Application of Jacobian® dynamic modeling software in systems biology

Glen H Ko and colleagues
Numerica Technology, Cambridge MA 02142


This will be a demonstration of the Jacobian® dynamic modelling software:


Extracting fundamental knowledge of biological pathways and biochemical reaction steps at the level of a sub-cell, whole-cell, tissue and/or disease through modeling, is an important promise of Systems Biology. To realize this promise, a dynamic modeling tool with the following capabilities is needed: highly efficient in building biological/biochemical models, computationally powerful to enable the user to easily perform various simulation and optimization modes, numerically robust to handle problems that are very stiff and hybrid (continuous and discontinuous events), and fast computational speed to handle increasing size of models.

Jacobian is dynamic modeling software, originally developed at MIT (and formerly called ABACUSS), which has the potential to meet all of the modeling requirements in Systems Biology. Jacobian has been successfully applied in a wide range of applications ranging from chemical, biochemical and polymerization reactions; engine combustion; energy generation such as fuel processing and fuel cells; and electronic material production by plasma etching.

In this presentation, we will (a) demonstrate the use of Jacobian in Systems Biology using examples from the literature, and (b) present some work-in-progress for future releases such as dynamic global optimization to estimate globally optimum model parameters, guaranteed, and multi-scale modeling in cancer biology.


B Schoeberl, C Eichler-Jonsson, E.D. Gilles and G Muller, "MAP kinase activated by surface and internalized EGF receptors", Nature Biotechnology 20:370-376 2002. PubMed


Glen H. Ko - Specializes on chemical reaction network and reactor modeling. Extensive consulting and collaboration experience with global companies and leading research institutes including AstraZeneca, BASF, Dow, GE, LG, Mitsui, Sumitomo, Toyota, ETHZ, MIT. Holds Ph.D. (1988) from MIT, B.A.Sc. (1984) from Brit. Col., both in Chemical Engineering

John E. Tolsma - Specializes in numerical algorithm and computational software development for dynamic modeling and optimization. Lead developer of Jacobian dynamic modeling and optimization software. Holds Ph.D. (1999) from MIT and B.S. (1993) from CalPoly both in Chemical Engineering

Taeshin Park - Specializes in dynamic model development and applications in diverse areas including polymerization, systems biology, chemical reactors. Lead developer of Jacobian for multi-scale modeling. Holds Ph.D. (1997) from MIT, M.S. (1991) and B.S. (1989) from Seoul National University, all in Chemical Engineering.