RBM Agenda

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

Towards Standards for Rule-Based Models

3:30-4:00 Michael Hucka (Caltech) An Overview of SBML

4:00-4:30 Nathan Addy (MSI) Experiences Converting Between BNG and Moleculizer Input Formats

4:30-5:00 Emek Demir (MSKCC) Rule based aspects in BioPAX

5:00-5:30 Michael Blinov (UCHC) 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

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

9:00-9:30 Jean Krivine (École Polytechnique) TBA

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 Ty Thomson (MIT) A Collaborative Process for Building and Documenting Biological Models

11:00-11:30 Talk 16

11:30-12:00 Talk 17

12:00-1:30 Lunch Sponsored by SFI

1:30-2:00 Talk 18

2:00-2:30 Talk 19

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