Mathematica 9 is now available
Services & Resources / Wolfram Forums / MathGroup Archive
-----

MathGroup Archive 2008

[Date Index] [Thread Index] [Author Index]

Search the Archive

Re: From reactions to differential equations

  • To: mathgroup at smc.vnet.net
  • Subject: [mg93385] Re: [mg93348] From reactions to differential equations
  • From: "Tamara Ursem" <tursem at gmail.com>
  • Date: Wed, 5 Nov 2008 04:56:52 -0500 (EST)
  • References: <200811041120.GAA29327@smc.vnet.net>

Hi Zac,

There is a Mathematica program called XCellerator that is written
specifically to transform reactions into ODEs.  See http://xcellerator.info/
and http://sourceforge.net/projects/xlr8r/ for more details. If you have
further questions, let me know or contact the developers (see
http://sourceforge.net/projects/xlr8r/).

Tami



On Tue, Nov 4, 2008 at 3:20 AM, zac <replicatorzed at gmail.com> wrote:

> Dear All,
>
> from some time now I=E1m working with more and more complex differential
> equations.
> Is there a package to transform a set of reaction-kinetic equations
> such as:
>
> {
> Subscript[a, i] + Subscript[b, j] -> Subscript[c, i, j],
>  Subscript[a, i] + Subscript[c, i, j] -> 2 Subscript[a, i] +
> Subscript[b, j],
>  Subscript[b, i] + Subscript[c, j, i] -> 2 Subscript[b, i] +
> Subscript[c, j]
> }
>
> to differential equations expressing the growth of a_i, b_i and c_i,j,
> regarding
> that I leave the parameters i and j undefined?
> I am fully aware of software packages like COPASI and Systems Biology
> that are available, but I think they are far more complex than what is
> needed here, and furthermore I would like to understand the method how
> these reactions are actually converted to diff.equations. Which I
> completely miss if I'm to rely on a concealed algorithm.
> I've already started to write a parser in Mathematica, but it became
> too cumbersome after a point to deal with indexed variables (without
> indices it is fairly simple), and I really don't want to invent
> something that (perhaps) already exists on the field.
> Any ideas?
>
> Istvan Zachar
>
>


  • Prev by Date: Re: Create a cumulative list
  • Next by Date: Re: Mathematica Help Urgent (Very New Beginner)
  • Previous by thread: From reactions to differential equations
  • Next by thread: Re: From reactions to differential equations