Software
The following table provides a list of the software used during the sessions and information on where to obtain it or how to install it.
The operating system used for preparing the sessions was Ubuntu22.04.
| Software | URL for software / version / installation |
| micromamba | curl micro.mamba.pm/install.sh | bash |
| firefox browser | sudo apt install firefox |
| Git | sudo apt install git |
| R-base | sudo apt install r-base |
| build-essential | sudo apt install build-essential |
| Pandas | micromamba install pandas==1.5.3 -c conda-forge |
| Numpy | micromamba install numpy==1.24.3 -c conda-forge |
| Jupyter | micromamba install jupyter==1.0.0 -c conda-forge |
| python-graphviz | micromamba install python-graphviz==0.20.1 -c conda-forge |
| matplotlib | micromamba install matplotlib==3.7.1 -c conda-forge |
| seaborn | micromamba install seaborn==0.12.2 -c conda-forge |
| CVXPY | micromamba install cvxpy==1.3.1 -c conda-forge |
| PySCIPopt | micromamba install pyscipopt==4.3.0 -c conda-forge |
| DecouplerPy | pip install git+https://github.com/saezlab/decoupler-py.git@4b3978f |
| Omnipath | pip install git+https://github.com/saezlab/omnipath.git@v1.0.7 |
| CORNETO | pip install git+https://github.com/saezlab/corneto.git@0.9.1-alpha.0 |
| Cylp | pip install cylp==0.91.5 |
| adjustText | pip install adjustText==0.8 |
| a browser (any modern) | apt install firefox chromium |
| Jupyter with Julia kernel (Julia at least version 1.6) | pip install jupyter |
| COBREXA (users will install themselves but it is better to test this in advance) | ‘import Pkg; Pkg.install(“COBREXA”)’ in a Julia-kernel notebook |
| pymaboss | micromamba install -c conda-forge -c colomoto pymaboss |
| Git | sudo apt install git |
| Perl | sudo apt install perl |
| R | sudo apt-get install r-base r-base-dev |
| povray | https://www.povray.org/download/linux.php |
| imagemagik | apt install imagemagick |
| PhysiCell | https://github.com/MathCancer/PhysiCell |
| PhysiBoSS | https://github.com/PhysiBoSS/PhysiBoSS |
| PROFILE: personalisation | https://github.com/sysbio curie/PROFILE |
| PROFILE_v2: personalisation and drugs | https://github.com/ArnauMontagud/PROFILE_v2 |
| PhysiCell ToolKit (PCTK or Tools4PhysiCell) | https://github.com/PhysiBoSS/pctk |
| Tools4PhysiBoSS Drugs | https://github.com/PhysiBoSS/tools4PhysiBoSS-Drugs |
| PhysiCell-COVID | https://github.com/pc4covid19/COVID19 |
| PhysiBoSS-COVID | https://github.com/vincent-noel/COVID19/tree/physiboss/v4 https://nanohub.org/resources/pb4covid19 |
| PerMedCoE COVID pipeline | https://github.com/PerMedCoE/covid 19 workflow |