RE: Archiving .fcs Data

Saving raw FCS files on a server isn't probably going to do a lot of
good two years from now unless you do a good job tracking the meta data
about the FCS files and the experiments they represent. You could
probably parse some of this information users will need to find the
files they want from the FCS header, assuming users are putting the
information they need there in a controlled fashion, but I would
advocate a more standardized approach. 

 

Depending on your needs, maybe something like the Free/Open Source Flow
Cytometry Laboratory Management System (flowLIMS) would be of interest. 

http://bioinformatics.fccc.edu/software/OpenSource/flowLIMS/flowlims.sht
ml 

 

It may also not be the case of "if you build it they will come". In my
experience, researchers tend to resist any extra work in annotating
their data to ease later retrieval, even if it could make their lives
(and their bosses lives) easier down the road in case they do need to
look at data from a critical experiment again and the original samples
are gone so can't be re-run. Unless there is buy-in from PIs from the
labs to enforce compliance,  the best intentions of the IT users group
won't mean anything to the biologists that just want to get on with
their experiments.

 

Best,

Ryan

 

Ryan Brinkman, PhD

Terry Fox Laboratory, British Columbia Cancer Research Centre

Assistant Professor, Medical Genetics, University of British Columbia

675 West 10th Avenue

Vancouver, BC V5Z ALL

Tel: (604) 675-8132

http://www.terryfoxlab.ca/

 

 

From: Robert Wadley [mailto:rbwadley@hotmail.com] 
Sent: Sunday, April 27, 2008 11:59 PM
To: cyto-inbox
Subject: Archiving .fcs Data

 

Dear Flow-ers,
 
I have been asked to gather a consensus about what to do with data.
 
I have always preferred to say it is the responsibility of the user to
save & store/archive their own data.
 
However, the IT users group here are suggesting that there should be
some sort of formal archiving.
 
I am currently working with my IT department to create a Cytometry
mini-server.  All the data generated from the Calibur, LSR II, Aria,
Fluostar, Confocal, and the fluorescent microscope would be saved to the
server. and the server would be backed up at regular intervals.  User's
would then extract their data from the server for saving, analysis or
other manipulation.  Presumably any archiving would be via the
mini-server too.
 
What do other research labs do?  
 
I know many have a similar approach to me - its all up to the user.  One
lab I visited simply trashed data when their drives were full,
automatically assuming the users had backed-up.  This is probably a
little too harsh!!
 
Regards
 
Rob Wadley
Cytometry & imaging Suite
MMRI
Brisbane. Australia

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