I’m not sure if the framing is quite right, but it should be inspirational: In Praise of Bad Programmers
http://cacm.acm.org/magazines/2010/1/55757-in-praise-of-bad-programmers/abstract
Category Archives: software engineering
Will this motive my colleagues?
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A problem I know
A key problem in supporting research software development is that funding agencies in many countries do not view software development as an intellectual exercise worthy of a research grant.
From http://www.nature.com/nphys/journal/v11/n5/full/nphys3313.html
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That Docker thing sounds promising
I missed this presentation, but I am going to figure out how to use Docker for reproducible research soon! http://benmarwick.github.io/UW-eScience-docker-for-reproducible-research/#1
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Some material on making a world map in Python
http://sensitivecities.com/so-youd-like-to-make-a-map-using-python-EN.html#.VMKgbUfF-Yt
https://www.packtpub.com/books/content/working-geo-spatial-data-python
I just want the outlines of selected countries… that should be easy, right?
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Pretty bug in mpld3
It’s not quite d3-broke-and-made-art quality, but I like the plot in this bug report: https://github.com/jakevdp/mpld3/issues/274#issuecomment-68576519
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PyMC2 function evals
PyMC2 has some tricky tricks for reducing function evaluations if possible. A question asked and answered on Stack Overflow investigates: http://stackoverflow.com/q/27714635/1935494 and I made a IPython Notebook with more details, too: http://nbviewer.ipython.org/gist/aflaxman/c07c5261bf22f6847098
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A little PyMC2 trick
Here is a little trick for getting around a pesky initialization issue in PyMC2 models, asked and answers on Stack Overflow when thing were quiet around here: http://stackoverflow.com/a/27724637/1935494
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Reproducible Computational Research by UW Folks
This interesting thing crossed my inbox during the quiet time between quarters:
Inspired by Dave and Randy’s presentations earlier in the quarter, our lab happened to publish two preprints today, both with supplemental GitHub repositories.
As mentioned several times, the reproducible part is hard. I would appreciate any feedback on our attempts to provide data and code, and how they might be improved. Of course you are welcome to comment on preprints if you wish.
1) Heare JE, Blake B, Davis JP, Vadopalas B, Roberts SB. (2014) Evidence of Ostrea lurida (Carpenter 1894) population structure in Puget Sound, WA. PeerJ PrePrints 2:e704v1 http://dx.doi.org/10.7287/peerj.preprints.704v1
GitHub Repo (Data and R scripts): https://github.com/jheare/OluridaSurvey2014
2) Indication of family-specific DNA methylation patterns in developing oysters
Claire E. Olson, Steven B. Roberts
bioRxivdoi: http://dx.doi.org/10.1101/012831GitHub Repo (IPython notebook): https://github.com/che625/olson-ms-nb/tree/1.0
Any feedback on how we might improve our Repositories is certainly welcome.
Very daring. I hope it was ok to share on my blog. I find this level of transparency inspiring.
The discussion that ensued indicates that there is still room for better tools to archive the computational environment where these analyses are being performed. I’ve always dreamed of doing my whole project in a virtual machine and then freezing it for posterity when I’m done. It would be the digital version of keeping a laptop on my shelf for each analysis. Easier said than done, however.
The discussion also resulted in a new wiki listing code products that accompany UW research projects: https://github.com/uwescience/reproducible/wiki/Code-Products
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Interactive Horizontal Bar Charts
Some notes on them here: http://nbviewer.ipython.org/gist/aflaxman/c93489dd19cee2eabf00
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PyMC3 with PyMC2
Did you know I have a fork of PyMC3 that you can run at the same time as PyMC2? I don’t keep it up to date, but people seem to want it every once in a while. Maybe this will help someone find it: https://github.com/aflaxman/pymc
import pymc as pm2 import pymc3 as pm3
Good for head-to-head comparisons…
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Healthy Algorithms 