Introduction
The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework, initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, and documentation are freely downloadable.
The source code and development of MBF is managed on this CodePlex site, but all downloads are hosted on the Microsoft Research site here:
http://research.microsoft.com/bio/mbf.aspx.
The MBF project is currently coordinated by a Technology Advisory Board, consisting of members from the academic community, industry and Microsoft.
Latest News
Microsoft Biology Foundation Workshop September 8-9 2011, Phoenix, Arizona
8/4/2011
We will be holding another 2 day workshop on MBF in September on the Arizona State University campus. The course will start at 9:00AM and will be located in the auditorium at
Biodesign Institute. You can view additional information and register for the course on our
events page. I'll post an additional course announcement sometime next week as well. Looking forward to seeing some of you there and hearing what you have to say about MBF V2.
MBF Coding Contest winner!
7/28/2011
We received a terrific entry for our MBF V2 Beta 1 coding contest from Kajal Das. As the winner of the contest he was awarded an Xbox 360 4GB with Kinect for his efforts. His DNA and RNA Sequence Annotation Studio application takes advantage of the GenBank and FASTA parsers, as well as GenBank Formatter and other features of our beta. His application allows one to:
View the complete sequence, including a nice zoom feature
View annotations either in whole or selectively
Create/edit/delete annotations
Save the modified sequence in GenBank format
You can see his project on CodePlex at
http://seqannotationstudio.codeplex.com/When asked about his experience using our beta he had this to say "First of all, I have been waiting for a long time for something like this to come from Microsoft. I had heard about BioPerl, BioJava, etc. Now, MBF opens up the path to new possibilities for the .NET developers." "Overall, I have had a great experience while working with MBF and developing the application using MBF. I enjoyed it thoroughly even being up till 2 o'clock in the morning for almost 10-12 days. "
Our congratulations go out to Kajal and we hope to see more of his work here on our project. Our version 2.0 is nearly ready, although I don't have a final date at this point in time.
Recap Microsoft Biology Foundation Workshop July 7-8 2011, Brisbane, Australia
7/13/2011
We had a small but enthusiastic audience for our 2 day workshop held in Brisbane, Australia last week. Besides the discussions on parsers, formatters and C# .NET our trainer managed to cover a bit of
Trident which garnered some interest among the students. We had attendees from
CSIRO,
Garvan Institute of Medical Research, and of course
UQ and
QUT. We hope to see some items aired during the course out on the discussion forum shortly as people digest the information provided. Many thanks to several people at QUT and UQ for assisting us in putting on a great workshop. The hospitality was very welcome. For those that registered and were unable to attend we will be having more workshops but perhaps not as convenient for those of you located in Australia. A reminder for those that haven't already submitted their entries for our coding contest, the deadline is this Friday July 15th at 5:00PM PST.
Schedule Update Microsoft Biology Foundation Workshop July 7-8 2011, Brisbane, Australia
6/30/2011
There has been a change to the start times for the MBF workshop held on July 7th and 8th in Brisbane. It will be at
09:00AM not 08:00AM as listed on our site. We will be in the large seminar room 3.142 Queensland Bioscience Precinct. The directions to the venue are
here. This change will also adjust our class schedule which we will communicate at the site. Looking forward to seeing many of you there.
Microsoft Biology Foundation Workshop 2011, Brisbane, Australia
6/2/2011
We are holding a two day MBF workshop in Brisbane, Australia on July 7th and 8th in conjunction with the
2011 Winter School in Mathematical and Computational Biology hosted by The University of Queensland. You can find details on the courses and a link to the registration site
here. The course will be focused on version 2 of MBF and the changes from version 1.
Post Beta 1 Drop now available under source code tab
5/19/2011
Our development team has been progressing on their push to complete version 2.0 of MBF. To that end, another milestone drop was just published under the source code tab. You should understand this is a milestone drop and as such will have issues and is not to be used for production work. Please do report any issues you encounter on the issue tracker tab. You should base any new contributions on this version of course.
