TL;DR: NIH are scaling back funding on model organism databases, which will degrade annotation quality. This can have far-reaching implications in many aspects of biology and computational biology. There’s a letter you can sign electronically, please do. <http://www.genetics-gsa.org/MODsupport> I am hoping to write a more detailed post on why this is important, but for the […]
Starting June 1, 2015, my lab is moving to Iowa State University in Ames, Iowa, and I’m very excited about this. I’ll be joining a growing cohort of researchers as part of a presidential “big data” hire the university has started a year ago. The research environment is superb, and there are some great bioinformaticians and genomics […]
If you haven’t read the transcript of Sean Eddy‘s recent talk “On High Throughput Sequencing for Neuroscience“, go ahead and read it. It’s full of many observations and insights into the relationships between computational and “wet” biology, and it is very well-written. I agree with many of his points, for example, that sequencing is not […]
A question to genome annotators out there. I need a simple genome annotator for annotating bacteriophage genomes in an undergraduate course. Until now, we used DNAMaster but for various reasons I would like to move away from that. Here’s what I need for class: 1. Annotate a single assembled linear chromosome, about 50,000 bp, 80-120 genes, no […]
I recently applied for a Moore Foundation grant in Data Science for the biological sciences. As part of the pre-application, I was asked to choose the top 5 works in data science in my field. Not so sure about data science, so I picked what I think are the most influential works in Bioinformatics, which […]
One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact […]
WikiProject Computational Biology/ISCB competition announcement 2013 The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology. A key component of the ISCB’s mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at […]
Yesterday I received an email from Kristjan Liiva, a student at RWTH Aachen University Germany. Kristjan has developed a really cool dashboard to analyze and visualize the development of collaborative OSS projects by mining their mailing lists and software repositories. (If the link doesn’t work, try again later; the project is heavily under development). The […]
The state of biology today: Our main problem is turning these DNA data into useful information. Finding genes and other functional genomic element, characterizing them, understanding their function and their impact on Life – all these are challenges that will remain with us for a long time, and which have revolutionized biology into the […]
A new paper from my lab and Patsy Babbitt’s lab in UCSF has recently been published in PLoS Computational Biology. It is something of a cautionary tale for quantitative biologists, especially bioinformaticians and system biologists. Genomics has ushered biology into the data rich sciences. Bioinformatics, developing alongside genomics, provided the tools necessary to decipher genomic […]
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 […]
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 […]
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 […]
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 […]