Re: Math and bio?

I didn't read all the links above yet but I was hoping there was a
good wikipedia entry on Rule-based modeling. I found an intro with
Agent-based modeling. I think they are the same thing.

Anyway, could I use one of these programs to do simple modeling like
how immune system function, organic chemical synthesis or other stuff
you find in textbooks?

On Sat, Dec 24, 2011 at 8:01 AM, Vincent Danos <vincent.danos@gmail.com> wrote:
> Hi
>
> In the same rule-based family, that is indeed very useful for
> combinatorial systems, there is also Kappa
> (http://kappalanguage.org, http://groups.google.com/group/kappa-users).
>
> The best model prize at iGEM'10 (see their model here:
> http://homepages.inf.ed.ac.uk/s0458094/CS2Bio11/)
> and '11 went to Edinburgh teams which were using an ad hoc spatial
> extension of
> Kappa (spatial Kappa: http://www.demonsoft.org/SpatialKappa/).
> Differently than coupling with Smoldyn,
> in spatial Kappa, you can execute rule-based in space without
> translating to ordinary reactions (of which there are
> typically too many to go the translation way).
>
> For your specific context, ie synaptic plasticity via transcriptional
> regulation of receptor populations in
> the post-synaptic density (PSD), depending on what scales and details
> you want to incorporate to the model,
> you will end up using vastly different tools.
>
> I am not a PSD expert, but it seems a key issue is the level of
> granularity you choose for describing Ca2+ signalling;
> there will be local concentrations of Ca2+ pairing with kinases fixed
> to the PSD and modifying the properties
> of other receptors in the neighbourhood. If you want to represent that
> (obviously a smaller time scale than
> transcription), then you need to map PSD in space and run a coupled
> model of ca2+ diffusion. Another issue
> is whether to represent the dynamic assembly of the PSD itself, and
> how realistic this assembly model should be
> (I think we know now that receptors sort themselves in a circular way
> and depending on their types live closer or further
> from the center of the synpatic contact).
>
> This article could be a good starting point to contemplate the rule-
> based option for
> a detailed model including some stylized version of PSD assembly:
> http://pubs.rsc.org/en/content/articlelanding/2011/mb/c1mb05152k
>
> For a higher-level view of synaptic plasticity, see references on this
> page:
> http://homepages.inf.ed.ac.uk/s0677281/Main.html
>
> Cheers
> Vincent
>
>
>
>
>
>
> On Dec 23, 4:12 pm, Keith Callenberg <keithcallenb...@gmail.com>
> wrote:
>> 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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