Difference between revisions of "Workflow"
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A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [http://en.wikipedia.org/wiki/Bioinformatics_workflow_management_system workflow management systems] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [http://en.wikipedia.org/wiki/Graph_(mathematics)#Directed_graph graph], where each [http://en.wikipedia.org/wiki/Vertex_(graph_theory) node] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise. | A '''workflow''' in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special [http://en.wikipedia.org/wiki/Bioinformatics_workflow_management_system workflow management systems] has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed [http://en.wikipedia.org/wiki/Graph_(mathematics)#Directed_graph graph], where each [http://en.wikipedia.org/wiki/Vertex_(graph_theory) node] represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise. | ||
| − | With BioUML users can either run pre-defined workflows or create their own for specific analysis purposes. | + | BioUML provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes. |
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| + | ==Pre-defined workflows== | ||
| + | |||
| + | BioUML, and especially the [[GeneXplain]] platform, facilitates standard analyses through a number of pre-composed workflows concatenating some of the most important modules, which also allows users to start with their first analyses right away, even before having learned all sophisticated details of the platform. | ||
| + | |||
| + | With any workflow the following steps are normally taken: | ||
| + | * importing data into the project (if necessary), | ||
| + | * data normalization (if necessary), | ||
| + | * selecting the appropriate workflow, | ||
| + | * specifying the input file(s), | ||
| + | * parameters setting, | ||
| + | * specifying the output directory, | ||
| + | * running the workflow, | ||
| + | * viewing the output. | ||
| + | |||
| + | A few pre-defined workflows in BioUML workbench are available as example data (''e.g. '''Data''' tab in navigation pane > data > Examples > ChIPMunk workflows''). [[GeneXplain]] offers a somewhat richer choice of ready-made workflows with all the links launching them right from the start page. | ||
| + | |||
== See also == | == See also == | ||
* [[:Category:Workflows|List of workflows]] | * [[:Category:Workflows|List of workflows]] | ||
Revision as of 18:14, 18 April 2013
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A workflow in bioinformatics can be defined as a series of computational or data manipulation steps. To compose and execute such sequences a variety of special workflow management systems has been developed. All such systems are based on an abstract representation of how a computation proceeds in the form of a directed graph, where each node represents a task to be executed and edges represent either data flow or execution dependencies between different tasks. Each system typically provides visual front-end allowing the user to build and modify complex applications with little or no programming expertise.
BioUML provides a workflow management system, which is intuitively handled through a simple drag-and-drop interface. With BioUML-related products users can either run pre-defined workflows or create their own for specific analysis purposes.
Pre-defined workflows
BioUML, and especially the GeneXplain platform, facilitates standard analyses through a number of pre-composed workflows concatenating some of the most important modules, which also allows users to start with their first analyses right away, even before having learned all sophisticated details of the platform.
With any workflow the following steps are normally taken:
- importing data into the project (if necessary),
- data normalization (if necessary),
- selecting the appropriate workflow,
- specifying the input file(s),
- parameters setting,
- specifying the output directory,
- running the workflow,
- viewing the output.
A few pre-defined workflows in BioUML workbench are available as example data (e.g. Data tab in navigation pane > data > Examples > ChIPMunk workflows). GeneXplain offers a somewhat richer choice of ready-made workflows with all the links launching them right from the start page.
