multicell

Python library to run biological simulations of 3D, multicellular tissues.

Installation instructions for Ubuntu 16.04.1

Install Ubuntu and update it. :

sudo apt update
sudo apt upgrade

Install required packages. :

sudo apt-get install git gitk python-pip scons zlib1g-dev libpng12-dev python-qt4 python-qt4-gl qt4-dev-tools libreadline-dev freeglut3 bison flex g++ libqt4-dev libqt4-opengl-dev libqhull-dev libreadline-dev pkg-config freeglut3-dev libann-dev liblapack-dev libmpfr-dev libblas-dev freeglut3-dev libboost-all-dev libeigen2-dev pyqt4-dev-tools python-sip-dev python-tk

Update pip (a Python module manager). :

pip install -U pip

Install Python modules with pip. :

pip install ipython==5.5 numpy scipy matplotlib jupyter pandas soappy scikit-image scikit-learn sphinx --user

Install deploy and sconsx. :

git clone https://github.com/openalea/deploy.git
cd deploy
git checkout 9ab468b5316ecdddcf38e17fce901cba09c018b5
python setup.py develop --user
cd ..
git clone https://github.com/openalea/sconsx.git
cd sconsx
git checkout 1ebd690c65a87d41c5be4eb68b51e6451fb27993
python setup.py develop --user
cd ..

Edit the .pam-environment file, which contains a definition of environment variables for your session. :

gedit .pam-environment

Paste the following if the file is empty, otherwise, edit accordingly. :

PATH DEFAULT=${PATH}:${HOME}/.local/bin
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/.local/bin

Save, log out of your session, and log back in for the changes to take effect.

Install openalea. :

git clone https://github.com/openalea/openalea.git
cd openalea
git checkout 7986945878f7fb78095265d5d9b97c32fbcc1f97
python multisetup.py develop --user
cd ..
git clone https://github.com/openalea/openalea-components.git
cd openalea-components
git checkout 4f86e0a0a157ea9428a348f11ffb53e012122a69
python multisetup.py develop --user
cd ..

Download vplants. :

wget https://github.com/jldinh/vplants/archive/refs/tags/v1.2.0.tar.gz
tar xzvf vplants-1.2.0.tar.gz
cd vplants-1.2.0

Edit multisetup.py (e.g. gedit multisetup.py): in the dirs section, comment every line (add a leading #), except ‘tissue’ (remove the leading #), save and close. Install vplants. :

python multisetup.py develop --user
cd ..

Install odesparse, a numerical integrator. :

wget http://www.simuplant.org/files/simuplant-server.zip
unzip simuplant-server.zip
cd RootGUIServer/odesparse_1
python setup.py install --user
cd ../..

Finally, install multicell. :

git clone https://github.com/jldinh/multicell.git
cd multicell
python setup.py develop --user

To start the examples, run:

jupyter notebook

Browse to the examples folder, inside of the multicell folder, and open one of the files.