Forum: How do you manage a large number of samples ( storage, analysis,...) ?
1
gravatar for Nicolas Rosewick
4.5 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

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 ?

hts forum samples • 1.8k views
ADD COMMENTlink modified 4.5 years ago by Alex Reynolds28k • written 4.5 years ago by Nicolas Rosewick7.9k

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

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum121k
0
gravatar for gyz151
4.5 years ago by
gyz1510
United States
gyz1510 wrote:

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).

ADD COMMENTlink written 4.5 years ago by gyz1510

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

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum121k
1

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

ADD REPLYlink written 4.5 years ago by Jean-Karim Heriche20k
0
gravatar for Alex Reynolds
4.5 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

LIMS - Laboratory Information Management System

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Alex Reynolds28k

see also Is There A Lims That Doesn'T Suck? ;-)

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum121k

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.

ADD REPLYlink written 4.5 years ago by Alex Reynolds28k
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