Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 364905
Title High-throughput bioinformatics with the Cyrille2 pipeline system.
Author(s) Fiers, M.W.E.J.; Burgt, A. van der; Datema, E.; Groot, J.C.W. de; Ham, R.C.H.J. van
Source BMC Bioinformatics 9 (2008). - ISSN 1471-2105 - 10 p.
DOI https://doi.org/10.1186/1471-2105-9-96
Department(s) PRI Bioscience
Bioinformatics
EPS-4
Publication type Refereed Article in a scientific journal
Publication year 2008
Keyword(s) workflows - services - tool
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.
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