RE: Creating a database of FCS files

The FCS header files have already been parsed and stored in a database(1).
The product was QCTracker from Phoenix Flow Systems.

Experience with the development of that product was one of the reasons for
the creation of CytometryML. Since the data in a CytometryML file is all
validated XML, it can be imported without any changes into commercially
available databases, spreadsheets and other applications.  The list mode
data and associated index files are stored as a simple array of
records(structs), which can be read by commercially available common
programming languages or manipulated by .Net object.  

1. R. C. Leif, R. Rios, M. C. Becker, C. K. Becker, J. T. Self, and S. B.
Leif, "The Creation of a Laboratory Instrument Quality Monitoring System
with AdaSAGE". Advanced Techniques in Analytical Cytology, Optical Diagnosis
of Living Cells and Biofluids, Ed. T. Askura, D. L. Farkas, R. C. Leif, A.
V. Priezzhev, , and B. J. Tromberg.. A. Katzir Progress in Biomedical Optics
Series Editor SPIE Proceedings Series, Vol. 2678, 232-239 (1996).

2. R. C. Leif, S. B. Leif, and S. H. Leif, "CytometryML, An XML Format based
on DICOM for Analytical Cytology Data ", Cytometry 54A pp. 56-65 (2003).

3. R.C. Leif, S.H. Leif, S.B. Leif, CytometryML, a markup language for
analytical cytology, in Manipulation and Analysis of Biomolecules, Cells and
Tissues, D. V. Nicolau, J. Enderlein, and R. C. Leif, Editors, SPIE
Proceedings Vol. 4962 pp 288-297 (2003).

-----Original Message-----
From: Adrian Smith [mailto:A.Smith@centenary.usyd.edu.au] 
Sent: Thursday, April 22, 2004 6:57 PM
To: cyto-inbox
Subject: Creating a database of FCS files

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