https://bugzilla.redhat.com/show_bug.cgi?id=1821069
Bug ID: 1821069
Summary: Review Request: python-steps - STochastic Engine for
Pathway Simulation
Product: Fedora
Version: rawhide
Hardware: All
OS: Linux
Status: NEW
Component: Package Review
Severity: medium
Priority: medium
Assignee: [email protected]
Reporter: [email protected]
QA Contact: [email protected]
CC: [email protected]
Target Milestone: ---
Classification: Fedora
Spec URL: https://ankursinha.fedorapeople.org/python-steps/python-steps.spec
SRPM URL:
https://ankursinha.fedorapeople.org/python-steps/python-steps-3.5.0-1.fc32.src.rpm
Description:
STEPS is a package for exact stochastic simulation of reaction-diffusion
systems in arbitrarily complex 3D geometries. Our core simulation algorithm is
an implementation of Gillespie's SSA, extended to deal with diffusion of
molecules over the elements of a 3D tetrahedral mesh.
While it was mainly developed for simulating detailed models of neuronal
signaling pathways in dendrites and around synapses, it is a general tool and
can be used for studying any biochemical pathway in which spatial gradients and
morphology are thought to play a role.
STEPS also supports accurate and efficient computational of local membrane
potentials on tetrahedral meshes, with the addition of voltage-gated channels
and currents. Tight integration between the reaction-diffusion calculations and
the tetrahedral mesh potentials allows detailed coupling between molecular
activity and local electrical excitability.
We have implemented STEPS as a set of Python modules, which means STEPS users
can use Python scripts to control all aspects of setting up the model,
generating a mesh, controlling the simulation and generating and analyzing
output. The core computational routines are still implemented as C/C++
extension modules for maximal speed of execution.
STEPS 3.0.0 and above provide early parallel solution for stochastic spatial
reaction-diffusion and electric field simulation.
Documentation can be found here:
http://steps.sourceforge.net/manual/manual_index.html
Fedora Account System Username: ankursinha
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