 '' | 9:00-9:30 ''Holger Conzelmann (University of Stuttgart)'' '''Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints''' | ||
9:30-10:00 '' | 9:30-10:00 ''Richard G. Posner (TGen)'' '''Mechanistic modeling of signaling pathways.''' | ||
10:00-10:30 '''Coffee Break Sponsored by SFI''' | 10:00-10:30 '''Coffee Break Sponsored by SFI''' | ||
10:30-11:00 '' | 10:30-11:00 ''Will Chen (Harvard)'' '''Phospho-dynamic Experiments and Computational Modeling of the ErbB Pathways''' | ||
===Towards Standards for Rule-Based Modeling=== | ===Towards Standards for Rule-Based Modeling=== | ||
Revision as of 19:16, 5 June 2007
Thursday, June 14
8:30-8:40 Opening Remarks
8:40-9:10 William Hlavacek (LANL) An Overview of Rule-Based Modeling
Software for Rule-Based Modeling
9:10-9:40 James Faeder (LANL) BioNetGen
9:40-10:10 Larry Lok (MSI) Moleculizer
10:10-10:40 Coffee Break Sponsored by SFI
10:40-11:10 Martin Meier-Schellersheim (NIH/NIAID) Simmune
11:10-11:40 Anika Öllrich (EBI) StochSim
11:40-12:10 Aneil Mallavarapu Little b
12:10-1:30 Catered Lunch Sponsored by SFI
1:30-2:00 Pat Lincoln (SRI) Pathaway Logic
2:00-2:30 Ozan Kahramano Pi-calculus
2:30-3:00 Pax Paxson (Matlab) Introduction to SimBiology and possible future enhancements for rule based modeling
3:00-3:30 Coffee Break Sponsored by SFI
Representational Issues in Rule-Based Modeling
3:30-4:00 Sohyoung Kim (NIH/NCI) Depicting combinatorial complexity with the molecular interaction map notation
4:00-4:30 Stephen Racunas (Penn State) Representation and Evaluation of Biochemical Hypotheses
4:30-5:00 Ty Thomson (MIT) A Collaborative Process for Building and Documenting Biological Models
5:00-5:30 Jean Krivine (École Polytechnique) TBA
5:30-5:45 Day 1 Summary and Thoughts About Day 2 (Hucka)
6:30 Dinner at Ristra Sponsored by SFI
Friday, June 15
Applications and Computational Aspects
8:30-9:00 Vincent Danos (CNRS) What is so special about biological signalling?
9:00-9:30 Holger Conzelmann (University of Stuttgart) Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints
9:30-10:00 Richard G. Posner (TGen) Mechanistic modeling of signaling pathways.
10:00-10:30 Coffee Break Sponsored by SFI
10:30-11:00 Will Chen (Harvard) Phospho-dynamic Experiments and Computational Modeling of the ErbB Pathways
Towards Standards for Rule-Based Modeling
11:00-11:30 Michael Hucka (Caltech) An Overview of SBML
11:30-12:00 Nathan Addy (MSI) Experiences Converting Between BNG and Moleculizer Input Formats
12:00-1:30 Lunch Sponsored by SFI
1:30-2:00 Michael Blinov (UCHC) TBA
2:00-2:30 Emek Demir (MSKCC) Rule based aspects in BioPAX
Open Discussion of SBML Level 3 Proposals
2:30-3:30 Presentation of SBML Level 3 Proposal (Blinov) Followed by Discussion
3:30-4:00 Coffee Break Sponsored by SFI
4:00-? Open Discussion about Level 3 and Other Topics in Rule-Based Modeling. Preparation of a conference report to be submitted to Molecular Systems Biology. Future meetings?
Saturday, June 16
Morning Departure