Data and materials availability All data necessary to understand, assess, and extend the conclusions of the manuscript must be available to any reader of Science. All computer codes involved in the creation or analysis of data must also be available to any reader of Science. After publication, all reasonable …read more
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I recently attended an NSF BIO directorate meeting about cyberinfrastructure needs. Here's a list of training & education challenges identified at that meeting:
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- development and adaptation of tools to archive data and metadata from diverse sources to enable data mining
- integration of structured and unstructured data from heterogenous data sources
- discussion …
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Here's a data analysis question for all you Big Data folk.
A beachcomber is interested in obtaining up to 10 examples of every type of shell present on a beach. The shells are individually easy to find, but some types are really rare and some are really abundant. The beachcomber …
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(Or, "A better way to publish bioinformatics.")
We just got word that our paper, "Scaling metagenome assembly with probabilistic de Bruijn graphs" [ arXiv ] [ github ] has been accepted for publication in PNAS. (Yay!) I just posted the final version to github, and the arXiv PDF should be updated to the third …
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At our 2012 course on Analyzing Next-Generation Sequencing Data, we talked quite a bit about future sequencing technologies, as well as about what analyses are reasonably cookbook (and which ones aren't).
Here are my thoughts -- yours welcome!
The basic conclusions about sequencing tech were these:
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I've just moved my blog over to Pelican, a static blog generator that takes in reStructuredText and spits out, well, this! I'm now using Disqus for commenting, too.
The main motivations for the move (apart from slightly better theming) were to escape dynamic-blog-land in favor of static-blog-land, while enabling a …
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About a year ago, I came across a really interesting Science paper entitled "Rapid and inefficient isolation of single cells from soil". In it, the authors -- from a well-known lab at UC Davis -- described how they used low-percentage agarose gels to extract thousands of individual cells from a soil sample …
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