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MDL Meeting Notes. 2002-09-25 and 2002-09-26 at MIT. Participants.

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mdl meeting notes

MDL Meeting Notes

2002-09-25 and 2002-09-26 at MIT

participants
Participants

Drew 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)

summary key talking points

Summary - Key Talking Points

1. Model Type Examples

2. Model Definition Language Specification, Requirements, & Vocabulary

3. BioSPICE System Integration

how to get things moving
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
lesson from the past
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
model types discussion
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
model types points of contact
Model Types - Points of Contact
  • Chemical Kinetics Endy

Normal/ODE (Tyson, Others), Fine-grained/Stoch (Cox), Complexes (Endy)

  • Static / graph / Flux balance Church, Lincoln, Lok?, Hucka
  • Automata (cell movement) Schoeberl, Kaiser
  • Markov Cox?
  • 2d/3d PDE diffusion Virtual Cell, Finney?
  • S-system (power law format ODE) Mishra
  • Hybrid systems Lincoln, Sokolsky
  • 4D: structural/cell dynamics Church
  • Boolean, Digital, Discrete event Hucka
  • Shape/4d ray trace Endy Mcell?
  • Electrophysiology ODE Zak
  • Delay differential equations Zak

BioSPICE.org sandbox folders Lincoln

model types by halloween
Model Types - By Halloween
  • Chemical Kinetics Endy (SBML)

Normal/ODE (Tyson, Others), Fine-grained/Stoch (Cox), complexes (Endy)

  • Static / graph / Flux balance Church, Lincoln, Lok?, Hucka (SMBL)
  • Automata (cell movement) Schoeberl, Kaiser (SBML)
  • Markov Beckwith, Cox? (no)
  • 2d/3d PDE diffusion Virtual Cell, Arkin, Finney? (no)
  • S-system (power law format ODE) Mishra (SBML composition?)
  • Hybrid systems Lincoln, Sokolsky (no…?)
  • 4D: structural/cell dynamics Church (no)
  • Boolean, Digital, Discrete event Hucka (SBML)
  • Shape/4d ray trace Endy, Mcell? (no)
  • Electrophysiology ODE Zak (no…VCell?)
  • Delay differential equations Zak (SBML)

(SBML) == SBML does/will handle, (no) == SBML does not handle

working groups discussion
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)
biospice components
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
data modeling added working group
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
mdl discussion cliff s list
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
what is needed
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
slide15
Map out the space
    • What are the gaps?
  • System integration
  • Overall functionality
  • The art of how they fit together
what mdl is not
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
mdl definition
MDL definition
  • Comes from use cases
    • Model development
    • Model creation / editing / evolution
    • Domain extensibility
    • Simulation (numeric)
    • Analysis (symbolic)
    • Models as a useable tool for browsing, etc

Personal organization

    • Models a presentation or communication mechanism

Whiteboard

    • Producing a formal representation is useful

MDL can play a role in that intellectual activity

  • End of October
mdl use cases
MDL Use Cases
  • Model development

Model creation

  • Analysis

Symbolic and numeric (Simulation)

Model validation

Wet-lab experiment design

  • Models as a useful organization tool for browsing, etc

Personal organization

  • Models a presentation or communication mechanism

Whiteboard

  • Domain extensibility

Editing and evolution of models

  • Producing a formal representation is useful in itself

MDL can play a role in that intellectual activity

  • Model discovery (Regulography)
action items first draft oct 15
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
model development flow
Model Development Flow
  • Experimental design
  • Experimental data processing

Array sw, expression data management

  • Identification of players

Genomics sw, clustering sw

  • Annotation vis-à-vis known info

Genomic

  • Relationship inference

Bayesian

  • Generation of qualitative model

Model induction

  • Generation of quantitative model

Optimization

  • Simulation / analysis / prediction

Matlab, XS, BioReactor, Sensitivity analysis

  • Publication of model
collaboration
Collaboration
  • Diversity of Discipline, Organization, Location
      • MDL needs: defined vocabulary, mappings
      • MDL needs: ability to difference
      • MDL needs: version control annotation?
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