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The LabBase system for data management in large scale biology research laboratories
N Goodman1, S Rozen, L D Stein
1The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609-1500, USA, Whitehead Institute for Biomedical Research, Cambridge, MA, USA. nat@jax.org
Motivation:
The development of laboratory information management systems (LIMSs) for large scale biology research projects can be a challenging problem. Many such projects generate complex datasets via complex procedures that undergo continuous refinement. A key software challenge is to simplify the database-development task so that databases can be built and modified quickly enough to keep pace with changing project-requirements.
Results:
LabBase extends the facilities offered by relational database systems to simplify the task of creating databases for large scale biology research projects. LabBase provides a structural object data model, similar to ACEDB, and adds to this the concepts of Materials, Steps, and States: Materials are objects representing the identifiable things that participate in a laboratory protocol; Steps are objects reporting the results of a laboratory or analytical procedure; and States are objects denoting places in a laboratory protocol. The system provides a data definition language for succinctly defining laboratory databases, and operations for conveniently storing and retrieving data in such databases. The system also provides support for workflow management. LabBase is implemented in Perl5 and provides a natural interface for laboratory application programs written in Perl.
Availability:
The software is freely available. Contact the authors.
Contact:
nat@jax.org