Trello

Just heard about Trello from Joel and signed up! Looks promising; may be I can use it to manage things around in the lab and office! Let us see.

The first commandment of computing and some academic put-down

Via John  Hawks, here is a link to Titus Brown’s thoughts on anecdotal science and the need for sharing codes:

Closer to home, I think I can attribute some of my collaborators’ impatience with me to this attitude of mine. I want to do good, solid, robust computational science, as well as relevant biology; my schtick is, at least at the moment,computational methods. Since my collaborators tend not to be computationally focused, they don’t always get the point of all the computational work. Some of them are either more patient or more relaxed about the whole thing — if you’re wondering why Jim Tiedje is co-authoring papers on probabilistic de Bruijn graphs, well, that’s why . Some of them are less patient, and it’s why I would never recommend a bioinformatics analysis position to anyone — it leads to computational science driven by biologists, which is often something we call “bad science”.

What’s the bottom line? Publish your methods, which include your source code and your parameters, and discuss your controls and evaluation in detail. Otherwise, you’re doing anecdotal science.

Also via John Hawks, I got the link to this academic put down (Pullum on Chomsky):

For example, he claims that children have an innate grasp of the psychic continuity of persons, and his basis for the claim is that his grandchildren enjoy a story in which a baby donkey gets turned into a rock. It is surprising to see a point this feeble published even once, but Chomsky has now put it into print at least three times.

…

McGilvray invites Chomsky to explain how “Merge” brought humanity the gift of arithmetic.

The attempted exposition is a train wreck. Chomsky confuses the empty set with zero, binary operations with unary ones, functions with the sets on which they are defined, the natural numbers with their set-theoretic construction, and both with the theory of arithmetic. McGilvray drinks it all in – and appends a commentary note that unfortunately elaborates the second of Paul Benacerraf’s two celebrated non-equivalent set-theoretic reconstructions of the natural numbers, when Chomsky was struggling to outline the first. It is embarrassing – like overhearing a conversation between two undergraduates about a mathematics lecture that neither has understood.

Following the 141 pages of transcribed chunks of conversation are some lengthy appendices and commentary notes, mostly just pedestrian restatements of Chomsky’s increasingly eccentric linguistic doctrines, and together with the glossary, bibliography and index making up 56 per cent of the whole book.

At least half a dozen “interview” volumes of Chomsky’s unrehearsed musings have been published since Mitsou Ronat created the genre in 1977. This one is McGilvray’s fourth book-length homage to Chomsky by my count. He is entitled to his view that anything Chomsky can be induced to say should be typed up and distributed. But why are university presses publishing stuff like this, devoid of carefully framed ideas, results or scientific data about language?

Presumably the guaranteed sales from having Chomsky’s name on the cover are too tempting to resist. Buyers should beware.

As John Hawks has titled his post, this is chomping of Chomsky!

Parallel computing: a good resource

After CUDA, now I am getting interested in plain old parallel computing (mpi and stuff like that) as well as in openCL (thanks to a collaborator, Prof. Phanikumar). So, I found this webpage, especially, this piece to be very helpful.

The computing pleasures

I recently upgraded my desktop by enhancing the RAM (from 4 to 16GB)  and adding a GPU (GeForce GTX580) card. However, I had trouble in using all the RAM; it would show only 4G, and I learnt that I either have to update the kernel or load a 64bit version. I decided to go for the second option and, while at it, decided to load the Precise Pangolin (Ubuntu 12.04).

My initial attempts to load Pangolin failed because I did not turn on the noapic, nolapic and nomodeset options while loading Ubuntu. Once I got that right, rest has been a sail. I really, really like the feel of the Unity desktop even though I am still learning the tricks. On the whole a nice experience so far.

Now, I am able to get a simulation with 4096×4096 size running (which takes only half of the available memory)! This probably is the first time I am running such a large scale simulation; the previous big simulations used to stop at one quarter of this size (at 2048×2048) and I am very, very excited!

Next step is to figure out CUDA and start using the GPU for computations, and needless to say, I am looking forward to it.

