Soaplab2 is a refactoring and enhancement of a long-standing project Soaplab (that is still being used and maintained). Please check the details of the aims and reasons of the project on its original Soaplab pages until this Soaplab2 documentation is finished. The main reasons for Soaplab2 were captured in this email.

Soaplab2 (or Soaplab) is a tool that can automatically generate and deploy Web Services on top of existing command-line analysis programs. It is especially well suited for applications with well described input and output parameters, such as EMBOSS (a package of Open Source software for sequence analysis). Soaplab allows integration of many applications within a single programming interface.

Soaplab can also interoperate with other Web Services and can create Web Services on top of existing web resources (e.g. extracting data from a third-party web page and providing its data as a Web Service) - a sub-project called Gowlab. [ An old documentation available here. ]

What Soaplab solves

An executive summary who can benefit from using Soaplab can be expressed in three following questions. If you answer them affirmatively then Soaplab can help you:

  1. You have (or someone else has) one or more command-line programs (analysis tools) to offer
  2. You wish to access them from other computers, eventually over the Internet
  3. You wish to access them using your (or someone else) client programs, not just by filling the forms and clicking on web pages manually

Also, Soaplab will work for you with the modified first question: You wish to grab (screen-scrape) data from a web page (more about this in the Gowlab sub-project).

You do not need to be a programmer in order to benefit from Soaplab. Soaplab generates everything needed for creating and running your Web services from description files (which you have to create).


Even thought the work on Soaplab2 is still driven by Martin Senger, the original Soaplab author, any progress would be impossible without the help of others:

Peter Rice's group at European Bioinformatics Institute is the major driving force. Especially thanks to Mahmut Uludag, Alan Bleasby, Jon Ison, and Tom Oinn (you know Taverna, don't you?).

Equally helpful is Peter Ernst from the Sandor Suhai's group at German Cancer Research Center. Sebastien Moretti from University of Lausanne was helpful with testing and maintenance of batch test sets.

The funding and support come from various sources, depending mostly on the individuals involved. The significant contribution, especially in 2007, came from the International Rice Research Institute (including the Generation Challenge Programme), and from the BioinfoGRID project. Project was also supported by the European Comission through the EMBRACE Network of Excellence by its funding for the EBI Soaplab Web Services.

The tooltips library used in the Spinet client is credited to TwinHelix Designs. Most of the icons in the Spinet client were shamelessly stolen from the open-source project Eclipse.

The documents icons were created at

References for Soaplab and Soaplab2

Martin Senger, Peter Rice, Tom Oinn,
"Soaplab - a unified Sesame door to analysis tools",
Proceedings, UK e-Science, All Hands Meeting 2003, Editors - Simon J Cox,
p.509-513, ISBN - 1-904425-11-9,
September 2003

Senger M., Rice P., Bleasby A., Oinn T., Uludag M.,
"Soaplab2: more reliable Sesame door to bioinformatics programs",
The 9th annual Bioinformatics Open Source Conference, 2008

Last modified: Tue Aug 10 14:31:55 2010