Displaying posts categorized under

Science

Nature by numbers

Beautiful video showing the mathematical beauty of nature, or the natural beauty of math. Here’s what I managed to figure out: 0:08-0:44 – Fibonacci sequence 0:45-1:40 – The Golden Ratio 2:40 – Delauney triangulations leading to Voronoi diagrams (2:56 and to the end)

New poll: would you make your genome public?

Would you have your genome sequenced for free?  Conditions: you must license it for all use; a liberal CC-no attribution-like license which allows for commercial use as well. Also, your genome will be made public with many personal data  such as age, height, sex, weight, ethnicity, personal status (we want to find the “money making […]

Obesity: the role of the immune system

Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance  and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in […]

Colbert on Gene Patents

Recently, a judge in Federal District Court in Manhattan ruled that Myriad’s patents on BRCA1 and BRCA2 genes were invalid, being a “products of the law nature” and could be patented no more than, say, mount Everest. These two genes are associated with breast and ovarian cancer, and are used in testing for susceptibility to […]

AMOS on Ubuntu

AMOS is a suite of genome assembly and editing software. It includes assemblers, validation, visualization, and scaffolding tools.  I have been having some issues installing AMOS on Ubuntu  9.10.  Specifically, Ubuntu 9.10 has gcc 4.4, which breaks the compilation of the AMOS release version. However, the development version has been fixed to accommodate that. If […]

Peer review: the neverending story

It seems like there is no institution that is more criticized in science than that of the peer-review system — an no one that is less mutable. While published paper evaluation metrics are being  revised (such as the recently introduced PLoS article level metrics, or the Australian National Health and Medical Research Council abandonment of […]

I never metagenomics I didn’t like

“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2 “What-ever” —  Me In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic […]

M3 / Biosharing Meeting

A promising meeting you may want to attend. Full disclosure: I’m in the program committee for this one. ISMB SIG CALL FOR ABSTRACTS AND POSTERS – Deadline April 30 Metagenomics, Metadata and Meta-analysis / Biosharing A Special Interest Group (SIG) organized by the Genomic Standards Consortium (http://gensc.org) at ISMB 2010 on July 9-10, 2010 in […]

Paweł Szczęsny in TEDx Warsaw

Pawel on Open Science. Full disclosure: I consider sharing an office with this guy for over a year to be one of the best experiences of my postdoc.

Stupid Pi tricks for Pi Day

π approximation script, from Stephen Chappell. import sys def pi(): a, b, c, d, e, f = 1, 0, 1, 1, 3, 3 while True: if a * 4 + b – c < c * e: yield e a, b, c, d, e, f = a * 10, (b – c * e) * […]

JSUR is accepting submissions

I have written about the Journal of Serendipitous and Unexpected Results before and now this just popped in my inbox from JSUR’s Google group. Apparently JSUR is now open for business. JSUR Call for Participation Submit your short (2-4page) and full length manuscripts to the Journal of Serendipitous and Unexpected Results. Over the past month […]

Bioinformatics Blog Carnival #1

Yes! Why should the evolution people have all the fun with their blog carnival? (After all, it is only a theory.) It’s time for bioinformaticians to show what we are made of, and to have a carnival of our own. Bio::blogs had a good run some time ago. I decided to reconnect what is hopefully […]

A sh*tload of data

There are more microbial cells in our body than our own. Those microbes are not just passive hitchhikers or conversely, malicious agents of disease. They affect our well-being and health in a much broader spectrum than simply “bad” or “passive”. Among other things our gut microbes play an important role in digestion, have been linked […]

Blogosphere catches: Marco Island, finding Ada and blog carnivals

Some interesting events cropped up recently. The Marco Island Advances in Genome Biology and Technology meeting was heavily tweeted and blogged about.  Pacific Biosciences unveiled their third generation sequencer. Ostensibly, it can sequence reads of 20,000 length, but the fraction of actual long reads in a run, and their quality is still a bit hazy. […]

Most common weaknesses of grant applications

I’ve been cleaning out my Gmail from attachment-emails recently. (Why do people continue to send me video files when there’s YouTube?) Anyhow, Mickey Kosloff sent me this. In this pic, form meet function, being concise and to the point, as a good grant application should be.