Difference between revisions of "Workflow"

Revision as of 16:00, 19 April 2013

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 (see the list of workflows below) with all the links launching them right from the start page.

Creating your own workflows

To create a new workflow in BioUML workbench you first need to go to the Data folder (or a subfolder within) of your project in which the new workflow will be stored (e.g. Data tab in navigation pane > data > Collaboration > test project > Data folder). As soon as you click on the Data folder in the navigation pane, a number of operation icons appears in the navigation toolbar. The names of the operations are shown as tooltip text (just place the mouse pointer over an icon). Click on the New workflow option.

To create a workflow in geneXplain go to the Start page and click Create your own workflow under the list of pre-defined workflow groups.

At this point you will be asked to specify the name of the new workflow in the pop-up dialog box. Here you can also choose a different location to save the workflow by navigating the directories tree and creating (sub)folders.

As you press Ok in the dialog box, a new tab opens in the workspace, where you can design a new workflow diagram. The workflow diagram represents different analysis functions being connected by input and output files. The resulting directed graph visualizes the sequence of analysis steps in the workflow. The diagram also may contain parameters, which are to be defined by the user.

You can add nodes to the graph by dragging and dropping items directly from the Analyses tab of the navigation pane (Analyses tab > analyses > Methods > ...) or by using the toolbox within the tab. The toolbox contains icons for such types of nodes as analysis methods, analysis parameters, analysis expressions, cycles and analysis scripts as well as for the Select tool, directed edges, notes and note edges. To add a node from the toolbox click first on the icon, then within the workspace, set parameters in the Create new node dialog box and press Ok - the node will appear in the graph. To add an edge just click on the icon in the toolbox, specify the output and input nodes in the Create new edge dialog box and press Ok.

Upon clicking on any component of the workflow you can see the information about this particular element in the operations field below.

Six steps to compose a simple workflow

Complex workflows

Cycles and scripts

See also

• List of workflows