[BioC] [R] MatLab SimBiology

[David Winsemius]

I would have used the search strategy "stochastic". Despite the risk  
that such a strategy could bring up anything to do with statistics, it  
in fact brings me to Stefano Iacus' package sde (and refers to the  
accompanying book, "Simulation and Inference for Stochastic  
Differential Equations With R Examples"). Further links on that page  
were to:
http://bm2.genes.nig.ac.jp/RGM2/pkg.php?p=sde

.. which gives a better picture of the capabilities of that package.

Also a possible package of possible interest to this rather vague  
questioner might be:

http://crantastic.org/packages/PSM

And even though it is pitched to population biologists, I thought that  
a package that included a "decaying-dimerization reaction set, [and]  
linear chain system":

http://crantastic.org/packages/GillespieSSA

... might have examples of interest to biological chemists.

-- 
David.


On Oct 31, 2009, at 7:05 AM, Carlos Ortega wrote:

> Hello,
>
> Please look here:
> http://crantastic.org/search?q=biology
>
> <http://crantastic.org/search?q=biology>Regards,
> Carlos.
>
> On Fri, Oct 30, 2009 at 6:12 PM, <mauede at alice.it> wrote:
>
>> Is there any R package that implements the same capability of MatLab
>> toolbox called SimBiology ?
>> We are expecially interested in protein-protein interactions and  
>> network
>> analysis.
>> As far as I know SimBiology implements a system of ODEs reflecting  
>> the
>> kinetic chemical reactions.
>> We would be more interested in stochastic simulations.
>> Thank you in advance.
>>
>> Maura
>>
>>
>> tutti i telefonini TIM!
>>
>>
>>       [[alternative HTML version deleted]]
>>
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>
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>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT