Computers and Software

COMPUTERS:

    The FACSCalibur and Vantage are operated by Macintosh Power PCs. The FACScans and FACStar still utilize HP computers, but these computers will be changed before the year 2000. Off-line PCs, Macs and HPs are also available for off line data processing. All computers are connected by local network.

    Because of the need to keep account records of use of this core facility, a user is issued a password on the computer and as long as that individual is using the facility the clock is running and keeping track of the time used. A record of time and cost can be returned to the user for each session.

    Network file access: In order to accommodate the increasing number of users we have optimized their throughput by providing file access over a computer network. Since data acquisition is usually quite rapid but data analysis can be time consuming, especially when more complex multiparameter analysis is performed, we have always analyzed data off-line. We also do not charge users for analysis time, so they can take as long as desired to evaluate their data. It has been our goal to allow the investigators to perform these analyses in the convenience of their own laboratory. They can access their files over the institute network or by "sneakernet".

COMPUTER SOFTWARE:

    The facility has available, for its users, nearly all of the current software used to analyze data. This availability is primarily the result of the facility Director’s interest in new approaches and the concomitant beta testing provided by our staff. This keeps this facility with the latest in software program development. The following data analysis packages are currently being used by facility staff and investigators.

Becton Dickinson Immunocytometry Systems

• HP FACScan Research Program: This was the original software provided by BDIS to acquire and analyze five parameter data using the FACScan. It is still used by many users to collect data.
• HP LYSYS II: This program has more advanced features than the FACScan Research Program and is used to collect and analyze data.
• CELLQUEST: This data acquisition and analysis program operates in the Macintosh environment. It represents the first significant software offered by any company for this computer environment. This program is basically the same as LYSYS II in its analysis capability.
• ATTRACTORS: This multiparameter automated data analysis program in the Macintosh environment represents the first major advance by any company in data analysis. This entirely new approach utilizes a pattern recognition methodology rather than gates and marker. While not a true clustering program, once the user has defined the populations of interest in the form of a template that can be saved, subsequent files of the same type are automatically clustered using the statistical information defined by the user generated template. Thus, one might term the program a user interactive cluster analysis program. No software we have tested can outperform the speed with which this program analyzes data once the template has been defined. Unlike other clustering algorithms, this program is not sensitive to cell cluster frequency and can resolve a subset containing 25 cells as easily as one containing 2500 cells.

• WHPPC and HP Reader: These two programs are at the heart of our computer network because they provide for the rapid conversion of data files from the HP environment into the PC environment. WHPPC is the network version and HP Reader is the floppy disc version.
• WinList: This multiparameter data analysis program incorporates a fast and efficient data analysis engine with extensive graphics capability for viewing the data. Because of the Dynamic Data Exchange capability of Windows, spread sheet and data base programs can be run in the computer background for instant data exchange with WinList. Because our users have PCs this is by far our most popular program.
• Modfit: This program is designed to analyze DNA histograms and it has advanced capabilities for aiding the user in handling debris and "sliced" nuclei often found in preparations from paraffin. The program automatically links to WinList so that combining immunophenotyping with DNA content analysis can take place simultaneously.

• Multicycle: This DNA analysis program is similar to Modfit in capabilities. This PC based program is also popular among users and some use both to compare results. This comparison can be informative when data quality is poor because each program uses somewhat different algorithms for DNA histogram analysis.

    MacLas or WinLas: Management Science Associates has been designing data analysis software that will seamlessly analyze data using both the conventional approach as well as in an automated fashion. The current program under development offers the user the ability to produce templates or a clustering algorithm to produce them. Unfortunately, the clustering is sometimes wrong, so the user can interface to correct the clustering error in the final template. Because there is jitter in data, a normalization algorithm is used to adjust the list mode file to that of a standard reference space. This approach is then applied to all subsequent data of the same type for rapid analysis. One major feature that is not available from anyone, as far as we know, is the ability to link similar subsets resolved with one combination of antibodies with the same subsets found with another combination by an iterative statistical process. Once fully implemented, a series of panels can then be combined and correlated statistically as if all of the antibodies were in the same tube. This will provide for the complete description of the patient’s immunophenotype.
 
   

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