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Nathan Addy
Michael Blinov
Will Chen
Josh Colvin
Holger Conzelmann
Vincent Danos
Emek Demir
Jim Faeder
Walter Fontana
Bill Hlavacek
Questions about Larry's talk
Is diffusion in Moleculizer grid free?
How does Moleculizer handle steric clashes?
Would like to know more about the simple structural modeling efforts of the Stanford group that Larry mentioned - see simtk.org
what's an example an allosteric effect that Moleculizer handles better than BNG - resolve off line
Questions about Martin's talk
what delimits the region of the cell in which reaction generation is to take place?
Questions about Anika's talk
? = don't know or don't care. should be specified somehow to track the basis of a model (assumption or supported by data) but the two cases are functionally equivalent w.r.t. model generation/simulation
Pax
UserData field might be useful for RBM interface w/ SimBiology Incremental compilation feature to be added for simulation graphical representation of generalized reactions Can you create a rule set from a reaction network? Probably not.
Pathway Logic
Examples of how pathway logic is being used to study metabolism, enable metabolic engineering. Available? Building on BioCyc
Smoking gun = Denise Wolf and Adam Arkin model of B. subtilis sporulation model (parameter must be different for bistability) and multiple KOs affecting metabolic activity
Jean Krivine
'Don't care, don't write policy'
, = + or .
He's talking about context-free rules
1) choose rule by activity - scales with log(|R|) where R is number of rules 2) uniformly choose an instance of the rule, proportional to number of operations in the rule 3) negative update, constant cost 4) fire reaction and update, constant cost
contact maps
stories - event structures or pathways
How do stories depend on parameters? - depends on dynamics
influence maps (set of all rules used) - static information
Sohyoung
Lots of discussion. Are MIMs equivalent to contact maps?
Racunas
Hypothesis-centered, Contradiction-based modeling
Software tools:
HyBrow,
Reactome Proofreader,
HyQue: Knowledge Base Integration,
PaperSpot ("gossip" tool)
Next steps:
A library of negative results A fundamental unit of causal discourse
Aneil (little b)
how to represent, how to analyze
molecular complexity, location complexity reaction complexity
how do modeling assumptions affect the mathematical structure of a model?
wants to build database of pathway models - working with Will Chen
What is Rita?
print-eval consistency: objects print as code
realistic cellular lattices
complexes as labeled graphs - not released in little b yet
language is the currency of ideas
