Displaying posts tagged with


A Simple Genome Annotator?

A question to genome annotators out there. I need a simple genome annotator for annotating bacteriophage genomes in an undergraduate course. Until now, we used DNAMaster but for various reasons  I would like to move away from that. Here’s what  I need for class: 1. Annotate a single assembled linear chromosome, about 50,000 bp, 80-120 genes, no […]

Are you using this blog for teaching, studies or writing?

Dear readers (Yeah, I’m talking to both of you!) If you are a school teacher, college professor or any kind of other educator, trainer or science writer, and if you have ever used this blog in your line of work, please let me know. Also, if you are a student and used this blog as […]

Terrible advice from a great scientist

I am not inclined to write polemic posts. I generally like to leave that to others, while I take the admittedly easier route of waxing positive over various bits of cool science I find or hear about, and yes, occasionally do myself. But WSJ editorial from E.O. Wilson has irked me so much, I have […]

ROSALIND: an addictive bioinformatics learning site

  I just learned about this one: ROSALIND  is a really cool concept in learning bioinformatics. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once […]

Short note on getting students busy

I recently read this post about lacunae in  Bioinformatics.  One complaint was: I know that documentation is a thankless task. But some parts of the Bio[Java|Perl|Python] libraries are described only as an API? This became apparent to me when I had to teach the libraries to students. What does this module do and why does it do […]

ISMB 2012 Vignettes Pt. 3: Swag

Promotional materials are part of any conference. In scientific meetings, the swag usually comes from the booths of product promoters, science publishers, and scientific societies. It was a nice surprise to see a Federal funding agency, the US Department of Energy give away decks of cards. I’m a sucker for cards, so I took a […]

Crowdsourcing Genomics II: Unveiling HINdeR and Phrux

About this time last year, I posted about a new course I was going to teach, Phage Genomics. Briefly: Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And I get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, […]

Music Monday: Playing for Change

The Playing for Change Foundation is dedicated to musical education worldwide. From their mission statement: A decade ago a small group of documentary filmmakers set out with a dream to create a film rooted in the music of the streets. Not only has that dream been realized, it has blossomed into a global sensation called Playing […]

Crowdsourcing genomics

  Miami University has  joined the National Genomics Research Initiative (NGRI) offered by HHMI Science Education Alliance (SEA) in their Phage Genomics course. The students go directly into the lab, participating in an authentic research experience. In a full-year academic course they: isolate and characterize bacterial viruses from their local soil prepare the viral DNA […]

Are you up to the 2011 PhD Challenge?

The PhD Challenge asks graduate students to do their utmost in their submitted papers. You thought getting a paper accepted is hard? Try getting a paper accepted which contains the sentence “I smoke crack rocks”. That was the PhD challenge for 2010, and Gabriel Parent from Carnegie Mellon University has lived up to it with […]

Do you use Byte Size Biology to teach?

If you are a teacher / instructor in the broadest sense of the word and have used this blog in your instructional capacity, please take a couple of minutes to fill out this short survey below (Five questions only, short. Really! short!!) It is important for me to know the extent of BsB’s outreach and […]

BsB in high school science… nice

A  small spike on my blog traffic yesterday led me to look for the source via Google Analytics. (If you are a blogger, you should really use this tool, lots of useful traffic information.) Seems like most of the traffic came from the page of a high school science teacher at Badin High School in […]

Just “teach”

The celebrations of Darwin’s 200th birthday and 150 years for the publication of The Origin of the Species are in full swing. We are apes equipped with 10 digits on our forelimbs, which we use in just about everything we do. We like numbers that are multiples of 10; even better if they are 10 […]