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Five octopus vids

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: […]

Gene and protein annotation: it’s worse than you thought

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 […]

Going to GOA: pt. 1

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 […]

Byte Size Hedgehog

I don’t know whether to categorize this guy under microbiology or zoology. He’s so small!

Videos on sequencing

A few cool vids on sequencing. Company infomercials, but still entertaining and informative. Thanks to my student, David Ream, for finding these. Pyrosequencing: Helicos: SOLiD: BASETM nanopore sequencing:

Photosynthesis, phages and structures: there’s treasure everywhere!

Here’s a really cool work, published this September in Nature.. Why did I choose this work?  Well, it’s a major discovery, and it’s all done using bioinformatics, and fairly simple bioinformatics at that. The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and […]

The Warren L. DeLano Memorial Award for Computational Biosciences

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 […]

Cool shroom vids

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 Genomic Ark: 10,000 vertebrate genomes

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 […]

Warren DeLano

For those who are not in the structural biology community: Warren DeLano wrote and maintained PyMol, the software of choice for molecular visualization. Practically anyone who published anything requiring a biomolecular image used PyMol. It is a great piece of software, powerful and extensible. Warren was strongly committed to writing quality product that served the […]

Open Access: what’s in it for me?

One problem that I am facing is convincing colleagues of the utility of an Open Access publication. The usual arguments: more visibility, retention of the right to re-use material, the Greater Good, taxpayer access to taxpayer-funded research and so on don’t stick very well when faced with a $1500-$2500 or higher publication fee. These can […]

Short Bioinformatics Hacks: Glimmer Splitter

Glimmer is a program that predicts ORFs in bacterial and archeal genomes. The input is the assembled genome FASTA file, the output are several files of the predictions in different stages. The terminal output file is the .predict file. which looks something like this: >NODE_1_length_38001_cov_935.551880 orf00001 481      362  -2     1.45 orf00002      451      567  +1     0.59 […]

Weekly poll: favorite wolf metric?

One aspect of living in any kind of social setting is being assessed, rated and tested by one’s peers. Constantly. We are social creatures: we need to know who we are up against in any given setting. It is, after all, a matter of life and death, or at the very  of gene dispersal. We […]

A bioinformatician’s peeves (some of them)

As resident bioinformatician in many places over the years, I got many of requests to help. Anything from a short blast run to a full-fledged collaboration. I love that. I always like learning about new problems, and those requests may blossom into full research collaborations. So yes, drop me an email or step into my […]