Metadata-Version: 2.1
Name: ecell4-base
Version: 2.0.5
Summary: 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.
Home-page: https://github.com/ecell/ecell4_base
Author: Kazunari Kaizu
Author-email: kaizu@riken.jp
License: the GNU General Public License v2
Platform: UNKNOWN
Description-Content-Type: text/markdown

E-Cell System version 4
=======================

|   |  |
| ------------- | ------------- |
| Conda package for Windows, Mac and Linux | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/ecell4_base.svg)](https://github.com/conda-forge/ecell4_base-feedstock) |
| PyPI (wheel) package for Linux | [![PyPI](https://img.shields.io/pypi/v/ecell4_base.svg)](https://pypi.python.org/pypi/ecell4_base) |

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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](http://gfrd.org), [Spatiocyte](http://spatiocyte.org) (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.

[![DOI](https://zenodo.org/badge/6348303.svg)](https://zenodo.org/badge/latestdoi/6348303)

Licensing terms
===============

This product is licensed under the terms of the [GNU General Public License v3](https://github.com/ecell/ecell4_base/blob/master/LICENSE),
See also [LICENSE](https://github.com/ecell/ecell4_base/blob/master/LICENSE) for the software included in this product.

- Copyright (c) 2010-, RIKEN

All rights reserved.


