Software

High-throughput bioinformatics with the Cyrille2 pipeline system

Mark WEJ Fiers , Ate van der Burgt , Erwin Datema , Joost CW de Groot and Roeland CHJ van Ham

Applied Bioinformatics, Plant Research International, PO Box 16, 6700AA Wageningen, The Netherlands

author email corresponding author email

BMC Bioinformatics 2008, 9:96doi:10.1186/1471-2105-9-96

Published:	12 February 2008

Abstract

Background

Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible.

Results

We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1) a web based, graphical user interface (GUI) that enables a pipeline operator to manage the system; 2) the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3) the Executor, which searches for scheduled jobs and executes these on a compute cluster.

Conclusion

The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.