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High-throughput bioinformatics with the Cyrille2 pipeline system.

Fiers MW, van der Burgt A, Datema E, de Groot JC, van Ham RC - BMC Bioinformatics (2008)

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

View Article: PubMed Central - HTML - PubMed

Affiliation: Applied Bioinformatics, Plant Research International, PO Box 16, 6700AA Wageningen, The Netherlands. Mark.Fiers@wur.nl

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.

Show MeSH
The Cyrille2 system architecture. Main architectural layers are numbered (1–4). See the text for further description.
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Figure 2: The Cyrille2 system architecture. Main architectural layers are numbered (1–4). See the text for further description.

Mentions: The Cyrille2 system architecture is composed of four distinct layers (Figure 2). Layer 1 comprises the main functional and core software components. These core components make extensive use of a modular application programming interface (API) (layer 2). The API allows unified access to three system databases (layer 3). The biological database and the end-user interface that connect to it are third-party systems that can be integrated with the Cyrille2 system (layer 4). To allow tracking and debugging of a pipeline in operation, a centralized status and logging system is implemented. This provides a pipeline operator access to detailed information on the status of a pipeline run and errors that might have occurred.


High-throughput bioinformatics with the Cyrille2 pipeline system.

Fiers MW, van der Burgt A, Datema E, de Groot JC, van Ham RC - BMC Bioinformatics (2008)

The Cyrille2 system architecture. Main architectural layers are numbered (1–4). See the text for further description.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2268656&req=5

Figure 2: The Cyrille2 system architecture. Main architectural layers are numbered (1–4). See the text for further description.
Mentions: The Cyrille2 system architecture is composed of four distinct layers (Figure 2). Layer 1 comprises the main functional and core software components. These core components make extensive use of a modular application programming interface (API) (layer 2). The API allows unified access to three system databases (layer 3). The biological database and the end-user interface that connect to it are third-party systems that can be integrated with the Cyrille2 system (layer 4). To allow tracking and debugging of a pipeline in operation, a centralized status and logging system is implemented. This provides a pipeline operator access to detailed information on the status of a pipeline run and errors that might have occurred.

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

View Article: PubMed Central - HTML - PubMed

Affiliation: Applied Bioinformatics, Plant Research International, PO Box 16, 6700AA Wageningen, The Netherlands. Mark.Fiers@wur.nl

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.

Show MeSH