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Total waste of time, ep. 1

Warning: frivolously geeky and technical  post, which can be best defined as “science methodology esoterica”, and from which you can learn absolutely nothing useful.  If you don’t get what’s going on, then it’s probably for the best, because this is a complete waste of time. Specific Aim 1:  find the longest word in English composed […]

The Seven Deadly Sins and Seven Heavenly Virtues of Scientific Websites

When I say here “scientific websites”, I am not referring to education sites, science blogs, or scientific journal web sites. I am talking about sites scientists use for their day to day research. Sites like Entrez, EBI, FlyBase, ExPasy, PDB etc. The sites I just mentioned I deem quite virtuous, but there are many sinful […]

The Human Genome Variome Project and Google News Reader

Apparently sequencing two white males of European extraction does not make for a very good sample of mankind, and that if we really want to get a good view of what we are really like, we need to sequence a couple more. Maybe even, you know, a woman, or someone from India or China or […]

NIH Stimulus money: what is in it for Bioinformatics?

Following  Shirley Wu’s excellent post on the stimulus money at the NIH, I decided to do my bit, and post some bioinformatically relevant programs from the  Challenge Grants. I am defining bioinformatics rather narrowly here, and excluding most biomedical informatics, imaging technologies, clinical data management, etc. Also, many other topics would be supported to some […]

Baby it’s cold outside

Most of the Earth’s surface is colder than the inside of your refrigerator. Deep sea temperatures are almost universally 2-4C. That’s already 73%  of the Earth’s surface. Then add to that the  polar regions, mountain ranges and permafrost and you have about 85% of the Earth’s surface constantly at refrigerator or freezer temperatures. While there […]

Not dead, overloaded

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, […]

Ten years of coding with the snake

Biopython is entering its 10th year; the unofficial birthday is on September, since that is when the mailing list started: September 1999. I stumbled onto that list mid-September, 1999. I believe the Python version was 1.5, I was still working on SGI Irix, and I was an 0.3 PhD candidate. Today I am coding with […]

Now this looks a lot better!

In any data-rich science, data visualization is of prime importance.  Finding ways to visually depict data is challenging, as we have opposing demands: we would like to see the data in the whole, but also be able to zoom in and analyze the details; we would like to know how the many details add up […]

My own post genomic moment

Maybe I am slow on the uptake, but I never quite liked the term “post genomic”, and I used it very sparingly. (Yes, I do have that term in one of my better cited papers, smack in the first sentence of the abstract, but I never liked that).  Perhaps because of all the associated abuse […]

Peace on Earth

Here is a little trick I performed as a first year grad student a while ago and which I would like to share. My PhD adviser, Hanah Margalit was supposed to give a talk at a  joint Israeli-Palestinian meeting. (Hopefully, such days will be back soon and permanently!) The audience was rather broad, and included […]

More on Microbial Sequencing

(Continued from “On Microbial Sequencing“). Well, it’s really been a great meeting. The biology of pathogens, parasites and symbionts is amazing. Historically, the microbes that chiefly interested us were one of those three: those that causes disease in humans, animals (focus on domesticated animals), plants (again, mostly domesticated). However, as we are (alas, too slowly) […]

On Microbial Sequencing

This is the 9th year the NSF & USDA  hold  a workshop for their microbial sequencing program awardees. (Full disclosure: I am not one of them).  Most of the talks are by the awardees themselves, and there were some great talks. For me an interesting angle was it to see how software is being developed […]