Microsoft Biology Foundation Workshop 2011, Cartagena, Colombia
5/16/2011
Our third installment of the MBF training workshop is taking place in Cartagena, Colombia May 16th and 17th. This course incorporates the new features found in our V2 beta 1 release. Descriptions of the event are located here
http://research.microsoft.com/en-us/events/mbf2011-cartagena/default.aspx
MBF Coding Contest using MBF V2 beta 1
5/11/2011
We are holding a contest to find the best bioinformatics and genomics application built on our just released MBF 2.0 beta 1. The contest ends July 15th at 5:00PM with the winner announced on July 27th. You can see the contest details here
http://research.microsoft.com/en-us/projects/bio/mbfcontest.aspx. The winner will receive an Xbox 360 4GB console with Kinect.
Announcing the beta 1 release of MBF 2.0 today.
4/22/2011
For those of you who evaluated our developer preview in December of last year enjoy! This is the first significant update since MBF 1.0. We do appreciate the contributions made to date. Here are some highlights included in this beta.
- Increased capacity for de novo assembly of larger and more complex species than V1
- Addition of comparative assembly functions for characterizing genetic diversity within or between species
- Core object model improvements for smaller memory footprint and increased parallel processing
- Parity with all version 1.0 tools and features
- New command line tools to help with genome assembly
- Updated documentation
We will be having updated training based on our beta in the near future. As well as additional training courses. As always we appreciate your participation and feedback
Rick Benge for the MBF team
Thank you for a great MBF workshop, April 2011
Microsoft Biology Initiative and RENCI have hosted a two day workshop at the Renaissance Computing Institute in Chapel Hill, North Carolina.
Mark Smith
http://www.julmar.com/blog/mark, our instructor, did a great job of presenting the materials and engaging the audience regardless of the variety in programming backgrounds. Most attendees loved the code along sessions! You can find all the workshop samples in Mark's blog. You can also download all MBF training materials including slides and hands-on labs from
http://research.microsoft.com/en-us/projects/bio/training.aspx.
Announcing: MBF two-day workshop, April 19-20, Chapel Hill, NC
3/2011
The Microsoft Biology Initiative and the Renaissance Computing Institute (RENCI) are hosting a two-day workshop on the Microsoft Biology Foundation. The MBF workshop will be held at the Renaissance Computing Institute in Chapel Hill, North Carolina, on April 19 and 20, 2011. This workshop will include a quick introduction to Microsoft Visual Studio 2010, the .NET Framework, C#, and the MBF object model. Attendees will participate in hands-on labs and write a sample application that employs the file parsers, algorithms, and web connectors in MBF. The workshop is open to everyone and registration is free of charge. For complete details and registration please visit:
http://research.microsoft.com/en-us/events/mbf2011-chapelhill/.
Thank you for a great MBF workshop March 11
3/2011
We had a great turnout! Read all about it in our Microsoft Biology Initiative Blog:
http://blogs.msdn.com/b/mbi/archive/2011/03/16/thank-you-for-a-great-mbf-redmond-workshop-march-11.aspx
Announcing: MBF one-day workshop, March 11, Redmond, WA
2/2011
The Microsoft Biology Initiative is hosting a one-day workshop on the Microsoft Biology Foundation. The MBF workshop will be held at the Microsoft Conference Center in Redmond, Washington, on March 11, 2011. Attendees will participate in hands-on labs and write a sample application that employs the file parsers, algorithms, and web connectors in MBF. The workshop is open to everyone and registration is free of charge. For complete details and registration please visit:
http://research.microsoft.com/en-us/events/mbf2011/.
Announcing the release of MBF v2.0 Preview
12/2010
We are excited today to give you a preview of our V2 of the Microsoft Biology Foundation. This release is intended as development evaluation only.
In this release, we have fixed some bugs and have implemented / improved some of the below features (please note this is not a complete list, as some items are still in progress):
- BAM extension scenarios and paired end support
- MUMmer optimizations to support large genome assembly
- Object Model changes to use ISequence : IList<byte>
- Optomization work:
- Memory profiling and analysis on MBF
- PaDeNA memory optimizations
- Sequence optimizations (including non-string & non-character)
- MUMmer optimization based on sequence
- Object Model optimizations
- More scenarios for collection of memory & perf profiles
To fully enjoy this release, and to avoid any conflicts, we strongly recommend that you fully uninstall the V1 of Microsoft Biology Foundation before installation of V2.
We also are aware of few issues in this code, the ones that might affect your installation are listed below:
- The DLL Version of MBF is incorrectly reported as 1.0.0.0
- The installer installs MBF in a directory called 2.1 (and not 2.0).
