e-BioFlow: improving practical use of workflow systems in bioinformatics

  • Authors:

  • Ingo Wassink;Matthijs Ooms;Pieter Neerincx;Gerrit Van Der Veer;Han Rauwerda;Jack A. M. Leunissen;Timo M. Breit;Anton Nijholt;Paul Van Der Vet

  • Affiliations:

  • Human Media Interaction Group, University of Twente, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Human Media Interaction Group, University of Twente, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Human Media Interaction Group, University of Twente, The Netherlands and Open University, Heerlen, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Microarray Department and Integrative Bioinformatics Unit, University of Amsterdam, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Laboratory of Bioinformatics, Wageningen University and Research, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Microarray Department and Integrative Bioinformatics Unit, University of Amsterdam, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Human Media Interaction Group, University of Twente, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands;Human Media Interaction Group, University of Twente, The Netherlands and Netherlands Bioinformatics Centre, Nijmegen, The Netherlands

  • Venue:
  • ITBAM'10 Proceedings of the First international conference on Information technology in bio- and medical informatics
  • Year:
  • 2010

Quantified Score

Hi-index 0.00

Visualization

Abstract

Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.