Software

Introduction

Several programs are available that are useful for various aspects of MCA, below are brief descriptions of some of these. 

Metabolic Simulators

These programs simulate the behaviour of metabolic pathways and then calculate the various MCA coefficients for the simulated states. They can be used for modelling, not just for control analysis.

  • Gepasi by Mendes (1993) is a free ms windows program for simulation of steady states and transient behaviour of biochemical pathways (including several compartments). it calculates all the enzyme elasticities, flux- and concentration-control coefficients, as well as their unscaled versions (Reder 1988) for steady states.
  • SCAMP by Sauro & Fell (1991, Sauro 1993) is a free command line driven compiler of metabolic pathways for the atari st and ms-dos. scamp simulates steady states and transient behaviour of metabolic pathways and calculates all the coefficients of mca (for both steady states and transient states, see Acerenza et al. 1989 for the latter).
  • MIST by Magnus Ehlde (1995) is a free MS Windows 3.1 simulator that can calculate control coefficients of the simulated pathways.
  • MetaModel by cornish-bowden & hofmeyr (1991) is an ms-dos simulator of the steady states of metabolic pathways. metamodel calculates the control coefficients of the steady states. a test version of metamodel 3 is available from ftp://bmshuxley.brookes.ac.uk/pub/software/ibmpc/metamod3/.
  • DBSolve by Igor Goryanin is a free windows 95 and nt (intel only) simulator with links to the EMP database.
  • SCoP is a commercial simulation program oriented towards biological applications. It can be used to simulate metabolic systems (there is no information about its capabilities for calculating elasticity and control coefficients).

Programs for Calculation of MCA Coefficients

In this class are programs that apply some matrix method to calculate enzyme elasticities, control coefficients or response coefficients.

  • CONTROL by Letellier et al. (1991), uses the Reder (1988) matrix method to calculate control coefficients from values of elasticities. CONTROL is available for MS-DOS.
  • MetaCon by Thomas & Fell (1993) uses the Fell & Sauro (1985, Sauro et al. 1987) matrix method. It calculates algebraic expressions of the control coefficients as functions of the elasticities and can substitute polynomial expressions or numerical values for any or all variables (metabolite concentrations, fluxes and enzyme elasticities). This program is also capable doing sensitivity analysis of control coefficients. MetaCon runs under MS-DOS and is available from ftp://bmshuxley.brookes.ac.uk/pub/software/ibmpc/metacon/

General Mathematics Programs

This type of programs are not specific for MCA but can be used for that purpose. Most are commercial (but there are good free packages too).


Last updated: March 28, 2013 at 16:36 pm