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The development and production management team


Published on 9 March 2020
Bioinformatics Rules Driven System (BIRDS)

The volume of the data generated by the new sequencing technologies is constantly increasing. It is therefore increasingly necessary to automate the processing and concatenating of the data. In response to that need we are developing a Bioinformatics Rules Driven System (BIRDS). 

BIRDS is advantageous in several respects:

  • BIRDS only triggers processing when the requisite resources are available. A resource may be a file, database, URL, etc.
  • BIRDS uses the Jboss Drools search engine to initiate and concatenate processing. Use of the search engine enables adaptation of each workflow on the basis of the downstream functional requirements. Moreover, incorporation of functional logic in the rules enables great flexibility with respect to implementation and simplifies maintenance.
  • BIRDS was designed from the outset to automatically manage a large number of processing operations in parallel and has the the capability of interacting with various types of computation cluster managers (LSF, SLURM, etc.). BIRDS is thus particularly suitable for production contexts.
  • BIRDS incorporates an error management system at each stage of the process, which enables initiation of actions as a function of the requirements of each workflow.
  • BIRDS retains a detailed history of processing operations and offers a web job management interface (status reports, re-initiation, etc.)