Bioinformatics workflow management systems

A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a specific domain of science, bioinformatics.

There are currently many different workflow systems. Some have been developed more generally as scientific workflow systems for use by scientists from many different dissiciplines like astronomy and earth science.

Examples

* BioBike is a biocomputing platform based upon the KnowOS (Knowledge Operating System) e-science technology. Written entirely in Lisp, KnowOS's main distinguishing feature is "through-the-browser" programmability.
* DiscoveryNet is a £2m EPSRC-funded project to an e-Science platform for scientific discovery from the data generated by a wide variety of high throughput devices at Imperial College London
* Geodise - Grid Enabled Optimisation and Design Search for Engineering (GeoDise)] developed at the University of Southampton
* Kepler enables scientists in a variety of disciplines like biology, ecology and astronomy to compose and execute workflows. Kepler is based on the Ptolemy II system for heterogeneous, concurrent modeling and design. Ptolemy II was developed by the members of the Ptolemy project at University of California Berkeley. Although not originally intended for scientific workflows, it provides a mature platform for building and executing workflows, and supports multiple models of computation.
* Medicel Integrator Workflow [http://www.medicel.com/documents.php?file=workflow_data_sheet] is a cluster-enabled bioinformatics workflow design and execution application. It can be used stand-alone or integrated with a biology data warehouse.
* Pegasus is a flexible framework that enables the mapping of complex scientific workflows onto the grid developed at the Information Sciences Institute at the University of Southern California
* Pegasys is a software for executing and integrating analyses of biological sequences, developed by the University of British Columbia.
* Taverna workbench is an open source worfklow system that enables scientists (typically, though not exclusively, in bioinformatics) to compose and execute scientific worfklows. It has been developed as part of a £5.5m EPSRC project called myGrid based at the University of Manchester. Independently, other researchers have created Programming by example workflow development tools that are interoperable with Taverna.
* Triana is an open source problem solving environment developed at Cardiff University that combines an intuitive visual interface with powerful data analysis tools.
* Wildfire is a distributed, Grid-enabled workflow construction and execution environment] . It has a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids.
* Sight [http://bioinformatics.oxfordjournals.org/cgi/reprint/bth151v1] is a web agent - oriented workflow platform that historically has extensive means to integrate websites with ordinary web forms and HTML responses (there is also support for WSDL as well). The system has a GUI-based workflow composer that supports modules with multiple ports and allows to access data from the modules that stand earlier in workflow. Sight was developed in Ulm university using java and it currently released under GPL.

External links

* [http://dx.doi.org/10.1002/cpe.993 Taverna: Lessons in creating a workflow environment for the Life Sciences] This paper reviews some of the above workflow systems
* [http://dx.doi.org/10.1145/1084805.1084814 A taxonomy of scientific workflow systems for grid computing] from the ACM SIGMOD Record
* [http://www.embracegrid.info/ Portal of a joint European Grid and web-services project called EMBRACE] . Provides much information and many work-out bioinformatics examples and web-services.