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8:30-8:40 '''Opening Remarks'''
8:30-8:40 '''Opening Remarks'''


8:40-9:10 ''William Hlavacek (LANL)'' '''An Overview of Rule-Based Modeling'''
8:40-9:10 ''William Hlavacek (LANL)'' '''An Overview of Rule-Based Modeling'''
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3:00-3:30 '''Coffee Break Sponsored by SFI'''
3:00-3:30 '''Coffee Break Sponsored by SFI'''


===Towards Standards for Rule-Based Models===
===Applications and Computational Aspects ===
''This session is a catch-all and it's not quite right''


3:30-4:00 Michael Hucka (Caltech) '''An Overview of SBML'''
3:30-4:00 ''Holger Conzelmann (University of Stuttgart)'' '''Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints'''


4:00-4:30 ''Nathan Addy (MSI)'' '''Experiences Converting Between BNG and Moleculizer Input Formats'''
4:00-4:30 ''Ty Thomson (MIT)'' '''A Collaborative Process for Building and Documenting Biological Models'''


4:30-5:00 ''Emek Demir (MSKCC)'' '''Rule based aspects in BioPAX'''
4:30-5:00 ''Richard G. Posner (TGen)'' '''Mechanistic modeling of signaling pathways.'''


5:00-5:30 ''Michael Blinov (UCHC)'' '''TBA'''
5:00-5:30 ''Will Chen (Harvard)'' '''Phospho-dynamic Experiments and Computational Modeling of the ErbB Pathways'''


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==
===Representational Issues in Rule-Based Modeling===


8:30-9:00 ''Sohyoung Kim (NIH/NCI)'' '''Depicting combinatorial complexity with the molecular interaction map notation'''
8:30-9:00 ''Sohyoung Kim (NIH/NCI)'' '''Depicting combinatorial complexity with the molecular interaction map notation'''
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10:00-10:30 '''Coffee Break Sponsored by SFI'''
10:00-10:30 '''Coffee Break Sponsored by SFI'''


10:30-11:00 ''Ty Thomson (MIT)'' '''A Collaborative Process for Building and Documenting Biological Models'''
10:30-11:00 ''Jean Krivine (École Polytechnique)'' '''TBA'''
 
===Towards Standards for Rule-Based Modeling===


11:00-11:30 ''Jean Krivine (École Polytechnique)'' '''TBA'''
11:00-11:30 Michael Hucka (Caltech) '''An Overview of SBML'''


11:30-12:00 ''Will Chen (Harvard)'' '''Phospho-dynamic Experiments and Computational Modeling of the ErbB Pathways'''
11:30-12:00 ''Nathan Addy (MSI)'' '''Experiences Converting Between BNG and Moleculizer Input Formats'''


12:00-1:30 '''Lunch Sponsored by SFI'''
12:00-1:30 '''Lunch Sponsored by SFI'''


1:30-2:00 ''Richard G. Posner (TGen)'' '''Mechanistic modeling of signaling pathways.'''
1:30-2:00 ''Michael Blinov (UCHC)'' '''TBA'''


2:00-2:30 ''Holger Conzelmann (University of Stuttgart)'' '''Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints'''
2:00-2:30 ''Emek Demir (MSKCC)'' '''Rule based aspects in BioPAX'''


2:30-3:30 Presentation of SBML Level 3 Proposal (Blinov) Followed by Discussion
2:30-3:30 Presentation of SBML Level 3 Proposal (Blinov) Followed by Discussion

Revision as of 04:49, 4 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

Applications and Computational Aspects

This session is a catch-all and it's not quite right

3:30-4:00 Holger Conzelmann (University of Stuttgart) Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints

4:00-4:30 Ty Thomson (MIT) A Collaborative Process for Building and Documenting Biological Models

4:30-5:00 Richard G. Posner (TGen) Mechanistic modeling of signaling pathways.

5:00-5:30 Will Chen (Harvard) Phospho-dynamic Experiments and Computational Modeling of the ErbB Pathways

5:30-5:45 Day 1 Summary and Thoughts About Day 2 (Hucka)

6:30 Dinner at Ristra Sponsored by SFI

Friday, June 15

Representational Issues in Rule-Based Modeling

8:30-9:00 Sohyoung Kim (NIH/NCI) Depicting combinatorial complexity with the molecular interaction map notation

9:00-9:30 Vincent Danos (CNRS) What is so special about biological signalling?

9:30-10:00 Stephen Racunas (Penn State) Representation and Evaluation of Biochemical Hypotheses

10:00-10:30 Coffee Break Sponsored by SFI

10:30-11:00 Jean Krivine (École Polytechnique) TBA

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

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

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