ecell4-base 2.1.0b1

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.

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.