Proteins are the machinery of life, and they facilitate most of life’s functions. Traffic into and out of the cell? Protein pumps, pores and channels. Respiration? Proteins. Metabolism and catabolism? Proteins. Immune system, signaling, development… all complex networks of interacting proteins. Understanding a protein’s structure can tell us a lot about how it performs its […]
A few one-liners to kick off the workweek: To order a set of fasta files by the number of sequences each one contains. If anyone knows how to put a tab as the output delimiter, please let us know: grep -c “>” fasta-files/*.fna | cut –fields=1,2 -d “:” –output-delimiter=” ” | sort -k 2 -nr […]
UPDATE: I submitted this post to the National Evolutionary Synthesis Center’s sponsored contest for a travel award to ScienceOnline2010. Let’s see how it goes… #scio10 In a previous post about Hatena we saw what might very well be the beginning of a (beautiful?) [:ttip=”symbiosis where one partner lives inside the cell of the other” id=”10″]endosymbiotic[:/ttip] […]
Intelligent Systems in Molecular Biology (ISMB) is a large international gathering of computational biologists, mostly from the bioinformatics side: genomics, structural bioinformatics, computational genomics, etc. This year there is a friendfeed room for microblogging ISMB 2009. So if you are not in Stockholm, or also if you are, look it up. Most of the microbloggers […]
First, a non-bioinformatic one liner, which is very relevant to most of us working on 3 different machines simultaneously, not including the 80 in our cluster. ssh-ing and giving your password each time is painful, and makes it almost impossible to do scripted file transfers, like backups. A good solution is shared key ssh in […]
In any programming gig, and that includes bioinformatics, a lot of repeat scriptology comes cropping up. I decided to share some of that, pro publico bono, and also because I hope to start some sort of ongoing cookbook for short bioinformatics hacks. If you have any cool short scripts you like to share, please email […]
There has been a lot of buzz recently about Wolfram’s new product, the Wolfram Alpha (WA). After attending a webinar on WA, I was given a preview account, and started messing around with it. In case you were wondering, that is the extent of my involvement with Wolfram Research, LLC, I don’t even have a […]
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 […]
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 […]
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 […]
