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README.txt
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README.txt
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G. Antunes and E. De Schutter: A stochastic signaling network mediatesthe probabilistic induction of cerebellar long-termdepression. Journal of Neuroscience 32: 9288-9300 (2012).We provide two versions of the model script, ltd.py andltd_updated.py, which were created for different versions of STEPS:- current versions of STEPS and any version from 1.2 on: use ltd_updated.py- old versions of STEPS (before 1.2): use ltd.pyThe work described in the paper was done with a pre-release version ofSTEPS, equivalent to version 1.0.0. The ltd-py script is includedmainly for reference, we strongly advise to use ltd_updated.py withthe most recent STEPS version. We deem the two scripts to benumerically equivalent for the respective STEPS versions.The differences between STEPS versions 1.2 and above, and STEPSversions below 1.2, are in how some reaction constants areinterpreted. For a zero-order reaction (in STEPS this is a reactionwhich has no reactants) the unit for the reaction constant in STEPS1.2 and above is M/s, which defines the molar concentration of theproduct(s) such a reaction will produce per second. In previousversions of STEPS the unit was /s and defined the number of moleculesof the product(s) produced per second.For a 2-dimensional reaction, that is a reaction where all reactantsare situated in a 'patch', units are based on square meters (sincethere is no 2D equivalent of the liter). Therefore, for a 2nd-orderreaction the units in STEPS 1.2 and above are m^2/(mol.s). All otherreactions are unaffected.Please refer to STEPS documentation athttp://steps.sourceforge.net/manual/manual_index.html for furtherinformation about STEPS.To install STEPS please visit:http://steps.sourceforge.net/STEPS/Download.html This script requiresthat you also have NumPy, SciPy and Matplotlib installed.At the end of the simulations, 5 figures will be plotted sequentiallyusing Matplotlib. If you don't have Matplotlib installed, please checkthe Python documentation to obtain information on how to save theresults of the simulations, and use Matlab or a similar program toopen them.