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SCAMP: A metabolic simulator and control analysis program

1991; Pergamon Press; Volume: 15; Issue: 12 Linguagem: Inglês

10.1016/0895-7177(91)90038-9

1872-9479

Herbert M. Sauro, David A. Fell,

Gene Regulatory Network Analysis

Previously developed metabolic simulation programs have concentrated on providing the facility to make time-dependent simulations of metabolic networks; few have been concerned with the steady state and even fewer with any steady state analysis, in particular metabolic control analysis. Here we describe a new simulation program SCAMP, which includes the facility to make time-dependent simulations, but in addition incorporates many of the concepts of metabolic control analysis. SCAMP makes available all the coefficients defined in the control analysis of Kacser and Burns [1] and Heinrich and Rapoport [2]. Thus control coefficients, response coefficients (including the conserved cycle coefficients defined by Hofmeyr et al. [3]) and elasticities (including kappa and pi elasticities [4]) can all be calculated easily. Two other special facilities have also been incorporated; conserved cycle identification and the inclusion of a simple data base of enzyme rate laws. SCAMP will accept models in terms of mass action reactions, user-defined (or data base-defined) rate law reactions or differential equations. SCAMP was primarily implemented for the Atari ST microcomputer since the ST supports a large continuous memory map. However, it is possible to run SCAMP on an MS-DOS type microcomputer provided there is at least 640K of memory. We also supply a simple command shell which integrates the various parts for both the Atari and MS-DOS version. The Atari version also includes a useful graphics plotting package.