Despite our best attempts to remove species from the face of the Earth, there is still quite a bit of life out there and it is still quite diverse. Also, there are still quite a few people who want to document, describe and make the rest of us aware of the magnitude and diversity of […]
I just spent the better part of a Saturday playing with Foldit. Foldit is an ongoing experiment in finding protein structures by harnessing the power of the mob – or gamers, as is the case here. The player is presented with a backbone & sidechain configuration, with the secondary structures mostly pre-determined. The problem is […]
The source file associated with this post can be downloaded here. The last time I talked about how to read a GOA gene_associations file into a Python dictionary data structure. Our goal was to find all genes that are annotated as hydrolases in the GOA gene_associations file. The tricky part is, most enzymes are not […]
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, […]
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: […]
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 […]
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!
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 […]
I am preparing an introduction-to-fungi class. Found this cool Aspergillus-related animation: Life on Earth never fails: Not sure what this is: Of course, there are the zombie ants I have written about before:
The first bioinformatics meeting I went to was in 1996 at the Nachsholim resort, north of Tel Aviv. I received a fellowship for the duration, and shared a room with the brilliant Golan Yona, then a grad student at the Hebrew University. I was doing biochemistry at the time and knew next to nothing about […]
