Some software development plans for Davis

I've been thinking a lot about what I want to do at UC Davis, and I would like to announce the following plans:

  1. I hope to write new and better transcriptome and metagenome assemblers. The current assemblers are hopelessly bad and I think we can probably eke out a 1% improvement, at least, by starting from scratch.
  2. I've been very disappointed with the workflow systems that are out there, so for people that want to run our new assembler, we'll be packaging that with a new workflow management system.
  3. We'll also be developing a new Web site for running analyses of biological data. Galaxy may have market penetration, but I really dislike their default CSS, and I think my lab can probably do a better job if we start from scratch.
  4. Needless to say, I'll need my own physical cloud hardware to run it all. So I'm planning a considerable expansion of our lab's cluster. I think we can probably make a big impact by writing our own virtualization management software, too; the existing systems are written by amateurs like Amazon and OpenStack, after all!

The bad news is that after some serious consideration, I have decided not to invest in a new mapping program; on top of the above it's a bit too much. I think I trust Heng Li's bwa, for now; we may revisit in a few months.

I will be seeking large scale NSF, NIH, USDA, and DOE funding for the above. Let me know if you want to sign on!


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