MDL Meeting Notes
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Transcript of MDL Meeting Notes
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MDL Meeting Notes
2002-09-25 and 2002-09-26 at MIT
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ParticipantsDrew Endy (MIT), Tom Knight (MIT),
George Church (Harvard), Oleg Sokolsky (UPenn), Daniel Zak (U.Delaware/ThomasJeffferson U),
Birgit Schoeberl (MIT), Jim Collins (B.U.), Jonathan Webb (BBN), Cliff Shaffer (VT),
Peter Finin (UPenn), Michael Hucka (Caltech), Andrew Finney (Caltech), Chris Cox (UTenn), Jesse S.A. Bridgewater (UCLA), Dennis A Dean
(Harvard), Katherine Gurdlier (BMU / Harvard), Jordan Fielder (MITRE), Olivia Tate (MITRE),
David Beckwith (UCLA), Daniel Segre (Harvard), Wayne Rindone (Harvard), Sriram Kosuri (MIT),
Clare Thiem (AFRL), Tom Garvey (SRI), Patrick Lincoln (SRI), Leon Chan (MIT),
Arch Owen (BBN), Bud Misra (NYU)
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Summary - Key Talking Points
1. Model Type Examples
2. Model Definition Language Specification, Requirements, & Vocabulary
3. BioSPICE System Integration
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How to Get Things Moving Group agreement on deadlines
• Use cases/MDL specification & requirements: – Oct 15 first draft– Halloween draft to MDL group
• Model types:– Halloween 12 different model types
Volunteer to be chief annoying person on model types: Cliff Shaffer
Volunteer to be chief annoying person on use cases/MDL requirements: Patrick Lincoln
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Lesson from the Past Model definitions need to support:
• Search – BLAST, etc.
• Merging – Dock two modeled components together
• Checking – Connect with other datatypes, compare independently
generated models
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Model Types - Discussion Chemical Kinetic
• Normal (Tyson/Shaffer/Kumar)• Fine-grained (Kosuri/Arkin)• Complexes (Lok/Finney/Faeder)• Markov models (Cox)…abstraction is research
3D• PDE (Arkin/Lowe/Przekwas)• Ray Tracing (Bartol/Stiles)
Flux Balance (Segres) Static Graph (Karp) Boolean/Logic (Lincoln) Bayesian inferred models (Gifford, Liao,
Lauffenberger) Diagramatic notations (Hucka, Schoeberl, Kohn) Other
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Model Types - Points of Contact
1. Chemical Kinetics EndyNormal/ODE (Tyson, Others), Fine-grained/Stoch (Cox), Complexes
(Endy)
2. Static / graph / Flux balance Church, Lincoln, Lok?, Hucka
3. Automata (cell movement) Schoeberl, Kaiser4. Markov Cox?5. 2d/3d PDE diffusion Virtual Cell, Finney? 6. S-system (power law format ODE) Mishra 7. Hybrid systems Lincoln, Sokolsky8. 4D: structural/cell dynamics Church9. Boolean, Digital, Discrete event Hucka10. Shape/4d ray trace Endy Mcell?11. Electrophysiology ODE Zak12. Delay differential equations Zak
BioSPICE.org sandbox folders Lincoln
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Model Types - By Halloween
1. Chemical Kinetics Endy (SBML)Normal/ODE (Tyson, Others), Fine-grained/Stoch (Cox), complexes (Endy)
2. Static / graph / Flux balance Church, Lincoln, Lok?, Hucka (SMBL)
3. Automata (cell movement) Schoeberl, Kaiser (SBML)4. Markov Beckwith, Cox? (no)5. 2d/3d PDE diffusion Virtual Cell, Arkin, Finney? (no)6. S-system (power law format ODE) Mishra (SBML composition?)7. Hybrid systems Lincoln, Sokolsky (no…?) 8. 4D: structural/cell dynamics Church (no)9. Boolean, Digital, Discrete event Hucka (SBML)10. Shape/4d ray trace Endy, Mcell? (no)11. Electrophysiology ODE Zak (no…VCell?)12. Delay differential equations Zak (SBML)
(SBML) == SBML does/will handle, (no) == SBML does not handle
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Working Groups - discussion Existing BioSPICE working groups: DB, EWG, MDL System-level integration (needed now)
• Identify overall map, components that make it up• System-level • Includes communication architecture (APIs)• E.g., “this is the API for a simulator”• Do it by layering, identify common functionality• Extensible interfaces
Model builder GUIs (community exists already) Simulators (community exists already?)
