This page lists a few projects exploring the simulation of cellular biochemistry, especially cellular regulatory networks, and some related topics such as methods for deriving regulatory networks from microarray data.
URL: http://www.zoo.cam.ac.uk/comp-cell/Papers/Shimizu02.pdf
Bio/Spice is a biological data analysis and modeling workspace and database based loosely on SPICE tools used by Electrical Engineers for the design and analysis of their circuitry.
http://ipsapp009.lwwonline.com/content/getfile/5030/4/3/fulltext.pdf
http://www.ee.princeton.edu/~rweiss/bio-programming/rweiss-phd-thesis.pdf
http://www.ee.princeton.edu/~rweiss/bio-programming/dimacs99-evocomp.pdf
Ramoni, Marco, and Paola Sebastiani, Bayesian Methods for Intelligent Data Analysis.
http://kmi.open.ac.uk/publications/tr.cfm?trnumber=67
http://www.math.umass.edu/~sebas/pdf-papers/genebook.pdf
http://www.genomethods.org/papers/statscience02.pdf
Our initial focus is on achieving interoperability between seven leading simulations tools: BioSpice (Arkin, 2001), DBSolve (Goryanin, 2001; Goryanin et al., 1999), E-Cell (Tomita et al., 1999, 2001), Gepasi (Mendes, 1997, 2001), Jarnac (Sauro, 1991; Sauro and Fell, 2000), StochSim (Bray et al., 2001; Morton-Firth and Bray, 1998), and Virtual Cell (Schaff et al., 2000, 2001).
http://www.sbw-sbml.org/sbw/docs/icsb2000/hucka-et-al-icsb2000.pdf
The Sytems Biology Markup Language (SBML) is discussed in:
http://bioinformatics.oupjournals.org/cgi/reprint/19/4/524.pdf
and in
http://www.sbw-sbml.org/sbml/docs/presentations/i3c-may-2003/sbml-status.pdf
The AfCS-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in cell signaling, the "brainchild of Al Gilman of the University of Texas Southwestern Medical Center in Dallas."
http://www.signaling-gateway.org/
http://www.nature.com/nature/links/021212/021212-4.html
"But it has become clear that the proteins don't work individually, but instead assemble fleetingly into molecular machines, the components of which are shared between pathways. (See Nature, 417, 894-896; 2002)."
"The analysis by Superti-Furga and his colleagues used some 1,700 bait proteins, representing almost 30% of the yeast's total complement of expressed genes, and defined 232 distinct complexes." (Half comprised 1 to 5 proteins, 18% comprised 6-10, 15% were 11-20, 6% were 21-30, 4% were 31-40, and 6% were comprised of over 40 proteins....and 40% of the proteins were involved in more than 1 complex.)
GNA (Genetic Network Analyzer) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a regulatory network using knowledge about regulatory interactions in combination with gene expression data.
At present, GNA consists of a simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential equations. The simulator has been implemented in Java 1.3 and has been applied to the analysis of various regulatory systems, including the network controlling the initiation of sporulation in B. subtilis
http://www.hgmp.mrc.ac.uk/Registered/Help/gna/what-is-gna.htm
Mor Peleg, Iwei Yeh, and Russ B. Altman. Modeling biological processes using Workflow and Petri Net models
Eric L.Haseltine and James B. Rawlings, Approximate Simulation of Coupled Fast and Slow Reactions for Stochastic Chemical Kinetics, Journal of Chemical Physics, Volume 117, Number 15, pp 6959-6969, October 2002
R. Maimon and S. Browning. Diagrammatic Notation and Computational Grammar for Gene Networks. Proceedings of the International Conference on Systems Biology., 2001.
Kohn, Molecular Biology of the Cell 1999, 10:2073.
List compiled by
Michael Grobe
May 2003