Genomics use cases


#1

I am evaluating SciDB for some bio-science/genomics use cases (we are building software/database “infrastructure” for high throughput sequencing at UNC-Chapel Hill), and I have been working my way through SciDB. I was wondering if there are papers or other documentation available about the specific application of SciDB to genomics, or if others are working in this area and would be willing to share their experiences.

Nassib


#2

I am also writing a paper about the application of SciDB to earth remote,but there are little relevant documents too. :frowning:


#3

Nassib & pingorya,

Thanks for the note.

First, there’s a small immediate, practical problem here. We (the SciDB core team) are actually working with a large pharma company on a genomics application. But for a number of reasons–chiefly, they don’t want us to talk about it–we can’t say a great deal.

And there are other, more general problems. The SciDB engine (in it’s current form) is only 6 months along, so not many people have had a chance to try it out on the problems your pointing it at. And second, we’re mostly DBMS hackers, not geographers or Bio-IT types. So we’re a bit tongue-tied when it comes to proposing solutions and ideas in spaces that lie a long way outside our comfort zone or area of expertise.

Perhaps it would be best if you could try us with some specific questions; describe the application, the data you’re looking at, the problems you’re addressing, and so on. Then we can explain how SciDB fits (or doesn’t).

KR
Pb