DBsolve: An Interactive Workbench For Mathematical Simulation of the

Igor Goryanin igor at turtle.stack.net
Thu Jul 17 13:36:18 EST 1997


DBsolve: An Interactive Workbench For Mathematical Simulation of the 
Cellular Metabolism After Genome Sequencing


Mathematical simulation of the cellular metabolism 
is the next step after genome sequencing 
and metabolic reconstruction.
The main objective of the simulation is to translate
the genome information into the complex dynamic behavior
of a sequenced cell and its functional subsystems. 
To solve problems under way to this goal DBsolve 
software package was developed.
It combines: 
1.  Automation of the large-scale mathematical models derivation,
2.  Solving and parameter continuation of the non-linear algebraic
systems,
including metabolic control analysis,
3.  Solving the non-linear stiff systems of ordinary 
differential equations (Ode's) ,
4.  Bifurcation analysis of the steady states of Ode's systems,
5.  Optimizing solutions of the models as algebraic equations or
Ode's and finding model parameters values.
The package has been successfully used for modeling and optimization
for glycolytic system of Mycoplasma genitalium, reconstructed from the
corresponding sequenced genome http://www.cme.msu.edu/WIT. It is
successfully used for metabolic modeling of different metabolic pathways
and a set of enzyme reactions mechanisms.
Availability
New trial DBsolve version for Windows 95 is free available via our 
server http://sirius.iteb.serpukhov.su/~igor.
Contact E-mail address: igor at turtle.stack.net




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