(updated to point to http://arxiv.org/).
Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
Abstract:
The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we …read more
There are comments.
I'm writing this on my way back from Stockholm, where I attended a workshop on the 4th Paradigm. This is the idea (so named by Jim Gray, I gather?) that data-intensive science is a distinct paradigm from the first three paradigms of scientific investigation -- theory, experiment, and simulation. I was …
read moreThere are comments.
(and some related thoughts on reproducibility in computational science)
In a recent news article on the "data deluge" in biology, I was quoted as saying "It's not at all clear what you do with that data. Doing a comprehensive analysis of it is essentially impossible at the moment." So, naturally …
read moreThere are comments.
This blog post was inspired by two recent events.
First, in response to a NY Times article about the "data deluge" affecting biologists, one of my Facebook friends said something like "stop whining about how hard it is to analyze the data and do some good experiments instead!" I vehemently …
read moreThere are comments.
I'm just on my way back from a JGI workshop on metagenome informatics, and I thought I'd take the opportunity to write up a short review.
The workshop was, frankly, excellent. We saw a bunch of talks on metagenome assembly (my current interest) as well as single-cell sequencing approaches, and …
read moreThere are comments.
As sequencing gets cheaper and cheaper, one would expect the answer for how to best sequence (and assemble!) any given genome would change. Most biologists assume something along these lines: everyone else has achieved some standard coverage (say 10x, or 100x) for their genome, so all we need to do …
read moreThere are comments.
There's been a lot of hooplah in the last year or so about the fact that our ability to generate sequence has scaled faster than Moore's Law over the last few years, and the attendant challenges of scaling analysis capacity; see Figure 1a and 1b, this reddit discussion, and also …
read moreThere are comments.