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- Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John Doyle, Hiroaki Kitano +37 others
- Bioinformatics
- 2003

MOTIVATION
Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.
RESULTS
We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical… (More)

MOTIVATION
Realistic simulation of the kinetic properties of metabolic pathways requires rate equations to be expressed in reversible form, because substrate and product elasticities are drastically different in reversible and irreversible reactions. This presents no special problem for reactions that follow reversible Michaelis-Menten kinetics, but for… (More)

The idea of metabolic efficiency is widely known in biochemistry , and appears in some form or other in many textbooks (e. Rather less common is any discussion of what the calculation of a metabolic efficiency actually means [though an excellent one may be found in Atkinson (1977)1, presumably because it is regarded as intuitively obvious. The simplest, and… (More)

MetaModel is a user-friendly program for calculating steady-state fluxes and metabolite concentrations of metabolic systems on the IBM PC and compatible computers. For any steady state that is obtained, one can then calculate a matrix of elasticity coefficients at that steady state, or a matrix of control and response coefficients. It thus offers a simple… (More)

The claim by Savageau et al. (1987 a, b, Math. Biosci. 86, 127-145, 147-167) that the theory of metabolic control associated with Kacser & Burns (1973, Symp. Soc. Exp. Biol. 27, 65-104) and with Heinrich & Rapoport (1974, Eur. J. Biochem. 42, 89-102) is no more than a special case of the biochemical systems theory of Savageau and colleagues is examined. It… (More)

It is now widely accepted that mathematical models are needed to predict the behaviour of complex metabolic networks in the cell, in order to have a rational basis for planning metabolic engineering with biotechnological or therapeutical purposes. The great complexity of metabolic networks makes it crucial to simplify them for analysis, but without… (More)

- Ranjit Randhawa, Clifford A Shaffer, John J Tyson, M Hucka, A Finney, H M Sauro +40 others
- 2006

1 Abstract Today's pathway models are small compared to the amount of information known about a particular cellular pathway, in part because current modeling languages and tools are unable to handle significantly larger models. Thus, most pathway modeling work today focuses on building small models of individual pathways since they are easy to construct and… (More)

It would not be appropriate for me, as convener of this discussion, to express any forcible opinions about the controversial aspects of metabolite channelling. Moreover, as an outsider in the field, or at best a newcomer to it, I realize that in expressing any view at all I run the risk of exposing my ignorance without much illuminating the subject. I shall… (More)

The probability of the sequence YRY(Ni)YRY occurring most frequently with the same i value in seven out of nine gene classes is reassessed and found to be about 1.3 X 10(-8), more than 4000 times greater than the value calculated by Arquès & Michel (1987), but still much too small for chance to be a reasonable explanation for the observation. Even if the… (More)

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