Ganesh Swami

While browsing through various tutorials on typography, I came across the “right” way to use bullets. I’m not too sure about using this style though. Indenting bullets is more commonly seen in print and on the web, and attempting to use the right style will definitely stick out (for the wrong reasons.)

I came across a paper on the pre-print archive: “Introduction to protein folding for physicists.” Proteins are polymers of amino acids and the sequence of these amino acids completely determine the native three dimensional structure. The human genome project gives us the sequences of all proteins in the human body. In theory it should be possible to study diseases like Alzheimer’s that are caused by the misfolding. Right?

Unfortunately, the combinatorial nature of the problem makes it impossible to do a brute force search. This paper is a decent introduction to the vocabulary of molecular biologists. The abstract:

[...] we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day sta- tus of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we phys- ically define the problem stating the assumptions behind this (commonly implicit) definition. [...]

The author recognizes the inadequacies of implicit solvent models. He also asks a key question: is kinetic information important for determining which minima is chosen. This was a similar question that I had while doing my docking project. Most docking algorithms right now only use static information.

References:

• Introduction to protein folding for physicists, by Pablo Echenique. arXiv:0705.1845v1 [physics.bio-ph]

• Picture courtesy of Wikipedia

Jon Hicks has a quick introduction to various typography terms. Have you ever found yourself wondering what line-width, em and serif were? Or what font is appropriate for headings and content? Then, this presentation is for you. His presentation also has a list of related links.

I was surprised to find out that Lucida Grande is the default font on Max OSX. The default font in Keynote is Gill Sans, so I assumed it was same throughout. Gill Sans is one of my favorite fonts.

I can never forget Helen Keller’s quote:

The best and most beautiful things in the world cannot be seen or even touched. They must be felt with the heart.

I come across so many things in the world that are just beautiful. I’ll try to post some of my experiences in this newly created category. It’ll mostly be pointers to things other people have created.

[I'll avoid the philosophical question about good science being art.]

Writing unit tests is generally considered good software engineering. You can even take it to an extreme: “write test, write code, refactor” with Test Driven Development. It’s not enough to just write tests — we must also check the effectiveness and quality of the tests themselves. How many relevant paths are we taking in the module being tested. This is where tools like gcov come handy.

But this just makes me drool…

(via Juho Snellman)