Just submitted this on Thursday:
Next generation sequencers are beginning to impact agricultural biology. Over the next few years, next generation sequencing will produce incredibly large datasets that will address structural (e.g., SNPs, CNVs, indels, methylation, translocations) and functional (e.g., RNA expression, transcription factor binding sites) variation in …read more
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As part of a CiSE submission I'm working on, I interviewed the lead developer on a scientific software package today. This software package is mainly used for evolutionary studies, and has a small but devoted following - ~6 developers and ~12 users locally, plus a few dozen users outside of MSU …
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John Gall apparently said:
A complex system that works is invariably found to have evolved from a simple system that worked. The inverse proposition also appears to be true: A complex system designed from scratch never works and cannot be made to work. You have to start over, beginning with …read more
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I recently had the pleasure of being the technical reviewer for a new Apress offering, Beginning Python Visualization, by Shai Vaingast.
To quote from the apress page,
read moreWhat you'll learn:
- Write ten lines of code and present visual information instead of data soup.
- Set up an open source environment ready …
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The decision of python-dev to deprecate bsddb has left us in a bit of a pickle (hah!) over in the pygr project. We're looking for a replacement for bsddb for default storage of infrequently- (or never-) changed pickled Python objects. Some of the parameters under consideration are:
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- Python version availability …
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The latest hot shit idea for making a protein-protein interaction database leaves me lukewarm.
A few months ago I met with a genomics group, and we had a back-and-forth about genome annotation. The conversation went something like this:
them: "We have to improve the tools for annotating un-annotated genes!" me …read more
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We're going through the PyCon '09 review process, and participating in the process has been pretty interesting. (I joined the Program Committee in large part because I was told to put up or shut up after I critiqued PyCon '08. Ahh, the open source world... where you're encouraged to go …
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