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The power of single-cell genomics: the mysterious SR1 bacteria have a unique genetic code

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

  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

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

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

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 […]

Adding supplementary tables and figures in LaTeX

A problem I encountered now, when revising a paper and adding a supplement per the editor’s request. How do I number my tables and figures as Table S1, S2 etc.? A solution was provided in Stackexchange, but the syntax was not good for my version of LaTeX, and I don’t like \makeatletter (here’s why). Here […]

The Black Queen Hypothesis

“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

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”

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

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)

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

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

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 […]

Group review, continued

I love it when other people use my ideas, especially before I think them up. After my previous post advocating group review of scientific articles, it was pointed out to me that two journals are already using group reviews to referee their papers. One is Frontiers (which is a collection of journals, rather than a […]

Group review of papers?

So I’ve been catching up on my paper reviewing duties this weekend. To those outside the Ivory Outhouse, “reviewing a paper” means “anonymously criticizing a research article considered for publication in a scientific journal”. (For those of you familiar with the process, you can jump to the text after the first figure.) Here’s how science […]