How To Install python3-steps on Fedora 36

In this tutorial we learn how to install python3-steps in Fedora 36. python3-steps is STochastic Engine for Pathway Simulation

Introduction

In this tutorial we learn how to install python3-steps on Fedora 36.

What is python3-steps

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

We can use yum or dnf to install python3-steps on Fedora 36. In this tutorial we discuss both methods but you only need to choose one of method to install python3-steps.

Install python3-steps on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install python3-steps using dnf by running the following command:

sudo dnf -y install python3-steps

Install python3-steps on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

After updating yum database, We can install python3-steps using yum by running the following command:

sudo yum -y install python3-steps

How To Uninstall python3-steps on Fedora 36

To uninstall only the python3-steps package we can use the following command:

sudo dnf remove python3-steps

python3-steps Package Contents on Fedora 36

/usr/lib/.build-id
/usr/lib/.build-id/47
/usr/lib/.build-id/47/fdaba5d22f6081a5ead6016e1a621747909ef5
/usr/lib64/python3.10/site-packages/steps
/usr/lib64/python3.10/site-packages/steps-3.6.0-py3.10.egg-info
/usr/lib64/python3.10/site-packages/steps/API_1
/usr/lib64/python3.10/site-packages/steps/API_1/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/geom.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/geom.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/model.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/model.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/quiet.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/quiet.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/rng.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/rng.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/solver.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/__pycache__/solver.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/geom.py
/usr/lib64/python3.10/site-packages/steps/API_1/model.py
/usr/lib64/python3.10/site-packages/steps/API_1/mpi
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__pycache__/solver.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/__pycache__/solver.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/mpi/solver.py
/usr/lib64/python3.10/site-packages/steps/API_1/quiet.py
/usr/lib64/python3.10/site-packages/steps/API_1/rng.py
/usr/lib64/python3.10/site-packages/steps/API_1/solver.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/cubit_support.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/cubit_support.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/geom_decompose.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/geom_decompose.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/meshctrl.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/meshctrl.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/meshio.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/meshio.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/metis_support.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/metis_support.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/morph_support.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/morph_support.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/sbml.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/sbml.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/steps_cubit.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/steps_cubit.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/steps_shadow.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/__pycache__/steps_shadow.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/cubit_support.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/geom_decompose.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/event_parser.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/event_parser.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/matlab_parser.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/matlab_parser.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/simulate.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/__pycache__/simulate.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/event_parser.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/matlab_parser.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/matlab_support/simulate.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/meshctrl.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/meshio.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/metis_support.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/morph_support.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/sbml.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/steps_cubit.py
/usr/lib64/python3.10/site-packages/steps/API_1/utilities/steps_shadow.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual
/usr/lib64/python3.10/site-packages/steps/API_1/visual/Colors.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/Control.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/DynamicComponent.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/PartitionViewer.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/Plotting.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/SimDisplay.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/StaticComponent.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Colors.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Colors.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Control.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Control.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/DynamicComponent.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/DynamicComponent.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/PartitionViewer.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/PartitionViewer.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Plotting.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/Plotting.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/SimDisplay.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/SimDisplay.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/StaticComponent.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/StaticComponent.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_1/visual/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2
/usr/lib64/python3.10/site-packages/steps/API_2/__init__.py
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/_saving_optim.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/_saving_optim.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/geom.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/geom.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/model.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/model.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/rng.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/rng.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/saving.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/saving.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/sim.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/sim.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/simcheck.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/simcheck.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/utils.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/utils.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/visual.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/__pycache__/visual.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/API_2/_saving_optim.py
/usr/lib64/python3.10/site-packages/steps/API_2/geom.py
/usr/lib64/python3.10/site-packages/steps/API_2/model.py
/usr/lib64/python3.10/site-packages/steps/API_2/rng.py
/usr/lib64/python3.10/site-packages/steps/API_2/saving.py
/usr/lib64/python3.10/site-packages/steps/API_2/sim.py
/usr/lib64/python3.10/site-packages/steps/API_2/simcheck.py
/usr/lib64/python3.10/site-packages/steps/API_2/utils.py
/usr/lib64/python3.10/site-packages/steps/API_2/visual.py
/usr/lib64/python3.10/site-packages/steps/__init__.py
/usr/lib64/python3.10/site-packages/steps/__pycache__
/usr/lib64/python3.10/site-packages/steps/__pycache__/__init__.cpython-310.opt-1.pyc
/usr/lib64/python3.10/site-packages/steps/__pycache__/__init__.cpython-310.pyc
/usr/lib64/python3.10/site-packages/steps/cysteps.so
/usr/share/licenses/python3-steps
/usr/share/licenses/python3-steps/LICENSE.md

References

Summary

In this tutorial we learn how to install python3-steps on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).