The Uncanny Valley Every day, software appears to do more things that we thought were exclusively in the human realm. Like beating a grandmaster in chess, or carrying out a conversation. I say “appears” because there is obviously no self-aware intelligence involved, as this rather bizarre conversation between Cleverbots demonstrates. For humans, playing chess and carrying […]
I am finishing up a great weekend at HHMI Janelia Farm Research Campus. The occasion is an annual symposium celebrating the Phage genomics Course taking place in dozens of universities in the USA. Here are two of our students, Erich Goebel and Morgan Light, next to the poster they presented at the meeting: This post […]
Scientific Curator – Bioinformatics Interested individuals should apply on-line at www.jax.org/careers, referring to job posting #3256. Contact Jeannine Ross at ext. 6045 with questions. The incumbent in this position plays a critical role in data annotation and curation for the Gene Ontology (GO) and Protein Ontology (PRO) programs at The Jackson Laboratory in Bar Harbor […]
Here is a study that looked for a type of genes that the authors felt was neglected by classic genomic annotation. The research shows how to employed concepts in molecular evolution to validate the existence of these genes. Some background: the first question we ask after assembling a genome is: “where are the genes”? Not […]
Great meeting: Biocuration 2012, Georgetown University, DC. When I leave a meeting with my head exploding with new ideas and a need to try them all out at once, I know I got my money’s worth, and then some. Even a three hour flight delay followed by discovering my car with a dead battery […]
NSF grant funded, woohoo! Now I am hiring a programmer. So if you want to be part of a dynamic, growing lab, do lots of interesting stuff and upgrade yourself from just a great bioinformatician to a super-bioinformatician, this job’s for you. You’ll be working primarily on microbial genome evolution, including setting up a kick-butt […]
I just received an email from Julian Gough , one of last year’s CAFA participants. He started a Wikipedia initiative on protein function prediction, which are barely stubs at the moment. EDIT: He alerted me to the fact that protein function prediction has virtually no presence on Wikipedia. So all you protein function predictors out there, please contribute. Yes, […]
If you have a merged file of paired-end reads, here is a quick way to read them using Biopython: from Bio import SeqIO from itertools import izip_longest # Loop over pairs of reads readiter = SeqIO.parse(open(inpath), “fastq”) for rec1, rec2 in izip_longest(readiter, readiter): print rec1.id # do something with rec1 print rec2.id # do something […]
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 […]
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 […]
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 […]
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 […]
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 […]
