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Directories of Bio-data

These bio-data directory construction tools are based on LDAP for a computable, networked search/retrieval of bio-data objects (as opposed to flat file databanks or web pages). This test sample includes an experimental LDAP-SRS gateway for query and retrieval of bulk biodata via the Lightweight Directory Access Protocol (LDAP).

LDAP has several features favorable for data-grid computing including: efficiency with large numbers and volumes of objects, public standard query syntax that is based on shared schema, and mature software protocols and systems that include security, binary encoded transport, flexibility in employing multiple backend data servers (RDMBS, Berkeley-DB, Perl and Shell tools), where new ones (like the bioinformatics data search standard SRS) can be added with relative ease.

Directory Services Talks Software

Tests have been focused mainly on looking at efficiency of this for use in distributed (grid) computing. The general idea being for useful grid computing w/ biodata, one needs to be able to select and move quantities in the order of 100K - 1000K records, 1GB - 10 GB in size, to many computers quickly enough to make it better than running the computation on one central server. Though work remains to make this widely usable, those who are interested in testing SRS over LDAP can use it as a starting point.

The software here is experimental, a work in progress (July 2002).
For further information, please contact Don Gilbert (gilbertd@bio.indiana.edu)