cell modeling for microphysiology

Tom Bartol 3920aec22c Fix preservation of reaction names during export of data model to bngl		3 年之前
.externalToolBuilders	8989108381 Some Eclipse project changes	4 年之前
.settings	91eac53522 Added support for warning option molecule_placement_failure	3 年之前
appveyor_windows	fcf1427724 Changed license from GPL to MIT, removed some empty/unused files	3 年之前
docs	f4360894b7 Removed old pymcell3 files that caused github dependabot alerts	3 年之前
include	d8da410f8c Fixed case when a molecule escaped geometry after being created in a	3 年之前
libmcell	443c3e656c Added support for cancellation of reaction in a callback	3 年之前
libs	38e5e7c3e9 Cleaned up compilation warnings with gcc 10 (except for bison warnings)	3 年之前
src	7a89fe15b5 Update version.txt	3 年之前
src4	d8da410f8c Fixed case when a molecule escaped geometry after being created in a	3 年之前
utils	3920aec22c Fix preservation of reaction names during export of data model to bngl	3 年之前
.cproject	f96e0067bc Initial implementation of export_geometry to OBJ file format, name	3 年之前
.gitignore	001169a1c2 Merge remote-tracking branch 'origin/mcell4_mdl2datamodel' into	4 年之前
.project	e5c9081092 Renamed bnglib to libbng	3 年之前
.pydevproject	2693100e3f Added Eclipse project files	5 年之前
.travis.yml	8e9f95471b Add some comments to travis.yml	6 年之前
CHANGELOG.txt	443c3e656c Added support for cancellation of reaction in a callback	3 年之前
CMakeLists.txt	071ba661b8 Fixed MSVC compilation warning	3 年之前
Doxyfile	e7a04712a8 Fixed command to run doxygen	3 年之前
LICENSE.txt	fcf1427724 Changed license from GPL to MIT, removed some empty/unused files	3 年之前
README.md	2f10c6ca26 Replaced python with python3 for in build instructions	4 年之前
appveyor.yml	b32268a7b0 Fix yml formatting problem.	6 年之前
build_gperftools.sh	66e9afcd48 Added script to build gperftools	4 年之前

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. 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.

README.md