https://github.com/mcellteam/mcell

MCell Monte Carlo Simulator of Cellular Microphysiology
https://github.com/mcellteam/mcell

cellblender mcell simulation

Last synced: 3 months ago
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MCell Monte Carlo Simulator of Cellular Microphysiology

• Host: GitHub
• URL: https://github.com/mcellteam/mcell
• Owner: mcellteam
• License: other
• Created: 2013-05-23T20:59:54.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2024-03-04T18:20:15.000Z (over 1 year ago)
• Last Synced: 2024-04-29T09:22:46.735Z (about 1 year ago)
• Topics: cellblender, mcell, simulation
• Language: C++
• Homepage:
• Size: 85 MB
• Stars: 33
• Watchers: 22
• Forks: 10
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.txt
  • License: LICENSE.txt

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README

        
# MCell

## Overview

MCell (Monte Carlo Cell) development is supported by the NIGMS-funded

(P41GM103712) National Center for Multiscale Modeling of Biological Systems

(MMBioS).

MCell is a program that uses spatially realistic 3D cellular models and

specialized Monte Carlo algorithms to simulate the movements and reactions of

molecules within and between cells—cellular microphysiology. 

## Build Requirements:

### Ubuntu 16.04:

Run the following commands:

    sudo apt-get update

    sudo apt-get install cmake build-essential bison flex python3-dev swig libboost-all-dev

### Windows

Install the package manager chocolatey from https://chocolatey.org/install.

Follow the instructions listed on that page, which will have you copy a command

into PowerShell as an Administrator.

Once chocolatey is installed, open up a new PowerShell terminal as an

Administrator, and run the following commands:

    choco install -y git

    choco install -y python3

    choco install -y cmake

    choco install -y ninja

    choco install -y msys2

    choco install -y winflexbison

    choco install -y swig

    

Open a new PowerShell Administrator terminal and enter the following:

    msys2

This will open a different MSYS2 terminal (not a PowerShell terminal). In this

MSYS2 terminal, enter the following commands:

    pacman -Syuu

    pacman -S --needed base-devel mingw-w64-i686-toolchain mingw-w64-x86_64-toolchain \

                    git subversion mercurial \

                    mingw-w64-i686-cmake mingw-w64-x86_64-cmake

    pacman -Sy mingw-w64-i686-boost mingw-w64-x86_64-boost

Add CMake and MinGW64 to your [Windows PATH Environment

Variable](https://helpdeskgeek.com/windows-10/add-windows-path-environment-variable/).

If you have installed these dependencies with Chocolatey and your top level

drive is named `C:`, you can append (or prepend) the following paths into your

Windows PATH (Search "Control Panel"; View by small icons; System; Advanced System Settings;

              Environment Variables; User Variables; Path; Edit):

    C:\tools\msys64\mingw64\bin

    C:\Program Files\CMake\bin

## Building MCell Executable from Source (OSX, Linux, Windows)

Open a terminal (non-Administrator PowerShell for Windows users), clone the

mcell_tools repo and run:

    git clone https://github.com/mcellteam/mcell_tools.git

    cd mcell_tools

    python3 run.py

This will clone all the required repositories and run build of all the components.

Running 'python3 run.py --help' shows other options.

To build just MCell, run these commands after you ran the 'python run.py'.

    cd mcell_tools/work/build_mcell

    cmake ../../../mcell -DCMAKE_BUILD_TYPE=Release

    make 

### Testing MCell

    cd mcell_tests

    python3 run_tests.py

Running 'python3 run_tests.py --help' shows other options.