Re: Creating a database of FCS files

Thanks Marty.
It's good to hear this is being formally worked on as it's a tricky
concept that needs to be addressed from many sides. I'm speaking of
research as well as clincal cytometry. 21 CFR Part 11 is the direction
we industry types are heading. 

I would ask or as I do so often, beg or whine (depending on your
perspective), instrument manufacturers to get involved in this process.
Personal communications have indicated they are heading in that
direction, hopefully we'll see or hear of something new at ISAC. Summit
(DakoCytomation) has database functional integration and is the only Co.
so far that I know with that capability.

Offline analysis packages, my choice for data
analysis/presentation/compensation/transformation etc..., have the
capabilities to export data directly or easily by copy and paste in the
form of spreadsheets or tables. I have in the past relied on the help of
Bioinformatics gurus to parse and script (I vaguely know what this
means) the spreadsheet created to search for statistical significance. I
used to work on a rather large project involving tracking patient
populations over time and treatment regimine where we were in the range
of a 50k line spreadsheet. Anyone blessed with the ability to tweak
Excel could do the same analyses or comparisons rather easily.	I use
FlowJo religiously, and I have heard other Co's working with WinList
databasing with success, but that doesn't rule out others like FCS
Express etc...

There are database analysis packages available that should be able to
help, once the data is in spreadsheet form. You still need to do the
manul FACS compensation and analysis though...at least for now.

Hope this helps further the discussion.
Chris

Chris Groves
Wyeth Research
200 CambridgePark Drive
Cambridge, MA 02140
617-665-5539
cjgroves@wyeth.com

>>> Marty Bigos <mbigos@gladstone.ucsf.edu> 4/27/2004 12:05:04 PM >>>
Hi Adrian -

The need of a management system for flow cytometry (as well as 
microscope image) data has been apparent for quite some time. Not 
only would it help in the research aspects you mentioned, it could 
also provide many other functions, such as secured sharing of data, 
easy availability from any networked site,  etc.

For several years I have been fortunate to be involved with Bill Hyun 
of UCSF through an SBIR with a local software company in SF (Biotrue, 
Inc.) to develop such a system. We are in beta test now.

The product, (which doesn't have a formal name yet, but is informally 
called RDMS - Research Data Management System), will be announced at 
the ISAC meeting at the end of May. Biotrue will have a booth there 
to give demos of the product, and I will be giving a workshop talk on 
some of the ideas behind its design.

I do have a (small) financial interest in Biotrue, but even if I 
didn't I would recommend that you look at the product as a possible 
solution to your needs. You can contact Jenny Liu (JLiu@Biotrue.Net) 
for more information.

Marty
Marty Bigos
Director, Flow Core
Gladstone Institute of Virology and Immunology
Building 3 SFGH Rm 509
415-695-3832

>Hi all,
>
>Some of the users here have raised the desirability of having a 
>database of all the FCS headers from all their data files. They 
>could then, for example, search for all the files/experiments in 
>which they used a particular stain etc.
>
>Is anybody doing this? Would this be something that other people 
>would find useful?
>
>I would love to set something up but I don't have the requisite 
>skills or time at the moment.
>
>As a temporary measure I suggested they export the FCS header info 
>from FlowJo using using a table and then compile them all in another 
>program like excel. This works for a few experiments but it needs to 
>be automated (and easy) if it is going to be generally applicable.
>
>Any comments or suggestions?
>
>Adrian Smith
>Centenary Institute of Cancer Medicine and Cell Biology
>Sydney, Australia


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