RBM Agenda: Difference between revisions
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[[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== | ==Thursday, June 14== | ||
8:30-8:40 '''Opening Remarks''' | 8:30-8:40 '''Opening Remarks''' | ||
8:40-9:10 William | 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 | 9:10-9:40 ''James Faeder (LANL)'' '''BioNetGen''' | ||
9:40-10:10 | 9:40-10:10 ''Larry Lok (MSI)'' '''Moleculizer''' | ||
10:10-10:40 '''Coffee Break Sponsored by SFI''' | 10:10-10:40 '''Coffee Break Sponsored by SFI''' | ||
10:40-11:10 | 10:40-11:10 ''Martin Meier-Schellersheim'' (NIH/NIAID) '''Simmune''' | ||
11:10-11:40 | 11:10-11:40 ''Anika Öllrich (EBI)'' '''StochSim''' | ||
11:40-12:10 | 11:40-12:10 ''Aneil Mallavarapu'' '''Little b''' | ||
12:10-1:30 '''Catered Lunch Sponsored by SFI''' | 12:10-1:30 '''Catered Lunch Sponsored by SFI''' | ||
1:30-2:00 | 1:30-2:00 ''Pat Lincoln (SRI)'' '''Pathway Logic ''' | ||
2:00-2:30 | 2:00-2:30 ''Ozan Kahramano'' '''On Concurrent Computations in Petri Nets for Modelling Signalling Pathways''' | ||
2:30-3:00 | 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''' | 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: | 4:00-4:30 ''Stephen Racunas (Penn State)'' '''Representation and Evaluation of Biochemical Hypotheses''' | ||
5:00-5:30 | 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) | 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 ''Vincent Danos (CNRS)'' '''What is so special about biological signalling?''' | |||
9:30-10:00 | 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''' | 10:00-10:30 '''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=== | |||
11:30-12:00 | 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''' | 12:00-1:30 '''Lunch Sponsored by SFI''' | ||
1:30-2:00 | 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 | 2:30-3:30 Presentation of SBML Level 3 Proposal (Blinov) Followed by Discussion | ||
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