Halling-Brown, Mark D. and Shepherd, Adrian J. (2008) Constructing computational pipelines. Methods in Molecular Biology 453 (4), pp. 451-470. ISSN 1064-3745.
Abstract
Many bioinformatics tasks involve creating a computational pipeline from existing software components and algorithms. The traditional approach is to glue components together using scripts written in a programming language such as Perl. However, a new, more powerful approach is emerging that promises to revolutionise the way bioinformaticians create applications from existing components, an approach based on the concept of the scientific workflow. Scientific workflows are created in graphical environments known as workflow management systems. They have many benefits over traditional program scripts, including speed of development, portability, and their suitability for developing complex, distributed applications. This chapter explains how to design and implement bioinformatics workflows using free, Open Source software tools, such as the Tav-erna workflow management system. We also demonstrate how new and existing tools can be deployed as Web services so that they can be easily integrated into novel computational pipelines using the scientific workflow paradigm.
Metadata
| Item Type: | Article |
|---|---|
| School: | Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences |
| Research Centres and Institutes: | Bioinformatics, Bloomsbury Centre for (Closed), Structural Molecular Biology, Institute of (ISMB) |
| Depositing User: | Administrator |
| Date Deposited: | 04 Aug 2010 14:09 |
| Last Modified: | 02 Aug 2023 16:49 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/1087 |
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