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May, 2011

Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

May, 2011

  • Microsoft Research Connections Blog

    Bioinformatics Front and Center at MBF Workshop

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

    Attendees included representatives from BASF Plant Science, SRA International, and the University of North Carolina. 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. (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, 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 page.

    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 search and PHYLIP

     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, 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; 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 site. If you discover a problem, please report it under the Issue Tracker tab; if you have a question or suggestion, use the Discussions tab.

     Simon Mercer, Director of Health and Wellbeing Microsoft Research Connections 

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  • Microsoft Research Connections Blog

    Paradigm Shifting in Scholarly Communications

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    Earlier this year, Lee Dirks, Cheri Ekholm, and I attended Phil Bourne’s Beyond the PDF workshop at the University of California, San Diego. This workshop advanced the premise that scholarly communication can and should evolve from static and disparate data and knowledge representation, as embodied in today’s typical PDF representations of research papers, to a rich integrated content which grows and changes the more we learn. In the few months since this event, there’s been a great deal of activity: Martin Fenner and Mark Hahnel are working on Wordpress for Scientists, Peter Sefton has launched the Scholarly HTML effort, and our team here at Microsoft Research is hard at work on some great new features for our next release of the Article Authoring Add-in for Word (the beta release of version 3.0 is due this later this year).

    But even more important than developing tools or formats, we need to persuade the current generation of researchers to challenge the status quo. Scholars do see the value (to varying degrees) in sharing a greater level of detail of their research as a part of the scholarly communication process, recognizing that such communications enhance the scientific record and accelerate discovery. But active researchers are also players in a system that rewards the traditional research paper format to the exclusion of all else.

    A major thread in this conversation stresses the enormous potential of shared research data in facilitating experimental reproducibility and validation. Much ink has been spent in the past few years on the “data deluge” and the promise of new advances in science that are not based on the traditional hypothesis-experiment-analysis-conclusion paradigm, but rather start with previously unseen patterns, anomalies, or correlations within the existing wealth of collected data themselves as the catalyst for new investigations and experiments.    

    To this end, it is clear that the sharing of scientific research data holds great promise for the scientific discoveries of the future. And yet the system of academic research achievement does not yet recognize or reward researchers for sharing their data. Change is afoot, however, and the next generation will look back on this decade as one of profound transformation in determining which parts of the scientific research process are recorded and how researchers are rewarded.

    In the meantime, organizations like BioMed Central are stepping up to recognize those researchers who are on the vanguard of this movement. Microsoft Research has contributed to BioMed Central’s Research Awards for several years, and we are proud sponsors of the Open Data Award since its inception in 2010. This year’s award recognized biologist Tommi Nyman from Finland for the article, “How common is ecological speciation in plant-feeding insects? A 'Higher' Nematinae perspective,” published in the open-access journal, BMC Evolutionary Biology.

    Dr. Peter Murray-Rust (left); Jean-Luc Bouvé (center), accepting the Open Data Award
    Dr. Peter Murray-Rust (left); Jean-Luc Bouvé (center), accepting the Open Data Award
    on behalf of Dr. Tommi Nyman; and Alex Wade (right)

    Dr. Nyman and his colleagues published three additional data files with their article:

    • The collection data for their specimens and taxonomic and ecological background information
    • The sequence data used in phylogeny reconstruction and resultant phylogenetic trees
    • The data file and run parameters for Bayesian Evolutionary Analysis Sampling Trees (BEAST)

    The data are well labeled and readily understandable by other scientists; moreover, the authors showed great transparency in their work, particularly in their first additional data file, which fully documents how they sampled their insects. This level of openness is not commonly seen and it demonstrates real leadership. Their article serves as an outstanding example of how evolutionary biology research should be presented and the data published to enable other scientists to validate and build on the work.

    Microsoft Research is honored to be an ongoing sponsor of the Open Data Award, and we are thrilled to be able to play a role in encouraging the Open Data movement in this way.

    Alex D. Wade, Director for Scholarly Communication, Microsoft Research Connections

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