7.5. Workflow Interfaces

These include applications for combining more than one application into a workflow or pipeline. The applications in the pipeline and data they operate on might be on a local machine or distributed on the Internet. For example, Taverna handles workflows where each step might be a web service running anywhere in the world. It can, for example, use the SOAP protocol for data exchange. Input ports accept input data and data is written to output ports. Taverna understands how to find and use web services, and users can create their own workflows or exchange them.

The available workflow interfaces include:







Pipeline Pilot


BioWBI (Bioinformatic Workflow Builder Interface)

http://www.alphaworks.ibm.com/tech/biowbi and WsBAW (Web services for Bioinformatic Analysis Workflow)





7.5.1. Taverna


Taverna is a free software tool for designing and executing workflows. Taverna allows users to integrate many different software tools, including web services from many different domains. Bioinformatics services include EMBOSS in addition to those provided by the National Center for Biotechnology Information, The European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab and BioMOBY.

7.5.2. metalife


metalife job designer provides the functionality to query, explore, analyze and visualize sequences in the context of genomics and proteomics. It integrates EMBOSS, several types of BLAST search, secondary antigenicity and structure prediction algorithms and another 140 state-of-the-art algorithms for primary structure feature extraction.


Pipeline Pilot(tm) is a high-throughput data analysis and mining system for drug discovery informatics. It is based around a powerful client-server platform that lets you construct workflows by graphically combining components for data retrieval, filtering, analysis, and reporting. Different client interfaces to the Pipeline Pilot platform enable you to work in the environment that best suits your needs.

7.5.4. BioWBI and WsBAW

http://www.alphaworks.ibm.com/tech/biowbi and http://www.alphaworks.ibm.com/tech/wsbaw

Bioinformatic Workflow Builder Interface (BioWBI) is a web-based working environment from which one can build and execute bioinformatic workflows and share analysis processes.

Web Service for Bioinformatic Analysis Workflow (WsBAW) automates bioinformatics workflows via web services.

These two pieces of software allow their users to design and execute complex bioinformatic analysis processes. They wrap EMBOSS algorithms plus other bioinformatics algorithms.

7.5.5. G-Pipe


G-Pipe is a graphical pipeline generator that allows the definition of pipelines and parameterisation of its component methods using Pise web interfaces. The entire analysis protocol is stored in XML and a complete bioinformatic experiment (linked set of methods and parameters) can thereby be reproduced or shared among users. A Perl macro making use of Pise/Bioperl and implementing the pipeline can also be downloaded (for developers).

Download: ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz

7.5.6. Mobyle


Mobyle is a system that provides a web environment to define and execute bioinformatics analyses. It is the successor of Pise, aiming at extending the functionalities towards services interoperability and data integration, while optimizing the usability of the interface for a public of biologists.

The Mobyle system is based on a set of program descriptions that automate their use, from the construction of the web interface up to the job execution. Based on extensive user studies, the end-user interface was developed as a Web Portal that provides a global and integrated view of all the elements needed to perform analyses, such as the available programs, the submitted jobs and the data of interest.

Mobyle is distributed under the terms of the GNU GPLv2. Downloads and project information, as well as a list of available public servers, can be found at: http://bioweb2.pasteur.fr/projects/mobyle/.

Mobyle includes a set of program descriptions (XML files), including popular packages such as EMBOSS but also PHYLIP, ViennaRNA, etc. These descriptions are distributed under GNU Lesser General Public License, version 2.1 (LGPLv2.1).