<commit_before>====================== BioPreDyn software suite prototype ======================

This code is the deliverable 7.2 of the BioPreDyn project ("Prototype Software
for Testing: User-friendly version of prototype software for testing in a
setting for industrial applications").

For more information about the development tasks related to the BioPreDyn
project (and the content of the deliverable 7.2), please visit the developer's
wiki: https://thecosmocompany.com/biopredyn-trac/

For more information about the BioPreDyn project itself, please refer to the
official project website: http://www.biopredyn.eu/

1. Installation

1.1. Dependencies

* CMake (http://www.cmake.org/): software build system.
* git (http://git-scm.com/): version control system; required for cloning the
libSEDML repository on GitHub.
* Python (version 2.7 or more - http://www.python.org/)
* libSBML (http://sbml.org/Software/libSBML): library for SBML file
manipulation; do not forget to build the library with Python bindings enabled.
* libSEDML (https://github.com/fbergmann/libSEDML): library for SED-ML file
manipulation; clone the https://github.com/fbergmann/libSEDML.git repository
with git and build the library with CMake, as described in the README.md file.
* COBRApy (http://sourceforge.net/projects/opencobra/files/python/cobra/0.2.1/):
library of tools for systems biology model analysis, originally a Matlab
toolbox; a Python version is now available.
* COPASI (http://www.copasi.org) Python bindings: library for the simulation and
analysis of biochemical networks.

1.2. Known problems

* libSBML installation (Windows XP32): linking problem related to libiconv when
building the library with cosmo-externals (for libxml); the file encoding.h must
be modified in order to include <libiconv/iconv.h> instead of <iconv.h>.

* libSEDML installation (Ubuntu 11.10): Python files are not completely
installed after running the installation process. A way to complete the
installation consists in manually putting the required files in
${INSTALL_DIR}/lib/python*/dist-packages and respecting the following folder
hierarchy:
${INSTALL_DIR}/lib/python*/dist-packages/libsedml.pth
${INSTALL_DIR}/lib/python*/dist-packages/libsedml/_libsedml.so
${INSTALL_DIR}/lib/python*/dist-packages/libsedml/libsedml.py
${INSTALL_DIR}/lib/python*/dist-packages/libsedml.pyc

* COPASI python bindings installation (Ubuntu 11.10): no setup file can be found
in the package, it therefore cannot be installed as a system library. The same
solution than the one described for libsedml can be used (with COPASI files
instead of libsedml files of course); alternatively, Eclipse users can simply
link the copasi*_python*_linux_x86 folder as an external library (in the project
properties).

2. User guide

2.1 Usage

python main.py /path/to/input/file [options]

Options can be:
--help: Display this help message.
--cobra: Open the input file using the cobrapy library.<commit_msg>CellNOpt.wrapper installation documented in README.txt<commit_after>====================== BioPreDyn software suite prototype ======================

This code is the deliverable 7.2 of the BioPreDyn project ("Prototype Software
for Testing: User-friendly version of prototype software for testing in a
setting for industrial applications").

For more information about the development tasks related to the BioPreDyn
project (and the content of the deliverable 7.2), please visit the developer's
wiki: https://thecosmocompany.com/biopredyn-trac/

For more information about the BioPreDyn project itself, please refer to the
official project website: http://www.biopredyn.eu/

1. Installation

1.1. Dependencies

* CMake (http://www.cmake.org/): software build system.

* git (http://git-scm.com/): version control system; required for cloning the
libSEDML repository on GitHub.

* Python (version 2.7 or more - http://www.python.org/)

* libSBML (http://sbml.org/Software/libSBML): library for SBML file
manipulation; do not forget to build the library with Python bindings enabled.

* libSEDML (https://github.com/fbergmann/libSEDML): library for SED-ML file
manipulation; clone the https://github.com/fbergmann/libSEDML.git repository
with git and build the library with CMake, as described in the README.md file.
Note that libSBML is a pre-requisite for libSEDML.

* COBRApy (http://sourceforge.net/projects/opencobra/files/python/cobra/0.2.1/):
library of tools for systems biology model analysis, originally a Matlab
toolbox; a Python version is now available. Dependency:
 * pyGLPK solver (http://tfinley.net/software/pyglpk/).

* COPASI (http://www.copasi.org) Python bindings: library for the simulation and
analysis of biochemical networks.

* CellNOpt.wrapper (http://www.ebi.ac.uk/~cokelaer/cellnopt/wrapper/): Python
wrapper for CellNOptR, a package for signalling pathways optimization in R. It
requires:
 * R (http://www.r-project.org/)
 * rpy2 (http://rpy.sourceforge.net/rpy2.html), a Python interface for R.
 * pywin32 (http://sourceforge.net/projects/pywin32)

1.2. Known problems

* libSBML installation (Windows XP32): linking problem related to libiconv when
building the library with cosmo-externals (for libxml); the file encoding.h must
be modified in order to include <libiconv/iconv.h> instead of <iconv.h>.

* libSEDML installation (Ubuntu 11.10): Python files are not completely
installed after running the installation process. A way to complete the
installation consists in manually putting the required files in
${INSTALL_DIR}/lib/python*/dist-packages and respecting the following folder
hierarchy:
${INSTALL_DIR}/lib/python*/dist-packages/libsedml.pth
${INSTALL_DIR}/lib/python*/dist-packages/libsedml/_libsedml.so
${INSTALL_DIR}/lib/python*/dist-packages/libsedml/libsedml.py
${INSTALL_DIR}/lib/python*/dist-packages/libsedml.pyc

* COPASI python bindings installation (Ubuntu 11.10): no setup file can be found
in the package, it therefore cannot be installed as a system library. The same
solution than the one described for libsedml can be used (with COPASI files
instead of libsedml files of course); alternatively, Eclipse users can simply
link the copasi*_python*_linux_x86 folder as an external library (in the project
properties).

* CellNOpt.wrapper installation (Windows XP32): the CellNOpt library in itself
is not a problem; however, rpy2 is quite tricky to install on Windows platforms.
The following steps gave satisfying results on Windows XP 32 bits:
 * Install R 2.15.3 (other versions not tested - did not work with R 3.0.x)
 * Install rpy2: compiling the sources on Windows proved to be painful and
 eventually unsuccessful. The only - unofficial - working binary distribution
 of this library was found here:
 https://bitbucket.org/breisfeld/rpy2_w32_fix/issue/1/binary-installer-for-win32
 Install it then:
  * Add the path to R.dll to the PATH environment variable (in my case
  D:\Env\R-2.15.3\bin\i386)
  * Add the R_HOME environment variable (in my case D:\Env\R-2.15.3)
  * Add the R_USER environment variable (your Windows username)
 * Install pywin32 (http://sourceforge.net/projects/pywin32)
 * Install cellnopt.wrapper; the best way to do so consists in using the
 easy_install tool:
  easy_intall cellnopt.wrapper

2. User guide

2.1 Usage

python main.py /path/to/input/file [options]

Options can be:
--help: Display this help message.
--cobra: Open the input file using the cobrapy library.
{'fraction_non_alphanumeric': 0.09627831715210355, 'fraction_numerical': 0.01307982740021575, 'mean_word_length': 4.754072924747867, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 7, 'lorem ipsum': 0, 'www.': 10, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5036335', 'n_tokens_mistral': 2247, 'n_tokens_neox': 2113, 'n_words': 849}