Ming Chen wrote:
> It seems Gepasi and Jarnac have no such problem as they regard
> reaction network as a black-box?
No and NO! Neither Gepasi nor Jarnac treat reactions as black boxes!
They use tull kinetics for them. Please read the information for these
programs before you start to misrepresent them publicly!
Gepasi information is at http://www.gepasi.org
You can also download the program and read the help file.
There are also refereed publications describing it too:
Mendes, P. (1993) GEPASI: A software package for modelling the dynamics,
steady states and control of biochemical and other systems. Comput. Applic.
Biosci. 9, 563-571.
Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical
pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
Mendes, P. & Kell, D.B. (1998) Non-linear optimization of biochemical
pathways: applications to metabolic engineering and parameter estimation.
Bioinformatics 14, 869-883
--
Pedro Mendes
Virginia Bioinformatics Institute, Virginia Tech
1750 Kraft Drive, suite 1100, Blacksburg, VA 24060, USA
Phone: +1 540 2317411 Fax: +1 540 2311777
