A critical review on modelling formalisms and simulation tools in computational biosystems

Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks.Research supported by PhD grant SFRH/BD/35215/2007 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal program

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets

Abstract. In order to understand complex genetic regulatory networks researchers require automated formal modelling techniques that provide appropriate analysis tools. In this paper we propose a new qualitative model for genetic regulatory networks based on Petri nets and detail a process for automatically constructing these models using logic mini-mization. We take as our starting point the Boolean network approach in which regulatory entities are viewed abstractly as binary switches. The idea is to extract terms representing a Boolean network using logic minimization and to then directly translate these terms into appropri-ate Petri net control structures. The resulting compact Petri net model addresses a number of shortcomings associated with Boolean networks and is particularly suited to analysis using the wide range of Petri net tools. We demonstrate our approach by presenting a detailed case study in which the genetic regulatory network underlying the nutritional stress response in Escherichia coli is modelled and analysed.

Modeling Biological Pathways: A discrete Event Systems Approach

A discrete-event systems approach is proposed for the modeling of biochemical reaction systems. The approach is based on Petri nets, which are particularly suited to modeling stoichiometric transformations, i.e., the inter conversion of metabolites in fixed proportions. Properties of Petri nets and methods for their analysis are presented, along with their interpretation for biological systems. An example of the human erythrocyte metabolism is presented to illustrate the concepts of the methodology

BIOCHEMICAL STUDIES ON THE OCULAR LENS IN RELATION TO CATARACTOGENESIS. Progress Report No. 4, December 1, 1968--January 31, 1970.

This report presents biochemical studies on the ocular lens in relation to cataractogenesis

BIOCHEMICAL STUDIES ON THE OCULAR LENS IN RELATION TO CATARACTOGENESIS. Progress Report No. 15, February 1, 1971--January 31, 1972.

The experiments provided the data on cross saturation needed to evaluate the Michaelis-Menten constants for these cations and the Vmax of the carrier responsible for active transport into the lens