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