# Install¶

PSAMM can be installed using the Python package installer pip. We recommend that you use a Virtualenv when installing PSAMM. First, create a Virtualenv in your project directory and activate the environment. On Linux/OSX the following terminal commands can be used:

$virtualenv env$ source env/bin/activate


Then, install PSAMM using the pip command:

(env) $pip install psamm  When returning to the project from a new terminal window, simply reactivate the environment by running $ source env/bin/activate


The psamm-import tool is included in the main PSAMM repository. Some additional model specific importers for Excel format models associated with publications are maintained in a separate repository. After installing PSAMM, support for these import functions can be added through installing this additional program:

(env) $pip install git+https://github.com/zhanglab/psamm-import.git  ## Dependencies¶ • Linear programming solver (Cplex, Gurobi, GLPK or QSopt_ex) • PyYAML (for reading the native model format) • NumPy (optional; model matrix can be exported to NumPy matrix if available) PyYAML is installed automatically when PSAMM is installed through pip. The linear programming solver is not strictly required but most analyses require one to work. The LP solver Cplex is the preferred solver. We recently added support for the LP solver Gurobi and GLPK. The rational solver QSopt_ex does not support MILP problems which means that some analyses require one of the other solvers. The MILP support in GLPK is still experimental so it is disabled by default. ## Cplex¶ The Cplex Python bindings will have to be installed manually. Make sure that you are using at least Cplex version 12.6. If you are using a virtual environment (as described above) this should be done after activating the virtual environment: 1. Locate the directory where Cplex was installed (e.g. /path/to/IBM/ILOG/CPLEX_StudioXXX). 2. Locate the appropriate subdirectory based on your platform and Python version: cplex/python/<version>/<platform> (e.g. cplex/python/2.7/x86-64_osx). 3. Use pip to install the package from this directory using the following command. (env)$ pip install \
/path/to/IBM/ILOG/CPLEX_Studio1262/cplex/python/<version>/<platform>


Further documentation on installing Cplex can be found in the Cplex documentation.

Note

Python 3 support was added in a recent release of Cplex. Older versions only support Python 2. If you are using Python 3 make sure that you have the latest version of Cplex installed.

## Gurobi¶

The Gurobi Python bindings will have to be installed into the virtualenv. After activating the virtualenv:

1. Locate the directory where the Guropi python bindings were installed. For example, on OSX this directory is /Library/gurobiXXX/mac64 where XXX is a version code.
2. Use pip to install the package from this directory. For example:


## QSopt_ex¶

QSopt_ex is supported through python-qsoptex which requires GnuMP and the QSopt_ex library. After installing these libraries the Python bindings can be installed using pip:

(env) \$ pip install python-qsoptex