<commit_before>Installing SloppyCell
=====================

Dependencies
~~~~~~~~~~~~

Required to run
+++++++++++++++
* Python_
* Scipy_
* matplotlib_

Required to build
+++++++++++++++++
* Fortran77 compiler

Recommended
+++++++++++
* LibSBML_: Required for SBML import and export. Be sure to build ``--with-python``.
* Psyco_: A just-in-time compiler for python, Psyco will speed up integrations by about 50% on supported platforms.
* Graphviz_: SloppyCell can generate ``.dot`` files specifying network diagrams,which can be visualized using Graphviz. 
* IPython_: A dramatic improvement over the standard python shell.


Instructions
~~~~~~~~~~~~
.. topic:: On Windows

   1. Install required dependencies. We recommend installing the 
      `Enthought Python distribution <http://www.enthought.com/python/>`_ to 
      satisfy the Python and SciPy dependencies. Here is a version of
      `libsbml built against Python 2.3 <libsbml_for_python23_win.zip>`_.
   2. To build SloppyCell on Windows.

      a. Install `MinGW <http::/http://www.mingw.org/>`_
      b. Unpack the tarball. (``tar xzf SloppyCell-0.2.tar.gz``)
      c. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)
      d. Build SloppyCell. (``python setup.py build -cmingw32``) 

   3. Or try installing this `binary version <SloppyCell-0.2-win32.zip>`_
      (built by <NAME>).

      a. Un-zip the binary.
      b. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)

   4. Run the installation script. (``python setup.py install``) 
   5. Run the included test routines. (``cd ../Testing; python test.py``)

.. topic:: On OS X and Linux

   1. Install required dependencies.  
      (On OS X 10.3, we recommend installing 
      `MacEnthon <http://download.enthought.com/MacEnthon/>`_ which will install
      Scipy, matplotlib, and IPython. A pre-built version of g77 (Fortran77 
      compiler) for OSX 10.3 is available at http://hpc.sf.net.)
   2. `Download <http://sourceforge.net/project/showfiles.php?group_id=140498>`_ SloppyCell-0.2.tgz.
   3. Unpack the tarball. (``tar xzf SloppyCell-0.2.tar.gz``)
   4. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)
   5. Run the installation script. (``python setup.py install``) 
   6. Run the included test routines. (``cd ../Testing; python test.py``)

$Date$

.. _Python: http://www.python.org
.. _SciPy: http://www.scipy.org
.. _matplotlib: http://matplotlib.sourceforge.net/
.. _LibSBML: http://www.sbml.org/software/libsbml/
.. _IPython: http://ipython.scipy.org/
.. _Graphviz: http://www.graphviz.org/
.. _Psyco: http://psyco.sourceforge.net/
<commit_msg>Typo fix<commit_after>Installing SloppyCell
=====================

Dependencies
~~~~~~~~~~~~

Required to run
+++++++++++++++
* Python_
* Scipy_
* matplotlib_

Required to build
+++++++++++++++++
* Fortran77 compiler

Recommended
+++++++++++
* LibSBML_: Required for SBML import and export. Be sure to build ``--with-python``.
* Psyco_: A just-in-time compiler for python, Psyco will speed up integrations by about 50% on supported platforms.
* Graphviz_: SloppyCell can generate ``.dot`` files specifying network diagrams,which can be visualized using Graphviz. 
* IPython_: A dramatic improvement over the standard python shell.


Instructions
~~~~~~~~~~~~
.. topic:: On Windows

   1. Install required dependencies. We recommend installing the 
      `Enthought Python distribution <http://www.enthought.com/python/>`_ to 
      satisfy the Python and SciPy dependencies. Here is a version of
      `libsbml built against Python 2.3 <libsbml_for_python23_win.zip>`_.
   2. To build SloppyCell on Windows.

      a. Install `MinGW <http::/http://www.mingw.org/>`_
      b. Unpack the tarball. (``tar xzf SloppyCell-0.2.tar.gz``)
      c. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)
      d. Build SloppyCell. (``python setup.py build -cmingw32``) 

   3. Or try installing this `binary version <SloppyCell-0.2-win32.zip>`_
      (built by <NAME>).

      a. Un-zip the binary.
      b. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)

   4. Run the installation script. (``python setup.py install``) 
   5. Run the included test routines. (``cd Testing; python test.py``)

.. topic:: On OS X and Linux

   1. Install required dependencies.  
      (On OS X 10.3, we recommend installing 
      `MacEnthon <http://download.enthought.com/MacEnthon/>`_ which will install
      Scipy, matplotlib, and IPython. A pre-built version of g77 (Fortran77 
      compiler) for OSX 10.3 is available at http://hpc.sf.net.)
   2. `Download <http://sourceforge.net/project/showfiles.php?group_id=140498>`_ SloppyCell-0.2.tgz.
   3. Unpack the tarball. (``tar xzf SloppyCell-0.2.tar.gz``)
   4. Descend into the SloppyCell-0.2 directory. (``cd SloppyCell-0.2``)
   5. Run the installation script. (``python setup.py install``) 
   6. Run the included test routines. (``cd Testing; python test.py``)

$Date$

.. _Python: http://www.python.org
.. _SciPy: http://www.scipy.org
.. _matplotlib: http://matplotlib.sourceforge.net/
.. _LibSBML: http://www.sbml.org/software/libsbml/
.. _IPython: http://ipython.scipy.org/
.. _Graphviz: http://www.graphviz.org/
.. _Psyco: http://psyco.sourceforge.net/

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