G. Antunes and E. De Schutter: A stochastic signaling network mediates
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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
- 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