Scientific/engineering/mathematics software

A good list and contains several of my favourites: FFTW, GSL, Sage, Octave and R; scilab and gnuplot are missing though.

Optimizing software and not getting wet in the rain

A rather detailed manual on software optimization (C++) and other optimization resources; via Andrew at Statistical Modeling, Causal inference, and Social Science.

A link to a paper in European Journal of Physics as to whether you should walk or run in a rain — in Bombay, where, you get drenched even if you are under the umbrella, it might be a good idea to learn to enjoy the warm, big fat drops hitting you!

HowTo: write code

Meant for economists; but should work for everybody.

Start-up ideas: frighteningly ambitious ones

Paul Graham has pulled a Hilbert with this one!

SAGE: An open-source mathematics software extraordinaire

A couple of months ago, a friend of mine, Deep, recommended SAGE to me. I installed it and played with it at very low level — solve a set of algebraic equations, plot some functions and generally use it as a calculator.But I did not pay much attention to it.

For the past ten days, I am trying to work with SAGE to solve a problem which involves some piecewise polynomials, their differentiation and integration (I will share the worksheet sometime soon on the net); I am having lots of fun with the software.

I remember discovering maple several years ago (again, thanks to two friends, Sai and Pradeep) one Saturday afternoon and enjoying it. After a long time, I am having similar fun with SAGE.

I think, SAGE is the best software I have seen after LaTeX in terms of its usefulness to my research and teaching, and I strongly recommend it to you!

Stal was his name too!

Being a C programmer and GNU/LINUX fan, it would be wrong for me not to post this story about Dennis Ritchie that Mark Lieberman has shared:

The Unix culture favored short identifiers in general: programs like ed, cd, ls, cat, cc, sed, su; directory names like bin, lib, etc, dev; userids like dmr, bwk, mvm. Against this background, 14 characters is a long name; and as Brian Kernighan put it in Unix for Beginners (1979), “14 characters … is enough to be descriptive”. In order to have arbitrary-length file names, you’d need to add another layer of indirection to the file-system data structures; and as Richard Gabriel later wrote about the Bell Labs Unix ethos, “All reasonably expected cases should be covered. Completeness can be sacrificed in favor of any other quality. In fact, completeness must be sacrificed whenever implementation simplicity is jeopardized.”

However, Unix escaped from Bell Labs — that’s part of the story of how Dennis Ritchie helped change the world — and folks in Berkeley had looser (or at least different) moral standards. By 1982 or so, the Berkeley flavor of Unix had developed a file system with arbitrary (or at least much longer) possible file names. So one day, someone sent me a tar tape that had been made on a Berkeley system. And because they’d had the bad taste to take extensive advantage of those longer-than-14-character file names,  my attempt to un-tar the tape was a disaster.

Specifically, as I recall, the overlong file names were simply silently truncated; aside from often concealing their identity and purpose, this caused later files with the same initial 14 letters to overwrite earlier ones.

So I went around the corner to discuss this problem with my colleagues in the Unix research department. Someone patiently explained to me why the 14-character limit was, on balance, a Good Thing. Someone else — certainly not Dennis — may even have suggested that tar’s silent truncation of file names was the Right Thing to Do. Some inconclusive theological controversy ensued.

After talking it over with Dennis, I concluded that re-writing the V7 file system would be too much trouble, as well a violation of local cultural norms, but that modifying tar would be both fairly easy and culturally acceptable. So I got the source code, and hacked tar so that when it encountered over-long file names, it mapped them into 14-character versions guaranteed to be unique, at least insofar as 14 alphanumeric characters permitted, and at the end it wrote out a file giving the table of correspondences between the original file names and the new ones.

This allowed me to get at whatever it was that was on that foreign tape, so I was satisfied. I sent the code around by email to some people that I thought might be able to use it, with a brief note explaining what it was good for, and expressing the hope that this solution would be acceptable “even to those stalwart puritans in the unix research department”. Dennis wrote back that it was indeed acceptable, signing his response “Stal”.

And for some time after that, he continued to use that nickname in private email to me.