Workflow related links, from putting myGrid's Taverna e-science workflow workbench in the context of related work. The emphasis is on scientific workflow and semantic web service composition. Topics include workflows in science, scientific workflow systems (and particularly bioinformatic ones), semantic web services, general workflow links and workflow patterns. The page is organised for convenience rather than ease of reading; many people may want to start with general workflows rather than at the top. Other useful links on this TWiki include:

• WorkFlow#Useful_Links -
• TavernaTips - for links to more info on Taverna
• WorkflowAtGGF - Global Grid Forum workflow workshop Mar 2004
• WorkflowDefinitions

Contents

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Scientific Workflows

There is significant debate about whether scientific workflows have characteristics that differentiate them from business workflows. WorkFlowDifferences covers some of these arguments. The September 2005 edition of SIGMOD Record includes a special section on scientific workflows. Early papers include Scientific workflow systems and Scientific Workflows from the NSF workflow and process automation workshop May 1996, and State of the Art in Workflow from 1998

Scientific Workflow systems/projects

• Taverna http://taverna.sourceforge.net (see also TavernaTips) Bioinformatics workflow workbench
• Kepler http://kepler-project.org/ (old link http://kepler.ecoinformatics.org/ )
  • based on the Ptolemy Project, http://ptolemy.eecs.berkley.edu
• Pegasus http://pegasus.isi.edu/
• DiscoveryNet http://www.discovery-on-the.net/applications.html - also http://www.inforsense.com/
• Triana http://www.trianacode.org/ - also workflow part of wider GridLab project
• SPA (Scientific Process Automation) https://www-casc.llnl.gov/sdm/
• Geodise http://www.geodise.com/index.htm
• ICENI http://www.lesc.ic.ac.uk/iceni/index.html
• Askalon http://dps.uibk.ac.at/projects/agwl/ AGWL language
• http://www.gridnexus.org/ a GUI GridNexus and language JXPL
  • builds on eariler work on GeneBeans
• P-GRADE http://www.lpds.sztaki.hu/pgrade/main.php?m=1 Parallel Grid Run-time and Application Development Environment

For additional workflow systems see the general workflow links below, in particular the Scientific Workflows Survey from Indiana and the lists of projects and tools maintained by the Grid Workflow Forum

Bioinformatics workflow systems

Most of the above scientific workflow systems have been used for bioinformatics. There are also bioinformatics specific systems that often have a specific set of tools.

• http://zlab.bu.edu/SeqVISTA/ SeqVista pipeline management
• http://www.migenas.org/home/index.jsp MiGenAS Microbial Genome Analysis System of the Max Planck Society
  • The MiGenAS Workflow Engine presentation by Thomas Soddemann
  • Public access via anonymous guest login is possible - contact via web site for details
• http://www.bioinformatics.ubc.ca/pegasys/ Pegasys: workflow management for bioinformatics
• BioWBI http://www.alphaworks.ibm.com/tech/biowbi on IBM alphaworks
• INCOGEN VIBE (Visual Integrated Bioinformatics Environment). http://www.incogen.com/VIBE
• TurboWorx Enterprise – http://www.turboworx.com
• Pipeline Pilot http://www.scitegic.com/products_services/pipeline_pilot.htm
• Accelrys http://www.accelrys.com/technologies/informatics/bioinformatics/workflows/
• BioOpera from ETH Zurich http://www.iks.inf.ethz.ch/projects/bioopera/index_html/view
  • project ended December 2003, the followon JOpera http://www.iks.inf.ethz.ch/jopera is not bio-specific
• Wildfire http://wildfire.bii.a-star.edu.sg/wildfire/index.asp a graphical tool for building workflows preconfigured to use EMBOSS components
• ubertool a software system for the integration and analysis of molecular biological data based around modular workflows.
  • However, http://www.science-factory.com/ discontinued its operations from 31 August 2003 due to insufficient funding.

Scientific workflows general information

• LinkUp project has scientific workflows as a key theme
• Workflow Management Research Group (WFM_RG) of the Global Grid Forum
• SIGMOD Record September 2005 includes a special section on scientific workflows
• The Grid Workflow Forum is an open forum for information exchange and discussions about scientific and commercial approaches in the domain of Grid Workflows
• The Gridbus project aims "to create next-generation GRID computing and BUSiness technologies"
  • and has produced A Taxonomy of Workflow Management Systems for Grid Computing
• Survey on Grid Workflows - appears to have been removed 27 August 2006
• Scientific Workflows Survey from Indiana - includes a nice set of scientific / Grid workflow slides presented at GGF 9 in 2003
• WorkflowAtGGF - GGF10 grid workflow workshop, March 2004 - this had a good representation from Grid workflow systems
• e-Science Workflow Services - NeSC workflow workshop Dec 2003
• NSF workflow and process automation workshop May 1996

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Service Composition and Workflows

