A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. E-Cell has multi-algorithm, multi-timescale and multi-spatial-representation as its central feature.
Project description
E-Cell System version 4
Conda package for Windows | |
Conda package for Mac and Linux | |
ManyLinux2010 wheel | |
Build only (without packaging) |
What is E-Cell System?
E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like a cell.
E-Cell4 accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature.
Features
- Single particle simulations, i.e. The enhanced Green's Function Reaction Dynamics (eGFRD) method, Spatiocyte (a lattice-based method), and the Reaction Brownian Dynamics (RBD) method
- Ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm (the next subvolume method)
- Rule-based modeling
- Python programmable
Try online
You can try this package online with Google Colaboratory. Please refer to https://github.com/ecell/ecell4_docs
Quick start
Please refer to https://github.com/ecell/ecell4#quick-start
Installation
E-Cell4 does NOT support Python2.
E-Cell4 does NOT support pip install
on Windows and Mac.
Windows
Install Miniconda with Python 3.7 for 64-bit (from https://docs.conda.io/en/latest/miniconda.html) and run this command on Anaconda Prompt.
conda install -c ecell ecell4_base
Mac, Linux
Install Miniconda with Python 3.7 for 64-bit (from https://docs.conda.io/en/latest/miniconda.html) and run these commands on your Terminal app.
conda config --add channels conda-forge
conda install -c ecell ecell4_base
Linux environment where you can NOT use conda
We provide ecell4_base
wheel package only for Linux.
python3 -m pip install ecell4_base
If you want to compile ecell4_base by yourself
Please refer to https://github.com/ecell/ecell4_base/blob/master/azure-pipelines.yml
Citation
If this package contributes to a project which leads to a scientific publication, I would appreciate a citation.
Licensing terms
This product is licensed under the terms of the GNU General Public License v3, See also LICENSE for the software included in this product.
- Copyright (c) 2010-, RIKEN
All rights reserved.
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