A toolbox for running OptSlope, an algorithm for metabolic engineering

Dependencies:

• cobrapy (latest from https://github.com/opencobra/cobrapy)
• libSBML 5
• numpy 1.7.1
• matplotlib 1.2.1
• pysvg 0.2.2
• PuLP 1.5.4
• IBM ILOG CPLEX 12.6

Specific instructions for Ubuntu 13.10:

• Run the following commands in the terminal:

  • sudo apt-get install libsbml5-python
  • sudo pip install pulp
  • sudo pip install pysvg
  • git clone https://github.com/opencobra/cobrapy ~/git/cobrapy
  • git clone https://github.com/eladnoor/optslope ~/git/optslope

• Make sure that the current directory is in PYTHONPATH. This can be achieved by adding this line to ~/.bashrc: export PYTHONPATH=.:$PYTHONPATH

• Install CPLEX (we recommend applying to IBM Academic Initiative)