E-Science Support

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Introduction

NBIC has chosen to advocate an e-science approach to bioinformatics. E-science is about enhancing science. That can mean lots of things, but in the BioAssist context it means we advocate using and developing reusable components and sharable workflows in a Grid environment. Adopting such an e-science approach can be a challenge.

BioAssist offers the expertise of the e-science support group of SURFsara and core NBIC people. E-science support at SURFsara provides custom advice on using the Life Science Grid as well as deploying webservices and workflows in the grid environment.

Under the supervision of Marco Roos a few 'friends' have offered to help as well: Morris Swertz, Scott Marshall, Silvia Olabarriaga, Pieter Neerincx. They all have a background in both e-science and bioinformatics (Marco also Biology), Silvia Olabarriaga with experience in applying grid technology for medical applications, and Pieter Neerincx with BioMoby.

For communication you can use the mailing list bioassist-users@nbic.nl , and these BioAssist wiki pages.

Other user support

Direct support and mailing lists

  • Via myExperiment you can directly post questions and comments to the experts, related to Taverna workflows.
  • Do not hesitate to send questions to the Taverna-users mailing list or Taverna-hackers mailing list. Questions are usually answered quickly, and more profound issues feed directly into the development process of 'the myGrid family' (creators of e.g. Taverna and myExperiment; NBIC works closely together with myGrid). The same is true for the feedback mechanism on myExperiment.

Links to more information

  • Please consider joining the BioAssist_NL group. You can join and create any group you want, but through this group we can see the activity of our project in terms of workflows and web services (web service support on myExperiment is planned before the end of 2008, a joint project with EBI).
  • Franck Tanoh created a wiki for web services, this is his starting point for annotation
  • For beanshells look at the myExperiment Beanshell Collection that Pieter Neerincx set up.
  • Through the e-science support team for NBIC group on myExperiment you can contact the members that are active on myExperiment, and look at their profiles.

User driven development (use cases)

We invite you to use this page to share with us what analysis you want to do with a workflow. We will send out specific invitations, but feel free to add your own story. We especially would like to know what kind of information you find important while designing, running, and publishing your workflow, and how you would use that information.

Data transport

Getting big data sets over XML is not a good idea. As this is used in Taverna workflows this issue came up frequently. These are the current initiatives to address this issue:


Disclaimer

  • The wiki pages above are work in progress.