From 5664068ef6809e57440ad7a4bf1e1bddd8717318 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Fri, 20 Jun 2025 17:00:40 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.md | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ README.txt | 1 - 2 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 README.md delete mode 100644 README.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..992c49a --- /dev/null +++ b/README.md @@ -0,0 +1,48 @@ +G. Antunes and E. De Schutter: A stochastic signaling network mediates +the probabilistic induction of cerebellar long-term +depression. *Journal of Neuroscience* 32: 9288-9300 (2012). + +We provide two versions of the model script, ltd.py and +ltd_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.py + +The work described in the paper was done with a pre-release version of +STEPS, equivalent to version 1.0.0. The ltd-py script is included +mainly for reference, we strongly advise to use ltd_updated.py with +the most recent STEPS version. We deem the two scripts to be +numerically equivalent for the respective STEPS versions. + +The differences between STEPS versions 1.2 and above, and STEPS +versions below 1.2, are in how some reaction constants are +interpreted. For a zero-order reaction (in STEPS this is a reaction +which has no reactants) the unit for the reaction constant in STEPS +1.2 and above is M/s, which defines the molar concentration of the +product(s) such a reaction will produce per second. In previous +versions of STEPS the unit was /s and defined the number of molecules +of the product(s) produced per second. + +For a 2-dimensional reaction, that is a reaction where all reactants +are situated in a 'patch', units are based on square meters (since +there is no 2D equivalent of the liter). Therefore, for a 2nd-order +reaction the units in STEPS 1.2 and above are m^2/(mol.s). All other +reactions are unaffected. + +Please refer to STEPS documentation at +[http://steps.sourceforge.net/manual/manual_index.html](http://steps.sourceforge.net/manual/manual_index.html) for further +information about STEPS. + +To install STEPS please visit: +[http://steps.sourceforge.net/STEPS/Download.html](http://steps.sourceforge.net/STEPS/Download.html) This script requires +that you also have NumPy, SciPy and Matplotlib installed. + +At the end of the simulations, 5 figures will be plotted sequentially +using Matplotlib. If you don't have Matplotlib installed, please check +the Python documentation to obtain information on how to save the +results of the simulations, and use Matlab or a similar program to +open them. + +--- + +2025-06-20: Converted README to Markdown. \ No newline at end of file diff --git a/README.txt b/README.txt deleted file mode 100644 index c69864f..0000000 --- a/README.txt +++ /dev/null @@ -1 +0,0 @@ -G. Antunes and E. De Schutter: A stochastic signaling network mediates the probabilistic induction of cerebellar long-term depression. Journal of Neuroscience 32: 9288-9300 (2012). We provide two versions of the model script, ltd.py and ltd_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.py The work described in the paper was done with a pre-release version of STEPS, equivalent to version 1.0.0. The ltd-py script is included mainly for reference, we strongly advise to use ltd_updated.py with the most recent STEPS version. We deem the two scripts to be numerically equivalent for the respective STEPS versions. The differences between STEPS versions 1.2 and above, and STEPS versions below 1.2, are in how some reaction constants are interpreted. For a zero-order reaction (in STEPS this is a reaction which has no reactants) the unit for the reaction constant in STEPS 1.2 and above is M/s, which defines the molar concentration of the product(s) such a reaction will produce per second. In previous versions of STEPS the unit was /s and defined the number of molecules of the product(s) produced per second. For a 2-dimensional reaction, that is a reaction where all reactants are situated in a 'patch', units are based on square meters (since there is no 2D equivalent of the liter). Therefore, for a 2nd-order reaction the units in STEPS 1.2 and above are m^2/(mol.s). All other reactions are unaffected. Please refer to STEPS documentation at http://steps.sourceforge.net/manual/manual_index.html for further information about STEPS. To install STEPS please visit: http://steps.sourceforge.net/STEPS/Download.html This script requires that you also have NumPy, SciPy and Matplotlib installed. At the end of the simulations, 5 figures will be plotted sequentially using Matplotlib. If you don't have Matplotlib installed, please check the Python documentation to obtain information on how to save the results of the simulations, and