Displaying posts categorized under

Biology

Test driving the Wolfram Alpha

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 […]

The Seven Deadly Sins and Seven Heavenly Virtues of Scientific Websites

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 […]

Size matters. Life is Live.

1976: Prologue In July 27, 1976, the American Legion, a US military veterans association, held a large meeting at the Bellevue Stratford Hotel a hotel in Philadelphia PA, celebrating the USA’s bicentennial year. Within 2 days, guests  started falling ill with an atypical pneumonia. By the end of the week, 221 people were ill and […]

Did you know it’s DNA Day?

Short quiz and a movie for DNA day. 1) We celebrate DNA day because: a) Congress said so b) Francis Collins said so c) I said so 2) Who has DNA? a) CSI Miami b) James Watson c) Please, please, PLEASE let the  paternity test comes back negative… 3)  Nature vs. Nurture: which is more […]

Children’s science books: Bacteria Galore by Sunday at Four

Jonathan Eisen started something nice in his blog: a review of children’s science books. So I think I’ll follow suit, especially since my first review will combine two of Jonathan’s  faves:  Microbiology and Open Access.  The book is “Bacteria Galore by Sunday at Four” by Mel Rosenberg, a Professor of Microbiology at  Tel-Aviv University who […]

Reading entrails, 21st-century style

And the future is certain Give us time to work it out — Talking Heads – Road to Nowhere We are a species obsessed with knowing what the future holds. Our personal  future, the future of our kith and kin, our countries, and our planet. Humans have always been trying to predict their personal future. […]

Ribosomal paleontology

In the latter epoch of those  2 billion-odd years between non-life and life on early Earth, our ancestral molecular replicators were quite probably RNA, not DNA. There are many arguments for this RNA world hypothesis: RNA can store information in its sequence, and self -duplicate; it can also catalyze reactions as a ribozyme. So technically, […]

Multitasking Antibody

We learned in high school and/or undergrad biology that one antibody would bind to one antigen. This is what makes our immune system so effective: antibodies bind with high affinity to foreign proteins or other molecules. Not only that, but those antibodies are specific: they would bind only to a specific site on the foreign […]

The Human Genome Variome Project and Google News Reader

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 […]

Challenges with Data Quality, Sharing, and Versioning in Next-Generation Sequencing

An fine talk by David Dooling highlighting  some of the false impressions about second generation sequencing. A partial list: Why sequencing quality trump base pair output Why genomes are really probabilities rather than strings Why centralized repositories break down when it comes to second generation sequencing data. Collaborative Software development and versioning has been moving […]

NIH Stimulus money: what is in it for Bioinformatics?

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 […]

Killer Fungi and Zombie Ants

Once infected, the ant’s behavior is hijacked to act as a delivery system for the fungus, which is finding a good location to die and infect more ants.

On Molecular Viewers, or why I voted for RasMol

Beware the temptation to use the 45 and 120 degree angle pink and yellow light source, in combination with shiny plastic B-splines, which would make your protein model look like brothel decor

A very loose and circular association to π (Pi) Day

Happy Pi (π) Day! Americans write dates in the MM/DD/YYYY format instead of the DD/MM/YYYY format used by the rest of the world.  Usually a rather painful and confusing format if you did not grow up with it, causing checks to bounce and leases to expire for those who recently moved to the US, but […]