Python is a great language that has so many available libraries and packages, including several for bioinformatics. However, anyone that has spent any time installing SciPy, Numpy and other libraries knows that compiling ATLAS and other libraries can be needlessly complicated and frustrating. If there were only a Python distribution that came with all of those pre-built libraries and others, like matplotlib, for Linux, OS X and Windows...
Enter the Enthought Python Distribution (EPD, http://enthought.com/products/epd.php ). Python has a "Batteries Included" reputation, which means it comes loaded with all sorts of tools and functionality. Well, EPD is like "nuclear power plant included" (http://enthought.com/products/epdlibraries.php). EPD is produced and supported by Enthought, a scientific computing company that creates and uses very powerful tools for data analysis and visualization (http://www.enthought.com/). Many of these tools, like Chaco, Traits, Envisage and Mayavi are included in EPD (http://enthought.com/products/epd.php).
EPD is availabe for free to academics (http://enthought.com/products/edudownload.php) and can also be purchases at various subscription/support levels (http://enthought.com/products/getepd.php). I purchased an individual license for one year for $199.
Now I have access to all EPD releases and updates for OS X, Linux and Windows for a year. I use Python on all 3 platforms, so having a consistent, supported EPD install across all platforms is a no-brainer for me.
EPD installation is painfully simple. One bit of advice if you're going to install EPD on Linux--disable SELinux and reboot before installing EPD. Once I disabled SELinux my EPD install on Scientific Linux went smoothly.
The rest of my blogging around Python usage will assume an EPD install. The topics I will cover, like biopython, Galaxy and PyCogent will certainly work with a Python installation from www.python.org, but honestly, I don't have the time to answer a lot of distribution and platform-specific questions. If you're using EPD, I can address all of them easily. EPD is free to try, so I encourage everyone to take a good look at it.
Enthought also sponsors the annual SciPy conference which is being held in Austin, TX this year (http://conference.scipy.org/scipy2010/schedule.html). The conference begins next Monday, the 28th, and I am chairing a bioinformatics/biomedical session. I hope to see you there!
Article ID: SLN310885
Last Date Modified: 08/14/2018 02:22 AM
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