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<!DOCTYPE html>
<html><head>
<title>BioPUG - Resources</title>
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<a class="hide-phone" id="logo" href="index.html"><span>Bio</span>PUG UniMelb</a>
<ul>
<li><a href="sessions.html">Sessions</a></li>
<li><a href="resources.html">Resources</a></li>
<li><a href="getting-started.html">Getting Started</a></li>
</ul>
</nav>
<div class="content grid">
<h3>Resources</h3>
<p>This is a work in progess. If you have suggestions to add to this list, please contact <a href="mailto:[email protected]">Simon</a>.</p>
<ul class="tabs center">
<li class="first current"><a href="#general-resources">General Resources</a></li>
<li><a href="#python-resources">Python Resources</a></li>
</ul>
<div id="general-resources" class="tab-content">
<h4>General Resources</h4>
<h5>Web Resources</h5>
<ul>
<li><a href="software-carpentry.org">Software Carpentry</a> is all about teaching researchers the fundamentals of computing and programming, to increase their productivity. We will be closely following their syllabus.</li>
</ul>
<h5>Journal Articles</h5>
<ul>
<li><a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000589">Dudley JT, Butte AJ (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput Biol 5(12): e1000589. doi:10.1371/journal.pcbi.1000589</a></li>
<li><a href="http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030199">Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol 3(11): e199. doi:10.1371/journal.pcbi.0030199</a></li>
<li><a href="http://arxiv.org/abs/1210.0530">Wilson G <em>et al</em> (2012) Best Practices for Scientific Computing. arXiv:1210.0530</a></li>
<li><a href="http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424">Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424</a></li>
<li><a href="http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002598">Morin A, Urban J, Sliz P (2012) A Quick Guide to Software Licensing for the Scientist-Programmer. PLoS Comput Biol 8(7): e1002598. doi:10.1371/journal.pcbi.1002598</a></li>
</ul>
</div>
<div id="python-resources" class="tab-content">
<h4>Python Resources</h4>
<h5 id="python-installation">Python Installation</h5>
<p>A <a href="getting-started.html">Getting Started Guide</a> has been written to walk you
through the procedure of installing the required software. Please read it for further details.</p>
<h5>General Reference</h5>
<ul>
<li><a href="http://docs.python.org/2/">Python 2 Documentation</a>. Of particular interest, the tutorial and library reference, describing code included with a normal install of Python 2.7.</li>
<li><a href="http://docs.python.org/3/">Python 3 Documentation</a>. As above, but for Python 3. Of particular interest, the tutorial and library reference, describing code included with a normal install of Python 3, and differences to Python 2.</li>
<li><a href="http://wiki.python.org/">The Python Wiki</a>, containing links to extra guides and resources, books, documentation and books.</li>
<li><a href="https://pypi.python.org/">PyPI</a>, the Python Package Index, is a repository of modules written for Python to extend it, and promote reuse and collaboration.</li>
<li><a href="https://python-guide.readthedocs.org/en/latest/">The Hitchhikers Guide to Python</a> is still a work in progress, but is already an extremely valuable guide for setting up your environment and outlining particularly useful packages you can use for various tasks.</li>
<li><a href="http://www.slideshare.net/doughellmann/an-introduction-to-the-zen-of-python">The Zen of Python</a> sums up the guiding principles of Python's design, and should inform your coding as well.</li>
<li><a href="http://python.net/~goodger/projects/pycon/2007/idiomatic/handout.html">Idiomatic Python</a> is about having a conventional coding style, so that your code is clear and understandable. Following the idioms can often improve performance, as they take into account how Python is implemented.</li>
</ul>
<h5>Books</h5>
<ul>
<li><a href="http://www.greenteapress.com/thinkpython/thinkpython.html">Think Python</a> is free to download, but print copies are available. Concise and to the point, it's our primary reference text.</li>
<li><a href="http://www.amazon.com/gp/product/0596158068?ie=UTF8&tag=giofneyo-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0596158068">Learning Python</a> seems to be one of the better beginning to intermediate texts for Python. At UniMelb, we have <a href="http://proquestcombo.safaribooksonline.com.ezp.lib.unimelb.edu.au/9780596805395">electronic access</a> to the latest editon through the library, as well as an earlier editon or two in print.
<li><a href="http://shop.oreilly.com/product/9780596158118.do">Programming Python</a> is for when you have a strong base of Python knowledge to work from. Covers making more complex programs, and advanced skills. UniMelb also has free <a href="http://proquestcombo.safaribooksonline.com.ezp.lib.unimelb.edu.au/9781449398712">electronic access</a> through the library.</li>
<li><a href="http://shop.oreilly.com/product/9780596007973.do">Python Cookbook</a> is a reference containing idiomatic solutions to common problems. Again, UniMelb has free <a href="http://proquestcombo.safaribooksonline.com.ezp.lib.unimelb.edu.au/book/programming/python/0596007973">electronic access</a> through the library.</li>
<li><a href="http://shop.oreilly.com/product/9780596154516.do">Bioinformatics Programming Using Python</a> covers a wide range of techniques, focussing primarily on bioinformatics work. <a href="http://proquestcombo.safaribooksonline.com.ezp.lib.unimelb.edu.au/book/programming/python/9780596804725">Electronic access</a> is available through the UniMelb library.</li>
</ul>
<h5>Online Courses and Tutorials</h5>
<ul>
<li><a href="http://learnpythonthehardway.org/book/">Learn Python the Hard Way</a> isn't actually that hard, but can require a bit of time to go through and type out each of the examples (the core of the "Hard Way" courses is that you develop muscle memory doing this). Available online for free, or can pay for access to a PDF and videos.</li>
<li><a href="https://www.udacity.com/course/cs101">CS101 at Udacity</a> is an introductory Computer Science and Python programming course. Self-paced, with video lectures broken up with quizzes, and programming assignments.</li>
<li><a href="https://github.com/gregmalcolm/python_koans">Python Koans</a> use test-driven development (TDD) to teach you about many aspects of Python. A little difficult for the absolute beginner, but a valuable resource.</li>
</ul>
<h5>Practice Exercises and Projects</h5>
<ul>
<li><a href="http://pythonmonk.com/">Python Monk</a> offers an interactive, step by step introduction to Python. Very nice!</li>
<li><a href="http://newcoder.io/">New Coder</a> has a number of small projects for you to practise your skills with, completing various tasks. Well worth a look!</li>
<li><a href="http://rosalind.info/">Rosalind</a> provides challenges of various difficulties, all based around biology and bioinformatics. You can start slow with basic Python, and work your way up to phylogeny and genome assembly problems.
</ul>
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