[IPython-dev] Concise citations for the Scipy stack

Mark Voorhies mark.voorhies at ucsf.edu
Mon Feb 2 14:11:37 EST 2015

I'm putting together a set of "software tools" references for a paper that we are preparing to submit.
I am trying to balance acknowledging as much of our infrastructure as possible, while minimizing the
number of references that have no direct (i.e., unambiguously obvious to the reader) connection to the
methods section of the paper (e.g., citing Tornado, git, h5py, or MySQL is probably going too far; likewise,
I think it's reasonable to cite R but not rpy2).

Based on http://www.scipy.org/citing.html, I think a good minimal set (for a paper with heavy use of
IPython for matplotlib-based plotting, including KDEs from scipy.stats, and a lot of vanilla python
sequence/expression analysis code) is:

NumPy & SciPy
Stéfan van der Walt, S. Chris Colbert and Gaël Varoquaux. The NumPy Array: A Structure for Efficient Numerical Computation, Computing in Science & Engineering, 13, 22-30 (2011), DOI:10.1109/MCSE.2011.37

John D. Hunter. Matplotlib: A 2D Graphics Environment, Computing in Science & Engineering, 9, 90-95 (2007), DOI:10.1109/MCSE.2007.55

Fernando Pérez and Brian E. Granger. IPython: A System for Interactive Scientific Computing, Computing in Science & Engineering, 9, 21-29 (2007), DOI:10.1109/MCSE.2007.53



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