Forum:How do you manage a large number of samples ( storage, analysis,...) ?

Question

[Nicolas Rosewick]

Hi,

An open question : How do you manage a large number of samples in term of storage ( fastq, bam, vcf, ... ), of directory structure, DB, ... ? When the number of samples becomes big, it can be though to manage this in a clear and efficent way. Multiple species, multiple people have access to the data, etc...

So for you, what is the best way to manage this?

[Pierre Lindenbaum]

see How Do You Manage Your Files & Directories For Your Projects ?

Answer 1

[gyz151]

I have been using Google Spreadsheet for logging and sharing multi-species, specimen, taxonomic, and various other kinds of data. There are ~10 users involved. See: https://docs.google.com/spreadsheet/ccc?key=0Aoac4TcHWbdndER2Tml4S1lBZkNIdkExdEhoU3llU0E#gid=0

For physical specimens/DNA extracts, I standardize the workflow and I manage or closely monitor individual projects (currently more than 4).

[Pierre Lindenbaum]

... as long as it works....

[Jean-Karim Heriche]

...and you don't have to deal with privacy/security issues...

Answer 2

[Alex Reynolds]

LIMS - Laboratory Information Management System

[Pierre Lindenbaum]

See also Is there a Lims that doesn't suck? ;-)

[Alex Reynolds]

Our lab has a custom-built LIMS built off a Django stack. It works for us. I think we were doing the Google Spreadsheet thing until it became too unwieldy to do reports. No LIMS will be perfect out of the box, I'd think, since each lab will likely have a particular research focus that requires customization.