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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As part of the 2012 Analyzing Next-Generation Sequencing Data course, I've been trying out ipython notebook for the tutorials.
In previous years, our tutorials all looked like this: Short read assembly with Velvet -- basically, reStructuredText files integrated with Sphinx. This had a lot of advantages, including Googleability and simplicity; but …
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I just returned from a NESCent Catalysis meeting on Cephalopod Genomics. I was invited as a bioinformatics and genomics guy, and so I spent four days in North Carolina talking about the opportunities and challenges of sequencing cephalopods.
Cephalopods are a class of the molluscs, and include squid and octopus …
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This is a draft proposal of a policy to encourage pre-publication data release and data sharing within a community. This policy is based on discussions at the Cephalopod Genomics Workshop (a Catalysis workshop sponsored by NESCent).
Note, this is made available under a CC-BY-SA license permitting use and re-use with …
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