Hello,
I'm trying to figure out if there's an existing system that does what I'm looking for before I go and try to build my own. I'd like to put together a data management system for microarray and sequence datasets, that can be used to store sample annotation, raw data (microarrrays), analysis results (DE gene lists, QC info, PCAs, etc), and other notes. We're not a core and don't have our own sequencer so we don't need the workflow tracking features of most genomics LIMS. We've got over 1000 CEL files sitting in a folder, and desperately need to start associating metadata with them.
I've checked existing relevant threads on this at multiple bioinformatics community sites. Most recently I've looked into BASE and Gnomex, as well as considered using a wiki for the purpose. I don't think a wiki would be quite the right fit. The BASE UI is a little too complex and I think it would scare off our biologists who also want to be able to see what samples we have run. Gnomex could work, but the UI is flash-based, which might cause some issues in the future, since flash is generally being phased out in favor of HTML5. Also, while I like the general organizational scheme that Gnomex uses, it seems like it would get confusing with a lot of attachments to an experiment, or a lot of experiments.
We're not completely averse to commercial solutions- I requested a quote/demo of GeneSifter also- but free/open source is always an easier sell.
Is there anything that I've missed somehow? I just want to make sure I didn't overlook a good solution before I spend a few months building something new (or customizing something like Galaxy).
Thanks!
Does GEO suits your need?
GEO would not be appropriate- we don't intend to make all the data public, and it's not possible to associate analysis results.