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The paper on MDAnalysis was published as
- N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327, DOI: 10.1002/jcc.21787
The HTML version of the paper has so many indentation errors in the code example to make it almost completely useless for learning MDAnalysis. The PDF version is mostly correct although the final formatted version ended up with a few line breaks that are illegal in the Python syntax. The free PubmedCentral version (available April 2012, e.g. through PMID 21500218), however, contains perfectly formatted Python code.
The full list of errata can be found on the MDAnalysis website.