Package: wnpp Severity: wishlist * Package name : stochastirator Version : 0.0.1 Upstream Author : Eric Lyons * URL : http://opnsrcbio.molsci.org/stochastirator/ * License : GPL Description : an accelerated discrete reaction event simulator The Stochastirator represents the time-dependent behavior of biochemical reaction networks in accordance with stochastic chemical kinetics. Briefly, for a user-specified reaction netwrok, the program works by, 1. computing the "next time" each reaction will execute based on the unique number of substrate molecules (or combinations) and reaction propensity. 2. sorting the "next (reaction) time(s)" to determine which reaction next occurs. 3. executing the next reaction, thereby advancing the simulation time and updating the number of products and substrates involved in the reaction. 4. computing a new "next time" for the executed reaction and reactions whose number of substrate species (or combinations) were changed by the just executed reaction. 5. repeating steps 2-4 until the end time of the simulation is reached The next reaction time, t, is computed using the First Reaction Method developed by Gillespie in 1976. t=(1/a)ln(1/r) where, "a" is the reaction "propensity" (the product of the reaction "rate" and the number of unique reactant combinations), "r" is a random number drawn from a uniform distribution in the unit interval. -- System Information: Debian Release: 3.1 APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing') Architecture: i386 (i686) Kernel: Linux 2.6.8-1-686 Locale: LANG=it_IT@euro, LC_CTYPE=it_IT@euro (charmap=ISO-8859-15) -- Luca Brivio Web: http://icebrook.altervista.org Jabber: lucab83@jabber.org ________________________________________________________________________ "Homo sum: humani nil a me alienum puto" (P. Terentius Afer) ________________________________________________________________________
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