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Re: From reactions to differential equations

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  • Subject: [mg93385] Re: [mg93348] From reactions to differential equations
  • From: "Tamara Ursem" <tursem at>
  • Date: Wed, 5 Nov 2008 04:56:52 -0500 (EST)
  • References: <>

Hi Zac,

There is a Mathematica program called XCellerator that is written
specifically to transform reactions into ODEs.  See
and for more details. If you have
further questions, let me know or contact the developers (see


On Tue, Nov 4, 2008 at 3:20 AM, zac <replicatorzed at> 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

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