Although much of the original development of workflow systems was in the area of office automation, there has recently been most activity in the area of web service composition and enterprise integration. Introductory article from IBM on "Business processes and workflow in a Web services world". For example the ICAPS 04 workshop on Planning and Scheduling Web and Grid Services

Scientific Services

Workflows often used for service composition, hence a close relationship between services and workflow (workflows as composite services)

• WebServices and W3c Web Services Activity
• BioinformaticsWebServices

Semantic Web Services

The Dynamo project bibliography prodives useful links to semantic seb services literature. While workflow systems compose web services, there is also significant related work in Semantic Web Services. Semantic descriptions can be key to finding services to compose, and another significant overlap is in using semantics to compose web services on demand

• http://lsdis.cs.uga.edu/Projects/METEOR-S/WSDL-S/ WSDL-S (Adding Semantics to Web Services) from LSDIS and IBM
• http://www.daml.org/services/ Semantic Web Services home page (DAML programme) links to OWL-S (DAML-S), SWSL, SWSA
  • http://www.daml.org/services/swsl/ Semantic Web Services Language (SWSL) much material relevant to workflow langauges
  • http://www.daml.org/services/swsa/ Semantic Web Services Architecture (SWSA)
  • http://www.daml.org/services/use-cases.html Semantic Web Services use cases
• http://www.wsmo.org/ Web Service Modeling Ontology is used by a number of large European projects
• http://www.w3c.org/2002/ws/swsig/ W3C semantic web services interest group
• http://www.swsi.org/ Semantic Web Services Initiative
• http://www.daml.ecs.soton.ac.uk/SSS-SWS04.html Semantic Web Services Symposium
• http://www.mindswap.org/~bparsia/talks/2004/march-w3c-swig.html a useful set of slides from Bijan Parsia of http://www.mindswap.org/
• http://knowledgeweb.semanticweb.org/ EU Knowledge Web Network of Excellence
• http://dip.semanticweb.org/index.html Data, Information and Process Integration with Sematic Web Services
• http://kmi.open.ac.uk/projects/cashew/ CASHEW Composition and Semantic enHancEment of Web services

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General workflow links

WorkflowDefinitions

• http://www.workflowresearch.de/ looks a well organised up-to-date site of workflow related links
• The State of workflow by Tom Baeyens is an interesting paper with links to open source projects, commercial vendors, standards and further reading.
• State of the Art in Workflow Oct 1998, is another introductory article
• WfMC - Workflow Management Coalition have introductory material from a business perspective
• Workflow-based Applications by Frank Leymann and Dieter Roller (IBM Systems Journal 36(1), 1997) looks at workflow from its impact on applications development.

Workflow sites (mainly business consortia)

• http://www.wfmc.org/ WfMC - Workflow Management Coalition
  • The WfMC have had considerable success with their workflow reference model, but efforts towards more detailed standards (e.g. XPDL and Wf-XML) have met with less success. See http://www.wfmc.org/standards/docs.htm for details
• http://www.ebpml.org/ - an informative site on business process management and workflow, Jean-Jacques Dubray
  • Articles library is a good source on current topics
• http://www.e-workflow.org/ - workflow portal sponsored by WfMC and WARIA
• http://www.bpmi.org/ Business Process Management Initiative,
  • uses the term Business Process Management System (BPMS) rather than workflow management system, for detail see The Emergence of Business Process Management by Howard Smith et al from http://www.bpmi.org/library.htm
• Google directory workflow another starting point for workflow links

Also look at the workflow patterns site mentioned below

Workflow systems (including BPEL Engines)

This list mainly has research/non-commercial workflow systems and particularly those for composing web services

• YAWL Yet Another Workflow Language system, based on workflow patterns work
• METEOR-S Semantic Web Services and Processes
  • http://chief.cs.uga.edu/~jam/webwork/ additional information
• http://www.oracle.com/technology/products/ias/bpel/index.html Oracle BPEL Process Manager
  • formerly the Collaxa BPEL engine
  • XML coverpages report on the Oracle BPEL engine - include useful links
• http://www.smartcomps.org/twister/index.html Twister open source BPEL engine
  • http://www.smartcomps.org/twister/links.html useful links
  • http://sourceforge.net/projects/wf-twister/ Twister on sourceforge
• http://www.activebpel.org/ ActiveBPEL open source BPEL engine
• http://openwfe.sourceforge.net/ OpenWFE Open WorkFlow Engine
• http://wfmopen.sourceforge.net/ WfMOpen J2EE based implementation of a workflow facility (workflow engine) as proposed by the Workflow Management Coalition (WfMC)
• http://www.rolemodellers.com/radrunner/ RADRunner a Human Interaction Management system, rather than a pure workflow system.
• http://www.jopera.org/ JOpera for Eclipse: Process Support for more than Web services.

