Category Archives: Tips

Scientific software workflow

We know the big differences between trying out a calculation on a back of an envelope and writing a rigorous proof. Likewise, there are differences between prototyping in a Matlab script and writing a reliable pre that supports a reproducible research project. In a 15-minute presentation for a introductory workshop on scientific software at UW Madison math department, I showcased my own workflow on a simple example of plotting several solutions to an ODE in Matlab.

Repository for the workshop can be obtained by

git clone

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Upgrading to Emacs 23 from Carbon Emacs

Ever since I learned about Emacs+AUCTeX, it’s been the ultimate LaTeX editor for me. Since I don’t want to rehash everything said online about the glorious world of LaTeX editing with AUCTeX (and friends), here’s a link – Emacs as the ultimate LaTeX editor.

Until today, I used Carbon Emacs – Emacs 22 bundle for Mac OS X. It was perfect – everything important (AUCTex) was nicely bundled in, it kept me shielded from the cruel world of package installation. Until Emacs 23 came out and decided to put out its own Mac OS X bundle, which really obsoleted Carbon Emacs.

I resisted the change for a while, I said “well, people have written their PhD theses in Emacs 22 (and earlier), so WTH would I need Emacs 23”. I don’t have an answer to that question, but being a progressive ;), I decided to… progress. And update to Emacs 23. Since there are no bundled packages with the GNU distribution of Emacs for Mac OS X, I needed to update AUCTeX myself. Troubadours being gone, nobody was here to compose a song about my epic struggles, so this blogpost will be the reminder of how I did it. And learned to love the bomb. Continue reading

Converting a sequence of pngs to a Quicktime movie

Every now and then I’ll need to convert a series of graphs into a movie. For example, phase space of a dynamical system varies with a perturbation parameter and we’d like to see a “slide-show” of these graphs. As a Mac user, I’d like the format to be Quicktime so it plays extra-nice with Keynote and friends. Here’s a short guide on how to achieve this – written mostly so I don’t have to redo this from scratch every time I’d like to make a movie. And if it ends up helping you – mazel tov! Continue reading

Installing ATLAS with full LAPACK on 64 bit Linux

This is a walkthrough guide to installing ATLAS 3.8.3 with full LAPACK on 64 bit Linux. Hope you’ll find it useful. Continue reading

Software engineering proverbs