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Biology

Microbial marketing

An original viral (or rather, fungal and bacterial) marketing campaign for the movie Contagion. Although the film tells the story of a fictional viral outbreak, the marketers of Warner Brothers Canada kept it in the realm of microbiology by teaming up with 25 microbiologists and creating what is probably the first agar-plated billboard, which they […]

Friday fun story: extreme bug hunting on MIRA

MIRA is a really cool sequence assembly software, developed and maintained by Bastien Chevreux. MIRA has a large and active community, led by the funny and gracious Bastien, for whom no problem is too small, or too large. Recently MIRA seemed to have developed a stochastic bug, one of those which are a serious headache […]

Postdoc positions available at Rutgers University

Postdoctoral Research Scientist Rutgers University Joint Appointment: Institute of Marine and Coastal Sciences, BioMaPS and Dept. of Biochemistry and Microbiology Two 2-3 year Postdoctoral Research Scientist positions are available. We are looking for young scholars with experience in the areas of computational biology. In the scope of this project, we will uncover how the metal-containing […]

Of Mice and Men or: Revisiting the Ortholog Conjecture

I  have posted quite a few times before about the acquisition of new functions by genes. In many cases a gene is duplicated, and one of the duplicates acquires a new function. This is one basic evolutionary mechanism of acquiring new functions. Sometimes, gene duplication occurs within a species: part of the chromosome may be […]

Short bioinformatics hacks: merging fastq files

So you received your mate-paired reads in two different files, and you need to merge them for your assembler. Here is a quick Python script to do that. You will need Biopython installed.   #!/usr/bin/env python from Bio import SeqIO import itertools import sys import os # Copyright(C) 2011 Iddo Friedberg # Released under Biopython […]

Tweets from AFP/CAFA 2011

The AFP/CAFA 2011 meeting was held on July 15 and July 16. Yes, it was a huge success, and I’m not just saying that beacuse I am one of the organizers.  I will write up something more comprehensive soon; in the meantime, here are my tweets from the meeting. I am learning a lot about […]

ISMB 2011 tweets

ISMB this year had quite a few twiterrers. Hashtag: #ISMB. I tried to collect all the #ISMB tweets, so I wrote my own twitter scavenger script, but it seems to go only 3 days back.  I am not sure if this is a Twitter feature, or something with the library I am using (tweepy) or […]

CAFA Update

Nearly a year ago, I posted about the Critical Assessment of Function prediction with which I am involved. The original post from July 22, 2010 is in the block quote. After that, an update about the meeting which will be held in exactly 2 weeks. The trouble with genomic sequencing, is that it is too […]

Suggest a name for the next BIG journal

The Max Planck society, Howard Hughes Medical Institute and Wellcome Trust have announced their plans for a new journal for biomedical and life science research to be launched summer 2012. From the joint press release: The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as […]

Zombie science roundup

  I am fascinated with zombies. Always have been, but even more so since I took an interest in microbiology. The zombie apocalypse is the best known and best chronicled viral infection which hasn’t happened. But it could happen any day, so stock up on non-perishable food, medical supplies, water purification tablets, chainsaws, machetes, baseball […]

Life is not a tree, it’s more of a…

  OK, I think the tree of life is obsolete. I have been spending a lot of time looking at horizontal gene transfer, reading about it, looking at it in genomes until my eyes water and my brain dessicates, occasionally blogging about it and soon to be publishing about it. Life is not a tree. […]

Shavuot is a microbial holiday

  Tonight is Shavuot. That wonderful holiday which includes midnight studies, water-bombing and dairy products. Mmmmm…. cheese. A food product heavily embedded in the science of microbiology. Cheese is the founding product of the biotech industry (along with beer and bread). So here’s to Lactobacilli and Lactococci which are at the center of the production […]

In defense of ‘prokaryotes’

Fine, I get it. “Prokaryotes” is a wrong taxonomic term. It’s wrong to lump bacteria and archaea together. That would be like saying “eutoichic” to lump all bacteria, archaea, plants and fungi together because they have cell walls. (“τοίχος” =wall in Greek. My Google Translate-foo is STRONG!)  Still, there are so many things in common among […]

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 […]

Psychedelic Monday: Sploosh!

Music: Ozric Tentacles. Featuring marine life. Mix by Bonci. Highlights: 0:33 Dolphin chasing ring bubble 2:02 Humpback(?) tailfin 2:58 Whale shark swimming with dolphins 3:44 & 4:07 Humpback baleen-syncing 4:11 Manta Ray 5:58 Human and dolphin kiss