TitleBodyTechnical Expertise RequiredCostAdditional Information
Bitbucket

Bitbucket is a free hosting site for open-source computer program source code. Bitbucket supports version control, offsite backup, and access by multiple authenticated users.

Basic programming skillsFree
Kepler

Kepler is a scientific workflow application that enables scientists, engineers, analysts, and computer programmers to create, execute, and share models and analyses. Kepler is a java-based application that can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging "R" scripts with compiled "C" code, or facilitating remote, distributed execution of models. Using Kepler's graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a "scientific workflow"—an executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and components developed by the scientific community to address common needs.

Basic programming skillsFree
  • https://kepler-project.org/users/documentation
  • Ludäscher B., Altintas I., Berkley C., Higgins D., Jaeger-Frank E., Jones M., Lee E., Tao J., Zhao Y. 2006. Scientific Workflow Management and the Kepler System. Special Issue: Workflow in Grid Systems. Concurrency and Computation: Practice & Experience 18(10): 1039-1065.
  • Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis. Derik Barseghian and Ilkay Altintas and Matthew B. Jones and Daniel Crawl and Nathan Potter and James Gallagher and Peter Cornillon and Mark Schildhauer and Elizabeth T. Borer and Eric W. Seabloom and Parviez R. Hosseini (2010) Ecological Informatics. Volume 5. Pages: 42 - 50.
  • Scientific workflow design for mere mortals. Timothy McPhillips and Shawn Bowers and Daniel Zinn and Bertram Ludäscher (2009) Future Gener. Comput. Syst.. Volume 25. Pages: 541--551.
Taverna

Taverna is an open source family of tools for designing and executing workflows, created by the myGrid project. Written in Java, the family consists of the Taverna Engine (the workhorse), and the Taverna Workbench (desktop client) and Taverna Server (remote workflow execution server) that sit on top of the Engine.

Taverna allows for the automation of experimental methods through the use of a number of different services (such as Web services) from a very diverse set of domains – from biology, chemistry and medicine to music, meteorology and social sciences. Effectively, Taverna allows a scientist with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources.

Taverna Workbench 2.1.2 supports: copy/paste, shortcuts, undo/redo, drag and drop; animated workflow diagram; remembers added/removed services; secure Web services support; secure access to resources on the Web; up-to-date R support; intermediate values during workflow runs; myExperiment integration; and Excel and csv spreadsheet support.

Basic programming skillsFree

D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. Pocock, P. Li, and T. Oinn, Taverna: a tool for building and running workflows of services., Nucleic Acids Research, vol. 34, iss. Web Server issue, pp. 729-732, 2006.

T. Oinn, M. Greenwood, M. Addis, N. Alpdemir, J. Ferris, K. Glover, C. Goble, A. Goderis, D. Hull, D. Marvin, P. Li, P. Lord, M. Pocock, M. Senger, R. Stevens, A. Wipat, and C. Wroe, “Taverna: lessons in creating a workflow environment for the life sciences,” Concurrency and Computation: Practice and Experience, vol. 18, iss. 10, pp. 1067-1100, 2006.

J. Sroka, J. Hidders, P. Missier, and C. Goble, "A formal semantics for the Taverna 2 workflow model," Journal of Computer and System Sciences, vol. 76, iss. 6, pp. 490-508, 2009.

J. Zhao, C. Goble, R. Stevens, and D. Turi, "Mining Taverna's semantic web of provenance," Concurrency and Computation: Practice and Experience, vol. 20, iss. 5, pp. 463-472, 2008.

T. Oinn, P. Li, D. Kell, C. Goble, A. Goderis, M. Greenwood, D. Hull, R. Stevens, D. Turi, and J. Zhao, "Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community," , Taylor, I., Gannon, D., and Shields, M., Eds., Springer-Verlag London Ltd, 2006.

VisTrails

VisTrails is an open-source scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated---change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.

Basic programming skillsFree