https://cmsb.ics.uci.edu/ 2026-04-03T21:42:51+00:00 https://cmsb.ics.uci.edu/ https://cmsb.ics.uci.edu/lib/tpl/vector/images/favicon.ico text/html 2013-03-25T00:02:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://cmsb.ics.uci.edu/doku.php/wiki:book_i?rev=1364169739&do=diff Book I Table of contents * Chapter 1: Introduction to biological modeling * Chapter 2: Biological dynamics and reaction kinetics * Chapter 3: Emergent properties of small networks * Chapter 4: Molecular complexes and statistical mechanics * Chapter 5: Computation: Formulation, simulation, and inference * Chapter 6: Biological networks text/html 2013-04-03T21:55:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://cmsb.ics.uci.edu/doku.php/wiki:book_ii?rev=1365026157&do=diff Book II (a virtual book) Table of Contents * Chapter 1: Graphs and graph theory * Chapter 2: Stochastic processes and algorithms * Chapter 3: Advanced computation * Chapter 4: Dynamics and model analysis text/html 2013-04-03T22:24:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://cmsb.ics.uci.edu/doku.php/wiki:navigation?rev=1365027868&do=diff Book I Ch 1: Introduction Ch 2: Kinetics/Dynamics Ch 3: Small networks Ch 4: Molec. stat mech Ch 5: Computation Ch 6: Networks Ch 7: Morphodynamics Ch 8: Mito metabolism Integrative SB Appendix: Mathematics Book II (virtual) Graphs Stochastics Adv. computation Dynamics Software availability text/html 2013-03-24T23:09:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://cmsb.ics.uci.edu/doku.php/wiki:site_notice?rev=1364166571&do=diff Systems Biology: Computational and Mathematical Methods by E. Mjolsness, P. Baldi, and B. Shapiro text/html 2013-04-03T21:16:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://cmsb.ics.uci.edu/doku.php/wiki:software_availability?rev=1365023813&do=diff Software availability Used particularly in this book Cellerator * xCellerator, available at <http://www.xcellerator.info/> . This depends on Mathematica(R). * python variant * kmech * ssa * cellzilla Dynamical Grammars * plenum * cambium translation Widely used elsewhere