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CBMPy & PySCeS-CBM/Mariner installation instructions (Windows 32/64)

Python and base dependencies

Install Open Source scientific Python distribution available from http://www.pythonxy.com:

  • Run Python(x,y)-2.7.3.0.exe
  • Agree to licence
  • Select the type of install: Full
  • Use default directories and start menu options

Test installation:

  • Open a terminal
  • Execute "ipython"
  • In ipython shell, execute "import numpy, h5py, xlrd, xlwt"

No errors/warnings indicate successful installation exit with CTRL-D

Install IBM cplex optimization studio (Academic)

  • Run cplex_studio125.win-x86-32.exe
  • Select English language and accept licence
  • Set "Program" install directory to C:ILOGCPLEX_Studio124
  • Set "Samples" install directory to C:ILOGCPLEX_Studio124_samples
  • Allow default associations to be set and PATH update

Once installation is complete we need to install the Python bindings

  • Open a terminal
  • Execute "cd c:ILOGCPLEX_Studio124cplexpythonx86_win32"
  • Execute "python setup.py install"

Test installation, in the terminal:

  • Execute "cd "
  • Execute "ipython"
  • Execute "import cplex"
  • Execute "lp = cplex.Cplex()"
  • Execute "lp.solve()"

A succesful test should return:

In : lp.solve()
Tried aggregator 1 time.
No LP presolve or aggregator reductions.
Presolve time =    0.00 sec.

Exit ipython with CTRL-D

Install libSBML (sbml.org)

  • Run libSBML-5.6.0-win-py2.7-packages-x86.exe

Test installation

  • Open a terminal
  • Execute "ipython"
  • Execute "import libsbml"
  • Execute "libsbml.LIBSBML_VERSION_STRING"

A successful test should return:

In : libsbml.LIBSBML_VERSION_STRING
Out: '50600'

Exit ipython with CTRL-D

Install CBMPy (pysces.sf.net/cbm)

  • Run pyscescbm-0.6.2.win32.exe

Test installation:

  • Open a terminal
  • Execute "ipython"
  • Execute "import pyscescbm as cbm"

This should return:

In [1]: import pyscescbm as cbm

**********
Welcome to the PySCeS Constraint Based Modelling Toolkit (0.6.2 [r1147])
**********

GLPK not available

*****
Using CPLEX
*****

No module named CBGUI

GUI module not available

***
Multiple Environment Module (0.6.2 [r1147])
***

Exit ipython with CTRL-D

CherryPy, libXML and SOAPlib (www.cherrypy.org, lxml.de)

  • Run lxml-2.3.win32-py2.7.exe
  • Run CherryPy-3.2.2.win32.exe
  • Run soaplib-0.8.1.win32.exe

Test installation:

  • Open a terminal
  • Execute "ipython"
  • Execute "import cherrypy, lxml, soaplib" no errors or warnings should be generated
  • Exit ipython with CTRL-D
  • change directory to supplied soaplib tests e.g. "cd e:gsktestssoaplib"
  • Execute "python binary_test.py"
  • Execute "python primitive_test.py"

All tests should pass.

PySCeS-CBM/Mariner (pysces.sf.net/cbm)

  • Run pyscesmariner-0.7.3.win32.exe

To test installation:

  • Open two terminals and in both
  • Change directory to supplied pyscesmariner tests e.g. "cd e:gsktestspyscesmariner"
  • In terminal one run "run_server.bat" which should nowdisplay

E:gsktestspyscesmariner>python cbm_server_demo.py Mariner using E:gsktestspyscesmariner as a working directory Mariner server name: 10.0.2.15 Mariner using port: 31313

<snipped>

* Multiple Environment Module (0.6.2 [r1147]) *

PySCeSCBM/Mariner initialising ... this console is now blocked

In terminal two:

  • Execute "python cbm_client_demo.py"

This should end without errors and display done. Congratulations you have successfully installed CBMPy and PySCeS-CBM Mariner!

Source: README.rst.txt, updated 2012-12-03