RBM Agenda: Difference between revisions

Latest revision as of 18:22, 11 June 2007

All talks will be 25 minutes followed by 5 minutes for questions.

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

The objective for this session is to provide an overview of the tools available for rule-based modeling. Key questions for the speakers to address are 1) What biological features and questions motivated the development of the software? 2) What capabilities does the software provide? 3) What are specific examples where the approach/software have led to new insights? 4) What capabilities still need to be developed? 5) What are the essential entities and processes that you feel must be represented in any exchange format to support your modeling needs and software?

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) Pathway Logic

2:00-2:30 Ozan Kahramano On Concurrent Computations in Petri Nets for Modelling Signalling Pathways

2:30-3:00 Ricardo Paxson (Mathworks) 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 and Goals for SBML Level 3

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

@@ Line 1: / Line 1: @@
 [[Rule-Based_Modeling_of_Biochemical_Systems|Back to Main Workshop Page]]
+All talks will be 25 minutes followed by 5 minutes for questions.
 ==Thursday, June 14==
@@ Line 8: / Line 10: @@
 ===Software for Rule-Based Modeling===
+The objective for this session is to provide an overview of the tools available for rule-based modeling.  Key questions for the speakers to address are 1) What biological features and questions motivated the development of the software? 2) What capabilities does the software provide? 3) What are specific examples where the approach/software have led to new insights? 4) What capabilities still need to be developed? 5) What are the essential entities and processes that you feel must be represented in any exchange format to support your modeling needs and software?
 :10-9:40 ''James Faeder (LANL)'' '''BioNetGen'''
@@ Line 23: / Line 26: @@
 :10-1:30 '''Catered Lunch Sponsored by SFI'''
-:30-2:00 ''Pat Lincoln (SRI)'' '''Pathaway Logic '''
+:30-2:00 ''Pat Lincoln (SRI)'' '''Pathway Logic '''
-:00-2:30 ''Ozan Kahramano'' '''Pi-calculus'''
+:00-2:30 ''Ozan Kahramano'' '''On Concurrent Computations in Petri Nets for Modelling Signalling Pathways'''
-:30-3:00 ''Pax Paxson (Matlab)'' '''Introduction to SimBiology and possible future enhancements for rule based modeling'''
+:30-3:00 ''Ricardo Paxson (Mathworks)'' '''Introduction to SimBiology and possible future enhancements for rule based modeling'''
 :00-3:30 '''Coffee Break Sponsored by SFI'''
@@ Line 34: / Line 37: @@
 :30-4:00 ''Sohyoung Kim (NIH/NCI)'' '''Depicting combinatorial complexity with the molecular interaction map notation'''
 :00-4:30 ''Stephen Racunas (Penn State)'' '''Representation and Evaluation of Biochemical Hypotheses'''
@@ Line 54: / Line 56: @@
 :00-9:30 ''Holger Conzelmann (University of Stuttgart)'' '''Signal transduction and combinatorial complexity: Model reduction, reduced modeling and thermodynamic constraints'''
-:30-10:00 ''Richard G. Posner (TGen)'' '''Mechanistic modeling of signaling pathways.'''
+:30-10:00 ''Richard G. Posner (TGen)'' '''Mechanistic modeling of signaling pathways'''
 :00-10:30 '''Coffee Break Sponsored by SFI'''
@@ Line 62: / Line 64: @@
 ===Towards Standards for Rule-Based Modeling===
-:00-11:30 Michael Hucka (Caltech) '''An Overview of SBML'''
+:00-11:30 ''Michael Hucka (Caltech)'' '''An Overview of SBML and Goals for SBML Level 3'''
 :30-12:00 ''Nathan Addy (MSI)'' '''Experiences Converting Between BNG and Moleculizer Input Formats'''