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 > >

**References**:**From reactions to differential equations***From:*zac <replicatorzed@gmail.com>