Department of Horticulture and Landscape Architecture

Horticulture Home Page Agriculture Home Page Purdue Home Page CFPESP Home Page Computer Simulation of Metabolism Home Page Introduction Effects of Varying Rates and Pool Sizes - A Sample Program Consideration of Multiple Compartments Consideration of Cycles - The GS/GOGAT Cycle Compounds Receiving Several 13C Atoms from 13CO2 Isotopomers of the Citric Acid Cycle Supplied with 3-13C-Pyruvate Modeling Radioactive Precursor Uptake Kinetics Simulation of The Pathway of DMSP Biosynthesis in Enteromorpha intestinalis Simulation of The Pathway of Synthesis of DMSP in Spartina alterniflora Making Rates Linearly or Hyperbolically Responsive to Pool Size Changes Metabolic Engineering of Glycine Betaine Synthesis - Metabolism of 14C-Choline in Transgenic Tobacco Expressing Choline Monooxygenase in the Chloroplast Considering Feedback Inhibition Modeling Allosteric Behavior - Cooperative Substrate Binding Links to Other Metabolic Modeling Resources on the www References Sponsors

Computer Simulation of Metabolism Links to Other Metabolic Modeling Resources on the www Systems Biology Workbench Development Group JWS Online Cellular Systems Modeling Java Web Simulation and Metabolic Modelling Software [Brett Olivier and Jacky Snoep] The BioNOME Resource A repository of bio-computational models and observational data supported by Procter and Gamble and operated by the San Diego Supercomputer Center. Computer Simulation of Biochemical Kinetics Mendes, P. & Kell, D.B. (1996). Computer simulation of biochemical kinetics. In "BioThermoKinetics of the living cell" (eds. H.V. Westerhoff, J.L. Snoep, F.E. Sluse, J.E. Wijker and B.N. Kholodenko), pp. 254-257. BioThermoKinetics Press, Amsterdam Gepasi A program for the simulation and optimisation of the kinetics of systems of chemical and biochemical reactions (steady states and time courses) [Pedro Mendes] The Metabolic Control Analysis Web Includes a list of software for Metabolic Control Analysis [Pedro Mendes] Jarnac (SCAMP II): Post-Genomic Systems Biology Software Jarnac is an interactive and interpreted language for modelling integrated cellular systems, such as metabolic, gene regulation and signal transduction circuits [Herbert M. Sauro] E-Cell 3: A Multi-Algorithm, Multi-Timescale Simulation Software Environment KINSIM/FITSIM [Software developed by Dr. Carl Frieden's Lab., Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine] ModelMaker and ModelManager [Commercial PC based software tools for simulation modelling development and management] Software for Kinetics SAAM II Software "SAAM II is a new compartmental and numerical modeling program developed to help researchers create models, design and simulate experiments, and analyze data more quickly, easily, and accurately than ever before. Compartmental models are constructed graphically by creating a visual representation of the model. Numerical models are built by entering algebraic equations directly. SAAM II is especially powerful because of the unique way it integrates three important model development and testing features" [The SAAM Institute, Inc.] Protein Function and Biochemical Pathways (PFBP) Project A description of an on-going research and development project whose main output is the aMAZE database MMT - A Metabolic Modeling Tool for Metabolic Engineering [Jochen Hurlebaus, Wolfgang Wiechert1 and Ralf Takors] www www.hort.purdue.edu David Rhodes Department of Horticulture & Landscape Architecture Horticulture Building 625 Agriculture Mall Drive Purdue University West Lafayette, IN 47907-2010 Last Update: 8/20/03