Displaying posts categorized under
Science
It has not escaped Twitter’s notice that the Watson & Crick paper is 60 years old today . Sorry, too busy to be really creative, so here is a repost from 2009. Think of it as a transposon. Short quiz and a movie for DNA day. 1) We celebrate DNA day because: a) Congress said so […]
Automated Function Prediction: Submit your abstracts by Saturday
By Iddo on April 15th, 2013
You have until Friday Saturday, April 20th to submit your abstracts to the Automated Function Prediction meeting, an ISMB 2013 Special Interest Group and CAFA: Critical Assessment of Function Annotations. Keynote speakers: Patricia Babbitt, University of California, San Francisco. Protein similarity networks: Identification of functional trends from the context of sequence similarity Alex Bateman, European Bioinformatics […]
Terrible advice from a great scientist
By Iddo on April 13th, 2013
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 […]
The power of single-cell genomics: the mysterious SR1 bacteria have a unique genetic code
By Iddo on March 29th, 2013
Thanks to Mitch Balish for calling my attention to this one. SR1 bacteria are not exactly a household name, even among microbiologists. They were first discovered in contaminated aquifers, and since then they were found to be also in animal and insect guts, as well as in human mouths. They are even suspected of being […]
Minor revisions only
By Iddo on March 29th, 2013
A new journal, Molecular Metabolism has the following policies: one week for reviews, and three possible outcomes only: Reject, Accept, or Minor Revision. Good for them on both decisions. Bonus: your editors are Mr. Blonde, Mr. Blue, Mr. Brown, Mr. Orange and Mr. Pink. And they are professionals (although they may not tip).
Announcement: Automated Protein Function Prediction Meeting
By Iddo on March 18th, 2013
The Automated Function Prediction, an ISMB 2013 Special Interest Group meeting and CAFA: Critical Assessment of Function Annotations. July 20, 2013, Berlin Keynote speakers Patricia Babbitt, University of California, San Francisco Alex Bateman, European Bioinformatics Institute Anna Tramontano, “La Sapienza” University, Rome. Key dates: April 20, 2013: Deadline for submitting extended abstracts posters & talks May […]
Some omics words we would like to see
By Iddo on March 13th, 2013
Advertisomics: environmental sequencing aimed at obtaining popular press coverage with little or no scientific value. Samples obtained from an environment otherwise not of microbiological interest. “Hey, did you hear they swabbed the car wheels in the building’s parking lot and found that the microbes all cluster by tire brand name?” Celebromics: sequencing the genome or […]
Critical Assessment of Genome Interpretation, 2013
By Iddo on March 13th, 2013
From the organizers of CAGI 2013. I have been to the Critical Assessment in 2010 and 2011, and even participated as an assessor. It’s a fun meeting, and if your work involves prediction of phenotypes from genotypes, there is still time (just about) to accept some of the challenges. The Critical Assessment of Genome Interpretation […]
The Black Queen Hypothesis
By Iddo on March 2nd, 2013
“Well, in our country,” said Alice, still panting a little, “you’d generally get to somewhere else — if you run very fast for a long time, as we’ve been doing.” “A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same […]
A Belated Valentine’s Day Post
By Iddo on February 16th, 2013
This is romantic! So listen up! A 3D heart shape may be drawn using the following implicit function: Or, in Python: def heart_3d(x,y,z): return (x**2+(9/4)*y**2+z**2-1)**3-x**2*z**3-(9/80)*y**2*z**3 Trouble is, there is no direct way of graphing implicit functions in Python. But anything can be found on Stack Overflow. Putting it all together: #!/usr/bin/env python from mpl_toolkits.mplot3d import […]
“The thing doesn’t fit is the most interesting”
By Iddo on February 15th, 2013
Richard Feynman passed on Twenty five years ago today. His legacy lies not only in physics, but (to more people perhaps), in his ability to communicate science, and the love of science. One of my favorite Feynman moments is in this video. I show it to students in a course section I teach about the […]
The scientific process
By Iddo on February 10th, 2013
Found on 9gag.com. EDIT: as pointed out by Jason McDermott, hypothesis should probably be used here instead of theory.
Life Stands on the shoulders of Giants (Viruses)
By Iddo on February 6th, 2013
Back to ancient life, what exactly defines life, and where does life end and non-life begin. One of my favorite subjects, and one of which I am the least knowledgeable. Doesn’t stop me writing about it though. Viruses are… well… not really life. Or so says common wisdom. They have some elements of life: a […]
A bit more on writing bioinformatic research code
By Iddo on January 21st, 2013
There has been a lot of discussion recently on this blog and others on the need for robust scientific software. Most of the discussion I have been involved in comes from bioinformaticians, because, well, I am one. There has been plenty of talk about code robustness, sharing, and replicability vs. reproduciblity. I do not want […]
Reproducible research software: some more thoughts
By Iddo on January 13th, 2013
So there was a lot written over the blogosphere, twittersphere and what-have-you-sphere about the to publish code in scientific research. The latest volley was fired from a post at biostars.org from “JermDemo” which also mentioned my post on making accountable research software by forming a volunteer “Bioinformatics Testing Consortium”. (My post, not my idea). I won’t […]