Speaking of sampling bacteria, this ties in well with the previous post about GEBA. And by “well” I mean “in an alternate-universe/ altered-consciousness manner”. The voices in the song are sampled from this KFC employee training tape. The video won a prize in machinima.com. So if you like World of Warcraft, bacteria, KFC, sampled music, […]
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Iddo
After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of […]
The coconut using octopus has been making the news lately, as the first evidence of tool use by these animals. A good opportunity to post some vids of these cool creatures: UPDATE: the “first tool use” has been somewhat oversold. Thanks to Zen Faulkes for calling my attention to this. They are resourceful: Camouflage skills: […]
Google flew the green-starred flag of hope yesterday, in celebration of the 150th birthday of a man who constructed a whole language based upon hope. He called himself Doctor Hopeful, and he wanted that the language he created would help break down national barriers. He made it easy to learn, so that people would be […]
Sequencing centers keep pumping large amounts of sequence data into the omics-sphere (will I get a New Worst omics Word Award for this?) There is no way we can annotate even a small fraction of those experimentally and indeed most annotations are automatic, done bioinformatically. Typically function is inferred by homology: if the protein sequence […]
The University of Alabama at Birmingham issued a statement last week asking that 11 structures be removed from the Protein Data Bank, as they are quite possibly fabricated. Wow. Very little detail was given by UAB’s statement (below), or by the media. Apparently all the structures are tied to one person, HMK Murthy, who could […]
Floated in my email inbox recently. Bears blogging. Dear Editor, I would like to thank the editorial board and the referees for their comments and contributions to our manuscript. We have carefully considered the comments when rewriting the manuscript, and believe it to be much improved now… …Oh, screw this. Let’s cut the bull. Mmkay? […]
GOA, the Gene Ontology Annotation, provide Gene Ontology annotation to proteins in UniProt. It also provides GO annotations to several genome projects: Chicken, Arabidopsis, Fly, Human, Mouse, Rat and Cow. Anyone working on any of those genomes, or on UniProt and is interested in annotation, would most likely need to query GOA once in a […]
I don’t know whether to categorize this guy under microbiology or zoology. He’s so small!
I was recently reminded of this classic by Geoffrey James. Here are a few of my favorites. The whole text is available online. In the beginning was the Tao. The Tao gave birth to Space and Time. Therefore Space and Time are Yin and Yang of programming. Programmers that do not comprehend the Tao are […]
In no particular order or context. No personal stuff and by no means a complete list: WordPress (like, duh). Wikipedia (default for looking up new stuff) Wikis in general (great lab management tool. Don’t need LIMS) Open Access Publishing and Creative Commons licensing. FLOSS licensing (90% of the software I use, and 100% of what […]
Warren DeLano passed away suddenly and at a young age at his home Nov 3, 2009. He was the author of PyMol, a very popular molecular visualization program, and a strong advocate of open source software. The family of Warren Lyford DeLano has created a “In Memorium” page and blog. Also, a memorial award is […]
To say that Thirteen is a futuristic Chandlerian hardboiled-detective-fiction meets Gibson cyberpunk in a Swiftian satire of contemporary USA would be a cumbersomely loaded one-liner describing a no less loaded but sleekly streamlined novel. Saying that would also do injustice to Gibson, Chandler, Swift, the English language and especially Richard Morgan. This book has it […]
