Ruchira S. Datta

Ran out of power on my laptop and microblogged this talk from my Droid. Pleasantly surprised that this worked at all; go FriendFeed! - Ruchira S. Datta

Probably my comments were a bit more telegraphic than usual. - Ruchira S. Datta

Didn't see how to post from the Droid interface to, e.g., The Life Scientists room or Science 2.0 room; hence resharing now. - Ruchira S. Datta

I just noticed that I was still not writing complete sentences (as I usually do) when back on my computer. It's funny how habit works. - Ruchira S. Datta

Microbes are a kind of robust, self-repairing replicating computer w/ 4.6 Mbit OS. - Ruchira S. Datta

Transcript of Hessel's talk: http://gnusha.org/transcr... - Karthik Raman

E.g., McKerrow UCSF potential targets to reverse resistance; Chibale South Africa, Lipinski ex-Pfizer: known drugs and their targets - Ruchira S. Datta

Practically implement idealism. Initially Indira Gandhi had no drug patents in India... - Ruchira S. Datta

We don't yet know how to use genomics for drug development. - Ruchira S. Datta

Well, it's logical to assume that the sage guys want to expand to the Bay Area too :) - Attila Csordas

Given the latest personal genomics hearings, it might be a good time to revisit this. - Ruchira S. Datta

"Many have assumed that humans ceased to evolve in the distant past, perhaps when people first learned to protect themselves against cold, famine and other harsh agents of natural selection. But in the last few years, biologists peering into the human genome sequences now available from around the world have found increasing evidence of natural selection at work in the last few thousand years, leading many to assume that human evolution is still in progress." - Ruchira S. Datta

For some examples of EP controversy, see http://languagelog.ldc.upenn.edu/nll... and http://www.babelsdawn.com/babels_... . - Daniel Mietchen

The semifinals will be in Donahue Gym. Berkeley Revolution will play the Puerto Rico B-team, competing for a spot in the finals (later that evening) against the winner of the Puerto Rico A-team vs. Minnesota game. - Ruchira S. Datta

Vive la Revolution! - Ruchira S. Datta

Please fill out completely: all countries you have spied for, all aliases you use, and how long you intend to spy. - Ruchira S. Datta

SABLE predicts solvent accessibility, secondary structure and transmembrane domains from sequence, and is available either as a web server or downloadable software. I've used the downloadable version. It gives you output like this: SECTION_SA Relative solvent accessibility prediction 0 -> fully Buried 9 -> fully Exposed 3rd line -> confidence level (scale from 0 to 9, corresponding to p=0.0 or low confidence and p=0.9 or high confidence, respectively) > 1 60 PETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPE 554303030456533120403353504400510063462525302010333415565115 445797748835446827696545584696888765325443495976545584455574 > 61 79 DLDMEDNDIIEAHREQIGG 4151554110201221233 5545445568487445533 END_SECTION Edit: The cool syntax coloring is due to BioStar, the SABLE output is just ASCII text. :-) Also, if you don't have an existing structure, you could try looking for a homology model at ModBase. You may be able to use the linked ModWeb modelling server to build one if it... - Ruchira S. Datta

I upvoted David Quigley's recommendation of the Dalgaard book. I'd also recommend Modern Applied Statistics with S http://amzn.to/9SU7xx by Venables & Ripley. Despite the title, it's totally relevant to R. From the first page of the Introduction, "An Open Source system called R has emerged that provides an independent implentation of the S language. It is similar enough that almost all the examples in this book can be run under R." This book is pretty much the standard reference for R in book form. - Ruchira S. Datta

As others have pointed out, two genes are homologs if they evolved from a common ancestor. Two genes are orthologs of each other if, in the gene family tree, the last common ancestor of those two genes was a speciation event. Two genes are paralogs of each other if, in the gene family tree, the last common ancestor of those two genes was a duplication event. This is important to know because after duplication, the genes are more likely to separately evolve more specific functions (subfunctionalization) or even new functions (neofunctionalization). Berkeley PHOG provides a precomputed database of orthologs derived from PhyloFacts gene family trees using tree distances. The default, most stringent variant, PHOG-S, aims to predict only clusters of genes which are all superorthologs of each other, that is, there are no duplication events in the portion of the gene family tree containing them. This variant has high precision but relatively lower sensitivity. The thresholded variant,... - Ruchira S. Datta

Good to see your thoughts on orthology at BioStar. - Khader Shameer

@kshameer Thanks! Your post inspired me to answer my first BioStar question. - Ruchira S. Datta