🚀 go-pugleaf

I have used a program called Stella II for the Mac. It sounds like exactly what you are 
looking for. It is a simulation program based on differential equations you specify. I 
modeled a number of biological pathways with it, including the HPA axis, nerve impulses, 
and pharmacokinetics to name a few. Nice feature is that it only requires you to build a 
diagram consisting of "stocks" and "flows" (variables and diffy-qs); the program writes the 
equations in order of execution and can print them out. This is great if you have a text-unix 
translator and access to a workstation which could do the simulation much faster. The 
manufacturer slips my mind @ the moment, but if you can't find it, mail me and I'll see 
what I can do.

Walter Lech
UCLA Dept. of Medicine

I have used a program called Stella II for the Mac. It sounds like exactly what you are 
looking for. It is a simulation program based on differential equations you specify. I 
modeled a number of biological pathways with it, including the HPA axis, nerve impulses, 
and pharmacokinetics to name a few. Nice feature is that it only requires you to build a 
diagram consisting of "stocks" and "flows" (variables and diffy-qs); the program writes the 
equations in order of execution and can print them out. This is great if you have a text-unix 
translator and access to a workstation which could do the simulation much faster. The 
manufacturer slips my mind @ the moment, but if you can't find it, mail me and I'll see 
what I can do.

Walter Lech
UCLA Dept. of Medicine

In article <47dje1$hig@studium.student.umu.se>, peterl@umdix.umdc.umu.se
(Peter Lundberg) wrote:

>Does anyone have experience with programs for solving differential
>equations? There should be something for setting upp systems of
>equations, and boundary conditions in an easy manner, maybe in some
>graphical format.
>
>I would appreciate comments on ease of use, etc! I'm mainly interested
>in Mac-programs for simulating metabolism. Perhaps Mathematica is what
>I'm looking for?
>
>73, Peter
>
>O==O ================================== O==O
>O==O Peter Lundberg                     O==O
>O==O Email: peterl@umdix.umdc.umu.se    O==O
>O==O ============761.91141============= O==O

Peter, CVODE (in C) is available at netlib@ornl.gov This is a set of
routines to solve ODE's. Fortran versions exist at the same site (many
other solvers as well). CVODE can handle stiff ODEs as well as non-stiff.

If by metabolism you mean metabolic chemical reactions take a look at
react 3.21 (free) at infomeister.osc.edu under pub chemistry software MAC
(or OS2 or MSDOS). The program is compiled and ready to run. It takes
chemical reactions from a  text file like:

0.0102 enzyme + substrate --> complex_1
1e+5 complex_1 --> complex_2
0.3e2 * complex_2 --> enzyme + protein_a  

It builds the ODE's and solves using CVODE. The * above is used to flag a
reaction(s) to have the rate constant(s) (e.g. 0.3e2 above) adjusted by
least-squares using a set of experimental data (e.g. observed protein_a vs
time data), an optional feature.  Example data files are in the MAC
archive.

Output is suitable for Cricket, gnuplot  or Igor.

Memory is allocated dynamically- I've run as many as 275 reactions
involving 25 species in a model. Comments may be imbedded in the reaction
mechanism, names (e.g. complex_1) are arbitrary- user invented, etc. Best
of all it is absolutely FREE.

Mike W