Re: Math and bio?

It's not clear to me what kind of model you are looking for, but there
are two software packages that I think would be worth checking out.
BioNetGen (http://bionetgen.org/) is a powerful system for rule-based
modeling that allows you to write general rules that propagate into
many reactions. It can be paired with Smoldyn (http://
www.smoldyn.org/) to stochastically model the spatial dependence of
these reactions.

Keith Callenberg

On Dec 22, 2:18 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
> Quick comment, I know a lot of calculations for enzyme kinetics are based
> with the rate of diffusion being the limit... then you'd probably need info
> about protein localization... are they in vesicles or free-floating or
> membrane attached
>
> I will keep this in mind and try to dig something up
>
> Sent from my mobile Android device, please excuse any typographical errors.
> On Dec 22, 2011 9:20 AM, "Jonathan Nesser" <jonathan.nes...@gmail.com>
> wrote:
>
>
>
>
>
>
>
> > I've been getting into mathematical models lately, and have noticed
> > that many of these models don't really take into account the signaling
> > complexities of biology. To this end I was wondering if anyone could
> > point me in the direction of a general equation, etc. that models
> > either the process of selecting a gene to be transcribed in a cell
> > (all of the different transcription affinity and negating factors), or
> > of quantifying the amount of mobilization of an enzyme which is
> > activated through a complex enzyme cascade. A name of an equation or
> > modeling style would be enough to get me started, I haven't been able
> > to find much of anything beyond the idea of the stochastic general
> > equation and markov, non-markov type equations. To put a context to
> > this broad question, I'm interested in the ligand gated g protein
> > receptor cascades in neurons, and the control of receptor populations/
> > synapse modulation (synaptic placticity) at a genetic (or at any
> > other) level. Having looked over a goodly amount of articles it seems
> > to me like this has been mainly studied at a qualitative level, much
> > less so at a specific quantitative level. Sorry to pollute the board
> > with my neuroscience again :P, but I think this would be interesting
> > to the slightly higher level genetics researchers here as well. :)
> > Thanks for any information in advance, and I apologize for my
> > ignorance if this is a commonly understood topic, I don't really have
> > access to a professor of, well, anything. :)
>
> > Jonathan Nesser
> > diybioandneurosci.blogspot.com
>
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