General sources of open source workflow systems

• http://www.manageability.org/blog/stuff/workflow_in_java/view blog page on open source workflow engines written in java
• http://java-source.net/open-source/workflow-engines/taverna open source workflow engines in Java (from java-source.net)
• http://joe.lindsay.net/openworkflow.html
• http://jbpm.org/2/state.of.workflow.html

Languages proposed as candidate standards (BPEL, BPML, WS-CDL, PSL etc)

One overview of the complexity of workflow standards is given in Process Management Standards Overview (April 2003) or http://xml.coverpages.org/bpm.html

• BPEL http://www-106.ibm.com/developerworks/library/ws-bpel/ BPEL 1.1 from IBM May 2003
  • BPEL 1.1 from Microsoft May 2003
  • BPEL is promoted as a standard WSBPEL through OASIS http://www.oasis-open.org/committees/wsbpel
    • The OASIS WSBPEL charter provides a good overview of this standardisation effort
    • WSBPEL Issues List illustrates the finer details still to be resolved
  • A quick overview of BPEL4WS from IBM
  • BPEL has gained considerable commerical support, see example systems above. It was developed through the combination of IBM's WSFL and Microsoft's XLANG. Also known as BPEL4WS (the orginal proposal) and WSBPEL (the OASIS standard being developed).
• BPML avialable from http://www.bpmi.org/
  • BPMI originally stressed BPML as a superset of BPEL, but their BPM stack of Sept 2004 (see http://www.bpmi.org/aboutus.htm ) places WS-CDL, BPEL and their BPQL (Business Process Query Language) as alternatives between their BPMN, BPSM, and BPXL and the Web Services Stack
• WS-CDL http://www.w3.org/TR/ws-cdl-10/ Web Services Choreography Description Language from W3C Web Services Activity
  • Emphasis here is not on a executable language but describing peer-to-peer collaborations between Web service participants by defining their behavior from a global viewpoint
  • looks to have replaced WSCI WSCI http://www.w3.org/TR/wsci/ Web Service Choreography Interface W3C note 8 August 2002
  • and also WSCL http://www.w3.org/TR/wscl10/ Web Services Conversation Language W3C Note 14 March 2002
• XPDL see http://www.wfmc.org/standards/docs.htm from WfMC
  • http://www.wfmc.org/standards/XPDL.htm for commercial and open source systems using XPDL
  • http://www.wfmc.org/standards/wfxml_demo.htm Wf-XML addresses invoking asynchronous web services
• BPSS from ebXML available from http://www.ebxml.org/specs/#technical_specifications
• PSL http://www.mel.nist.gov/psl/index.html Process Specification Language although developed for a manufacturing systems integration perspective, this addresses many of the same issues.
• I-N-C-A http://www.aiai.ed.ac.uk/project/ix/inca/

but do read W.M.P. van der Aalst "Don't go with the flow:Web services composition standards exposed. Web Services - Been there done that?, Trends & Controversies", Jan/Feb 2003 issue of IEEE Intelligent Systems Ontoweb Process Content Standards for the Semantic Web is a state-of-the-art November 2001 report that illustrates the overlap between workflow language standards and those for the semantic web. See SWSL for additional information.

Workflow patterns

Wil van der Aalst has worked on using workflow patterns to compare workflow languages and systems.

• http://www.citi.qut.edu.au/yawl/index.jsp YAWL - Yet Another Workflow Language, based on workflow patterns work
• http://www.workflowpatterns.com - provides interactive animations of the 20 basic workflow patterns, documentation, and evaluations of systems, languages, and standards based on these patterns.
• http://www.workflowcourse.com - supports the English, Chinese, and Dutch versions of the book Workflow Management: Models, Methods and Systems. The site contains interactive examples, flash animations, slides, exercises, etc.
• http://www.processmining.org - explains the concept of process mining using animation and provides papers and slides on the topic.
• http://www.jopera.ethz.ch/docs/patterns - presents a set of Quicktime screen movies showing workflow patters as they are executed by JOpera for Eclipse.

The above three WWW sites contain animations, lecture materials, product/language evaluations, slides, papers and reports on topics related to Workflow Management (WFM) and Business Process Management (BPM) ["Wil van der Aalst" <w.m.p.v.d.aalst@tm.tue.nl> March 2004]

Notes

Related Twiki pages

• WorkFlow#Useful_Links
• WorkflowAtGGF
• LinkUp

Additional Links

• http://www.gray-area.org/Pubs/grid-flow.pdf Grid-Flow: A Grid-Enabled Scientific Workflow System
• http://www.nesc.ac.uk/technical_papers/UKeS-2003-01/index.html UK e-Science Gap Analysis includes section on workflow that mentions several projects
• http://dps.uibk.ac.at/index.pl/grid some useful Grid workflow links
• http://www.cc-pe.net/iuhome/workflow2004index.html information on CCPE special issue for Grid Workflow

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-- MarkGreenwood - 14 Jul 2005