Bioinformatics Front and Center at MBF Workshop

Published

(opens in new tab) (opens in new tab) (opens in new tab)On April 19 and 20, the Microsoft Biology Initiative (opens in new tab) welcomed a small, focused group to the Microsoft Biology Foundation Workshop 2011 (opens in new tab), held at the Renaissance Computing Institute (RENCI) (opens in new tab) in Chapel Hill, North Carolina. The workshop was a clinic in the use of the Microsoft Biology Foundation (MBF) (opens in new tab), an open-source Microsoft .NET library and application-programming interface for bioinformatics research.

Attendees included representatives from BASF Plant Science (opens in new tab), SRA International (opens in new tab), and the University of North Carolina (opens in new tab). The two-day workshop covered the basics of MBF, as well as more advanced topics, such as scalability and the new features in the beta 1 release of MBF version 2.0 (opens in new tab). (The full release of version 2.0 is planned for this summer.)

Mark Smith, our workshop instructor, did a great job of presenting the material and engaging the audience, which included participants with a variety of programming backgrounds. Attendees loved the code-along sessions, as well as the great introduction to Microsoft .NET Framework programming! Not surprisingly, there was considerable interest in the launch of our MBF coding contest (opens in new tab), where one lucky winner will receive an Xbox 360 with Kinect. Workshop samples, including slides and hands-on labs, are available on the Microsoft Biology Training (opens in new tab) page.

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Feedback

Participant input will help us make future MBF workshops more valuable. Here’s a sampling of participants’ feedback:

What did you enjoy most about the workshop?

  • The labs, which provided simple yet powerful examples of the types of programs that can be built

 What would you suggest we change/improve?

  • Add some performance metrics demonstrating why particular structures of classes make sense in different contexts
  • Provide more time to do the labs
  • Include more bioinformatics tools, such as FASTA (opens in new tab) search and PHYLIP (opens in new tab)

 How are you using MBF or planning to use MBF?

  • To display (parsed) genomic data, annotate, pipe into sequence analysis programs
  • Planning to extend it to handle PDB files
  • For sequencing analysis

Future Workshops

We will host a two-day MBF Workshop in Cartagena, Colombia (opens in new tab), May 16 and 17, 2011. We are also planning a workshop in Brisbane, Australia, July 7 and 8, during the 2011 Winter School in Mathematical and Computational Biology (opens in new tab); I will post details once they’ve been finalized. Additional workshops are in the planning stage; we will announce the dates and sites when they are finalized.

In the meantime, we encourage you to get involved in the MBF project. You can join the project and download source code from the Microsoft Biology Foundation CodePlex (opens in new tab) site. If you discover a problem, please report it under the Issue Tracker (opens in new tab) tab; if you have a question or suggestion, use the Discussions (opens in new tab) tab.

 —Simon Mercer (opens in new tab), Director of Health and Wellbeing Microsoft Research Connections 

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