Wed, 20 Aug 2008 22:11:03 BST CiteULike: julius qualitative http://www.citeulike.org/user/julius/tag/qualitative CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/julius/article/1885378 <i>Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1239-1249.</i> Executable cell biology Jasmin Fisher Thomas Henzinger doi:10.1038/nbt1356 Nat Biotech, Vol. 25, No. 11. (November 2007), pp. 1239-1249. 2007-11-08T17:06:30-00:00 2007 Nat Biotech 25 11 1239 1249 Nature Publishing Group qualitative http://www.citeulike.org/user/julius/article/1707784 <i>PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152.</i> From Pathways Databases to Network Models of Switching Behavior Baltazar Aguda Andrew Goryachev doi:10.1371/journal.pcbi.0030152 PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152. 2007-09-29T10:56:33-00:00 2007 PLoS Computational Biology 3 9 e152 bioinformatics boolean qualitative sysbio http://www.citeulike.org/user/julius/article/671360 <i>Bioinformatics, Vol. 19, No. 3. (12 February 2003), pp. 336-344.</i><br /><br />Motivation: The study of genetic regulatory networks has received a major impetus from the recent development of experimental techniques allowing the measurement of patterns of gene expression in a massively parallel way. This experimental progress calls for the development of appropriate computer tools for the modeling and simulation of gene regulation processes. Results: We present Genetic Network Analyzer (GNA), a computer tool for the modeling and simulation of genetic regulatory networks. The tool is based on a qualitative simulation method that employs coarse-grained models of regulatory networks. The use of GNA is illustrated by a case study of the network of genes and interactions regulating the initiation of sporulation in Bacillus subtilis. Availability: GNA and the model of the sporulation network are available at http://www-helix.inrialpes.fr/gna Contact: Hidde.de-Jong@inrialpes.fr 10.1093/bioinformatics/btf851 Genetic Network Analyzer: qualitative simulation of genetic regulatory networks Hidde de Jong Johannes Geiselmann Celine Hernandez Michel Page Bioinformatics, Vol. 19, No. 3. (12 February 2003), pp. 336-344. 2006-05-26T12:30:02-00:00 2003 Bioinformatics 19 3 336 344 qualitative sysbio http://www.citeulike.org/user/julius/article/616560 <i>Biosystems, Vol. 84, No. 2. (May 2006), pp. 91-100.</i><br /><br />This paper presents GINsim,1 a Java software suite devoted to the qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete mathematical and graph-theoretical concepts. GINsim encompasses an intuitive graph editor, enabling the definition and the parameterisation of a regulatory graph, as well as a simulation engine to compute the corresponding qualitative dynamical behaviour. Our computational approach is illustrated by a preliminary model analysis of the inter-cellular regulatory network activating Notch at the dorsal-ventral boundary in the wing imaginal disc of Drosophila. We focus on the cross-regulations between five genes (within and between two cells), which implements the dorsal-ventral border in the developing imaginal disc. Our simulations qualitatively reproduce the wild-type developmental pathway, as well as the outcome of various types of experimental perturbations, such as loss-of-function mutations or ectopically induced gene expression. GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks Gonzalez Gonzalez A Naldi L Sanchez D Thieffry C Chaouiya doi:10.1016/j.biosystems.2005.10.003 Biosystems, Vol. 84, No. 2. (May 2006), pp. 91-100. 2006-05-07T16:21:18-00:00 2006 Biosystems 84 2 91 100 qualitative sysbio