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**Biopython README file** "The Biopython Project":http://www.biopython.org/ is an international association of developers of freely available Python tools for computational molecular biology. biopython.org provides an online resource for modules, scripts, and web links for developers of Python-based software for life science research. Thanks to bioperl, we can also provide web, FTP and CVS space for individuals and organizations wishing to distribute or otherwise make available standalone scripts & code. This Biopython package is made available under generous terms. Please see the LICENSE file for further details. **For the impatient** To build and install Biopython, type: python setup.py build python setup.py test python setup.py install **System Requirements** o "Python 2.0":http://www.python.org/ or above o "Martel":http://www.biopython.org/~dalke/Martel/ (requires "mxTextTools":http://starship.python.net/~lemburg/mxTextTools.html) o "Numerical Python 15.3 or above":http://numpy.sourceforge.net/ (optional) This is only required if you want to use the classification tools. **Installation** *** Make sure Python and Distutils are installed correctly *** Installation should be as simple as going to the biopython directory, and typing: 'python setup.py install' If you need to do additional configuration, e.g. changing the base directory, please type 'python setup.py', or see the documentation for Distutils. For FreeBSD users, "Johann Visagie", mailto:firstname.lastname@example.org has made Biopython available in the ports tree. According to Johann: This means that a FreeBSD user with an up-to-date ports tree can now install BioPython as simply as: 'cd /usr/ports/biology/py-biopython ; make install' Fetching of the package as well as installation of all dependencies (Python itself as well as Distutils) will be handled automagically. **Testing** Biopython includes a suite of regression tests to check if everything's running correctly. To do the tests, type: drevil:~biopython/> python setup.py test If you have Tk installed, this will run a nice GUI that displays the results of the tests. Otherwise, you will see results on the command line. **Contributing, Bug Reports** Biopython is run by volunteers from all over the world, with many types of backgrounds. We are always looking for people interested in helping with code development, web-site management, technical administration, and whatever else comes up. If you wish to contribute, please visit the "web site":http://www.biopython.org and join our "mailing list":http://www.biopython.org/MailList.shtml If you wish to contribute a bug report, please submit them to the "online bug reporting form":http://www.biopython.org/biopython-bugs/ **Distribution Structure** AUTHORS -- An (incomplete) list of people who have contributed. Bio/ -- The python package that makes up biopython Doc/ -- Documentation LICENSE -- License information for this package MANIFEST.in -- Tells distutils what files to distribute NEWS -- Release notes and news README -- This file Scripts/ -- Miscellaneous, possibly useful, standalone scripts Tests/ -- Regression testing code setup.py -- Installation file. **To Do** (In no particular order...) - PDB parser - more regression tests - Zope-ify the web site - microarray data - deprecate Sequence.py If you see something here you would like to work on, please send mail to email@example.com! Thanks