Abstract
BackgroundThe power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms.DescriptionThe Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at ConclusionsOur development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data.
Highlights
The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms.Description: The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux
Oracle to PostgreSQL Once LAD was fully operational on Linux we undertook its migration to an open-source relational database that could support all the features that LAD required, such as support for transactions, foreignkey integrity constraints, indexes, and sequences
We plan to add MAGE-ML export capability such that data can be readily exported from LAD into other analysis programs that conform to the MIAME standard of data representation
Summary
Microarray experiments in all forms produce a great quantity of data. In addition to the primary microarray data, details about the biological samples that were analyzed must be correctly recorded and archived. Oracle to PostgreSQL Once LAD was fully operational on Linux (powered by Oracle) we undertook its migration to an open-source relational database that could support all the features that LAD required, such as support for transactions, foreignkey integrity constraints, indexes, and sequences. The Linux-supported, open-source relational database that met these requirements was PostgreSQL http://www.post gresql.org. PostgreSQL is an advanced open-source object-relational database management system that supports most SQL constructs These constructs include transactions, triggers, stored procedures, subselects, and user-defined types and functions. The use of PostgreSQL greatly reduces the level of complexity required to run a production microarray database due to the ease with which it can be installed and maintained This opens up the possibility of a larger community of developers becoming involved with a proven array data warehouse. In essence users are not restricted to LAD tools for analysis and may only utilize its intrinsic data loading capabilities while analyzing microarray data via custom-developed algorithms and interfaces
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