2010 Best Practices Competition IT & Informatics HPC

Published Resources for the Life Sciences
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reduces the amount of data users must enter, reduces errors and facilitates integration with
results from other assay platforms. HCS Road enables new types of experiments that were
not supported by our previous data management tools, including 1536-well HCS assays
and cell cycle analysis based on DNA content measures for individual cells. HCS Road
provides a single source for data from Cellomics Arrayscan, GE InCell and Evotec Opera
instruments. Finally, HCS Road facilitates the sharing of assays and analysis tools
between groups. Users can review assay data from other groups, determine whether a cell
line or fluorescent probe has been used before, and see how a hit from their assay
performed in previous experiments.
The data management solutions we implemented allow us to handle the large volumes of
data that HCS generates. Database partitioning reduces backup times and improves query
performance; network attached storage systems enable the storage and management of
large numbers of images; and the use of file-based storage with transient database loading
for cell level data allows us to analyze this unique result type while minimizing database
size.
CONCLUSIONS.
Successfully developing an enterprise-wide data management system for HCS results
presents challenges. The diversity of instruments, users and projects begs the question of
whether it is better to develop isolated systems tailored to the requirements of a single
group or instrument type. We concluded that the benefits of an integrated system were
worth the effort required. HCS Road currently supports multiple imaging platforms and
research groups and provides a single point of access for results and experimental
annotation. It facilitates the sharing of assays and data analysis methods between groups
and provides a rich and structured model for annotating cell-based assays.
We chose to develop our own system for HCS data management so that we could
accommodate our needs and workflows and could integrate it with other enterprise
databases. A consequence of this integration is that no two organization’s solutions will
look exactly the same. Large organizations will wish to accommodate their existing
workflows and databases whereas smaller organizations may need to implement some of
those functions within their HCS data management system. We believe that the
requirements and solutions we identified will be informative to other HCS users looking to
develop or purchase their own data management solution.
The system was built using technologies by multiple vendors who made several updates to
their architectures to make optimize the performance and reliability of the solution. The