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September 2003
 RE: Multiple kineticLaw Sections Per Reaction 11 Mar '06 05:29 --- Herbert Sauro wrote: > I also think there is a real problem, how would one know that > a given > rate law in an SBML model is valid for a stochastic model? How do you know if a given rate law is valid for a deterministic model? It isn't for SBML to decide which laws are sensible and which aren't. > As > far as I > know, and I please correct me if I am wrong, there are only a > very small > number of rate laws that have been shown to be usable for > stochastic > simulations. Not true. There isn't anything to show. You can use any rate law you like, just as for deterministic models. But let me clarify... First, the issue with rate laws is nothing to do with whether the model is deterministic or stochastic, but rather whether or not species are treated as continuous or discrete. So all of these issues are about continuous rate laws and discrete rate laws (which tend to be slightly different). So let's start with continuous rate laws. For a given reaction, say X -> Y you can write down any rate law you like, and continuous deterministic modellers never fail to amaze me with their creativity in this regard! ;-) Of course, not all laws you write down are completely sensible, and only a very small fraction have any vague attempt at theoretical justification. However, it is important to distinguish between laws that are consistent with the underlying theory and those that aren't. So for the above equation, you could write down the kinetic law "1". Now personally I would regard that as being an allowable rate law, and consistent with the SBML specification (and I have seen real models with constant rate laws), but most of us would consider it pretty dumb (assuming X isn't a boundary), because it doesn't have a root at zero, and therefore doesn't prevent X from going negative. Therefore in some sense a kinetic law of "1" isn't really consistent with the underlying theory. Now let's consider a more interesting example: 2X -> Y Here, the obvious continuous mass-action rate law would be of the form "kX^2" (though there are lots of other laws you could use). Among other things, this has the desirable property of having a (double) root at zero and therefore prevents X from going negative. However, if X is being treated as discrete, there is a problem with the above rate law. Because X takes on integer values and is changed by the reaction in steps of 2, you need a rate law with roots at both zero and one in order to prevent X from going negative. So pretty much any (non-negative) rate law with roots at zero and one is consistent with the discrete formulation. Now most people would use a law of the form "kX(X-1)", as this has a rigorous mass-action stochastic kinetic derivation, but there isn't any "rule" in discrete modelling which says you are only allowed to use laws with a rigorous justification, just as there isn't in the case of continuous rate laws. My own (admittedly controversial) opinion is that many of the rate laws used routinely by continuous modellers have only the most scant justification, so I don't see why discrete modellers should be forced to live by different rules. > I can't blindly read a SBML file, Level 1 or 2 > (and we use > level 2), and just plug all the equations into a, say, > Gillespie > simulator. Of course not! But this is nothing to do with there being any kind of problem encoding discrete models in SBML. It is an issue about _converting_ models designed for one framework to another framework. But models in both frameworks can be encoded perfectly well in SBML. > I think this is what the SBO idea will solve? Yes, SBO is supposed to help with the conversion problem. Yours, -- Darren Wilkinson email: darrenjwilkinson@btinternet.com home www: http://www.darrenjwilkinson.btinternet.co.uk/ work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/

SubjectPosterDate
Multiple kineticLaw Sections Per Reaction Bill Denney09 Mar '06 10:14
Re: Multiple kineticLaw Sections Per Reaction Hiroyuki Kuwahara09 Mar '06 16:18
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro09 Mar '06 17:09
RE: Multiple kineticLaw Sections Per Reaction Bill Denney09 Mar '06 18:30
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 01:01
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 04:15
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 09:54
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 10:16
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops10 Mar '06 10:28
Re: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:24
Re: Multiple kineticLaw Sections Per Reaction Tomas Radivoyevitch10 Mar '06 05:32
Re: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 10:32
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:02
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 09:39
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 10:36
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:10
Re: Multiple kineticLaw Sections Per Reaction Mike Hucka10 Mar '06 11:07
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 13:00
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 13:03
RE: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson10 Mar '06 13:51
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops10 Mar '06 15:04
Re: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 16:21
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops13 Mar '06 05:55
Re: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson13 Mar '06 12:09
Re: Multiple kineticLaw Sections Per Reaction Stefan Hoops14 Mar '06 05:08
Re: Multiple kineticLaw Sections Per Reaction Darren J Wilkinson14 Mar '06 11:21
response to "fast" attribute action item... Schaff29 Mar '06 08:22
response to "fast" attribute action item Schaff29 Mar '06 11:58
RE: Multiple kineticLaw Sections Per Reaction Bill Denney10 Mar '06 14:28
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 15:10
stochastic/ODE models Eric Mjolsness10 Mar '06 14:44
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere10 Mar '06 14:55
RE: Multiple kineticLaw Sections Per Reaction Herbert Sauro10 Mar '06 18:01
RE: Multiple kineticLaw Sections Per Reaction Mike Hucka11 Mar '06 00:41
RE: Multiple kineticLaw Sections Per Reaction  Darren J Wilkinson11 Mar '06 05:29
RE: Multiple kineticLaw Sections Per Reaction Bill Denney11 Mar '06 05:37
RE: Multiple kineticLaw Sections Per Reaction Nicolas Le Novere11 Mar '06 15:23
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