use Matlab or a similar program to open them. \ No newline at end of file From 86d5ae91fda05a7cd508ad0ff4e0b6553deb6414 Mon Sep 17 00:00:00 2001 From: rsakai Date: Mon, 7 Jul 2025 14:11:14 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 51 +++++++++++++-------------------------------------- 1 file changed, 13 insertions(+), 38 deletions(-) diff --git a/README.md b/README.md index 992c49a..30ef970 100644 --- a/README.md +++ b/README.md @@ -1,48 +1,23 @@ -G. Antunes and E. De Schutter: A stochastic signaling network mediates -the probabilistic induction of cerebellar long-term -depression. *Journal of Neuroscience* 32: 9288-9300 (2012). - -We provide two versions of the model script, ltd.py and -ltd_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 +G. Antunes and E. De Schutter: A stochastic signaling network mediates the probabilistic induction of cerebellar long-term depression. *Journal of Neuroscience* 32: 9288-9300 (2012). + +We provide two versions of the model script, ltd.py and ltd_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.py -The work described in the paper was done with a pre-release version of -STEPS, equivalent to version 1.0.0. The ltd-py script is included -mainly for reference, we strongly advise to use ltd_updated.py with -the most recent STEPS version. We deem the two scripts to be -numerically equivalent for the respective STEPS versions. - -The differences between STEPS versions 1.2 and above, and STEPS -versions below 1.2, are in how some reaction constants are -interpreted. For a zero-order reaction (in STEPS this is a reaction -which has no reactants) the unit for the reaction constant in STEPS -1.2 and above is M/s, which defines the molar concentration of the -product(s) such a reaction will produce per second. In previous -versions of STEPS the unit was /s and defined the number of molecules -of the product(s) produced per second. - -For a 2-dimensional reaction, that is a reaction where all reactants -are situated in a 'patch', units are based on square meters (since -there is no 2D equivalent of the liter). Therefore, for a 2nd-order -reaction the units in STEPS 1.2 and above are m^2/(mol.s). All other -reactions are unaffected. +The work described in the paper was done with a pre-release version of STEPS, equivalent to version 1.0.0. The ltd-py script is included mainly for reference we strongly advise to use ltd_updated.py with the most recent STEPS version. We deem the two scripts to be numerically equivalent for the respective STEPS versions. + +The differences between STEPS versions 1.2 and above, and STEPS versions below 1.2, are in how some reaction constants are interpreted. For a zero-order reaction (in STEPS this is a reaction which has no reactants) the unit for the reaction constant in STEPS 1.2 and above is M/s, which defines the molar concentration of the product(s) such a reaction will produce per second. In previous versions of STEPS the unit was /s and defined the number of molecules of the product(s) produced per second. + +For a 2-dimensional reaction, that is a reaction where all reactants are situated in a 'patch', units are based on square meters (since there is no 2D equivalent of the liter). Therefore, for a 2nd-order reaction the units in STEPS 1.2 and above are m^2/(mol.s). All other reactions are unaffected. Please refer to STEPS documentation at -[http://steps.sourceforge.net/manual/manual_index.html](http://steps.sourceforge.net/manual/manual_index.html) for further -information about STEPS. +[http://steps.sourceforge.net/manual/manual_index.html](http://steps.sourceforge.net/manual/manual_index.html) for further information about STEPS. To install STEPS please visit: -[http://steps.sourceforge.net/STEPS/Download.html](http://steps.sourceforge.net/STEPS/Download.html) This script requires -that you also have NumPy, SciPy and Matplotlib installed. +[http://steps.sourceforge.net/STEPS/Download.html](http://steps.sourceforge.net/STEPS/Download.html) This script requires that you also have NumPy, SciPy and Matplotlib installed. -At the end of the simulations, 5 figures will be plotted sequentially -using Matplotlib. If you don't have Matplotlib installed, please check -the Python documentation to obtain information on how to save the -results of the simulations, and use Matlab or a similar program to -open them. +At the end of the simulations, 5 figures will be plotted sequentially using Matplotlib. If you don't have Matplotlib installed, please check the Python documentation to obtain information on how to save the results of the simulations, and use Matlab or a similar program to open them. --- -2025-06-20: Converted README to Markdown. \ No newline at end of file +2025-06-20: Converted README to Markdown.