E-Cell System version 4
| Conda package for Windows, Mac and Linux |  |
| PyPI (wheel) package for Linux |  |
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 and Python3 32-bit.
ecell4_base package does NOT support pip install on Windows and Mac. Please use conda instead.
Windows, Mac, Linux
Install Miniconda with Python 3.7 for 64-bit (from https://docs.conda.io/en/latest/miniconda.html) and run the following command in Terminal app. (On Windows, Start Menu -> Anaconda3 (64-bit) -> Anaconda Prompt or Anaconda Powershell Prompt)
conda install -c conda-forge ecell4
Linux environment where you can NOT use conda (For example Google Colab)
We provide ecell4_base wheel package only for Linux.
(On Linux) You can install (or upgrade) ecell4_base and ecell4 with
python3 -m pip install ecell4 -U
If you need 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.