• Multiple simulators operating simultaneously, validation • Have affinity group meeting at Dec 02 PI meeting (Garvey)
Non-simulator analysis tools• Have affinity group meeting at Dec 02 PI meeting (Garvey)
Data modeling (Resources? Do this in future)
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BioSPICE Components Model building GUIs
• Reads and writes MDL Analysis tools
• Model analysis – Simulators
• Reads MDL, parameter values, configuration– Bifurcation, reachability, sensitivity analysis, elementary
modes • Data analysis
– Compare experimental data with output of simultators, parameter estimation, confidence
Control systems• Coordinate multiple simulators, multiple models• Version control, multiple runs, Chicago Chimera, make
Databases – connections Lab notebook End-to-end use cases: Hucka
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Data Modeling: Added Working Group?
From raw data to mechanism, rate terms and parameter estimates.
Metadata (model points back to dataset)• Version, author, …
Bayesian inference of models
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Notes on Model Definition Language Specification, Requirements, & Vocabulary
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MDL Discussion -- Cliff’s List What goes in a model definition language
• Metadata scheme• Graphical layout• Geometry / topology • Variables (species, things with names)• Bits of computation
– Named functions for use in rate laws
• States• Control (state transitions, compartment…)• Set of constraints• Objective function
– Might be a bit of computation
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What is Needed Need group that looks at components and
how they fit together Interagent coordination language:
• OAA is much improved, particularly performance
Inputs to simulator? But don’t need BioSPICE working groups
when there are already healthy communities • Model building (user interfaces), simulators
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Map out the space• What are the gaps?
System integration Overall functionality The art of how they fit together
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What MDL is Not Not data model Not process model Not integration language for components Not ontology for biology, biochemistry
• But we will produce a controlled vocabulary• But we may require an ontology
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MDL definition Comes from use cases
1. Model development2. Model creation / editing / evolution3. Domain extensibility4. Simulation (numeric)5. Analysis (symbolic)6. Models as a useable tool for browsing, etc
Personal organization
7. Models a presentation or communication mechanismWhiteboard
8. Producing a formal representation is usefulMDL can play a role in that intellectual activity
End of October
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MDL Use Cases1. Model development
Model creation
2. AnalysisSymbolic and numeric (Simulation) Model validationWet-lab experiment design
• Models as a useful organization tool for browsing, etcPersonal organization
• Models a presentation or communication mechanismWhiteboard
• Domain extensibilityEditing and evolution of models
• Producing a formal representation is useful in itselfMDL can play a role in that intellectual activity
1. Model discovery (Regulography)
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Action Items: First draft Oct 15 Webb and Hucka
• Use case guide and example Shaffer (Full Tyson example) Zak sensitivity analysis, experimental design Bridgewater (Simulation) (coupled
represselators) Dennis (brainstorming, collaboration) Experimental design, model validation (Cox) Model discovery, regulography (Beckwith) Model creation (Finney, Bridgewater) Mode switching, hybrid control need to be in
MDL
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Model Development Flow1. Experimental design2. Experimental data processing
Array sw, expression data management3. Identification of players
Genomics sw, clustering sw4. Annotation vis-à-vis known info
Genomic5. Relationship inference
Bayesian6. Generation of qualitative model
Model induction7. Generation of quantitative model
Optimization8. Simulation / analysis / prediction
Matlab, XS, BioReactor, Sensitivity analysis9. Publication of model
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Collaboration Diversity of Discipline, Organization,
Location– MDL needs: defined vocabulary, mappings– MDL needs: ability to difference – MDL needs: version control annotation?