We hope you enjoy this preview, and we would love to have your feedback via our
Community Forum or
Discussions in CodePlex.
The MBF Team
MBF development has moved to a new location
11/2010
Dear MBF contributors,
We have moved MBF's code forge to a TFS server in the Microsoft Extranet. We will continue to use CodePlex to share stable code drops for MBF, issue reporting, as well as the discussion forum in addition to our new community forum at
http://www.getsatisfaction.com/mbi. We will continue to distribute binaries from the project's main site at
http://research.microsoft.com/bio.
We encourage you to continue contributing to the MBF project with your issue reporting, comments, and suggestions in this CodePlex forum and our new community forum. You are also welcome to provide bug fixes and code contributions via CodePlex patches. If you are interested in becoming a code committer to the MBF project, please contact
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Thank you!
The MBF team
MBF development is moving to a new location!
10/2010
Dear MBF contributors,
We are in the process of transitioning the hosting of the MBF project source code to a new location. If you are planning on submitting any contributions at this point, we request that you hold on to them until our new location is ready. We cannot guarantee that any contributions made after today will be migrated to the new location. You will receive a notification when our new location is ready, no later than Nov 15th. This communication will include instructions on how to obtain credentials to continue to be a MBF contributor in our new location.
Thank you for your patience during this transition,
The MBF team.
Microsoft Biology Foundation v1.0 is Released!
7/2010
We are happy to announce that the first full, stable version of the MBF library has been released for download! Though the source code can be obtained, evaluated and/or used at any snapshot in time, we have made a concerted effort to provide a robust, stable version for use by those whose research requires a high level of quality. Because the CodePlex.com organization has enforced a strict policy of not allowing downloads which contain dependencies on closed-source binaries, the installers and overall project information page has been moved to
http://research.microsoft.com/bio/. This is the best place to go to find out details about the project, install the library and/or tools, and to keep informed about the latest in project news. The final v1.0 code changelist is here:
http://mbf.codeplex.com/SourceControl/changeset/changes/60869.
Thanks to all who made this release possible!
XConomy Article
5/2010
See this great article just written by Luke Timmerman
http://www.xconomy.com/seattle/2010/05/03/microsoft-builds-open-source-tool-for-biologists-drowning-in-data-an-on-ramp-for-customers-who-pay/. Good overview and answer's a lot of questions I'm sure folks are curious about.
MSR Tech Fest Demo: Bioinformatics Computing in the Cloud
3/2010
The Microsoft Biology Foundation and the Biology Extension for Excel plays a key role in exploring how Windows Azure can be leveraged for use in Bioinformatics Research. By downloading the latest version of the Biology Extension for Excel, access to the latest AzureBlast service can be explored.
About the Microsoft Biology Foundation
MBF has been constructed with specific goals in mind:
- Extensibility: MBF is designed to be extended. If you need functions that are not in the basic library, you will find them easy to implement in a way that works with the existing functions. We encourage developers who extend MBF to contribute their code back to the project as open source so that the community as a whole may benefit from their work. We also plan to continue to add features to MBF, extending it into new areas of biology and integrating it with other tools. Microsoft researchers are already using MBF in their research, as are an increasing number of academic partners; they will be making code contributions to extend the range and power of the Foundation, and we encourage you to do the same.
- Language neutrality: .NET allows different languages to be used for different purposes—so the accessibility of Visual Basic, the power of C#, the speed and conciseness of a functional language such as F#, or the ad-hoc scripting capabilities of Iron Python are all available, as are many others. Whatever .NET-supported language you choose, the code you write is compatible.
- Supporting best practices: MBF source is well-documented and designed to be a good example of how to program using C#. Algorithm implementations include a reference to the publications from which they are derived, so scientists can clearly understand what they do. In addition, MBF includes examples of how to integrate with other Microsoft technologies such as Windows Azure, Microsoft Silverlight, Microsoft Office, and the latest version of the .NET Framework.
- Cross-platform and interoperability: MBF works well on the Windows operating system and with a range of Microsoft technologies. We plan to work with the developer community to take advantage of the extensibility of MBF and support an increasing range of Microsoft and non-Microsoft tools as the project develops.
- Building community: MBF is an open source project, with code available for academic and commercial use free of charge under the OSI-approved Apache 2.0 license. We will provide forums for help, user feedback, feature requests, and bug reporting. MBF is open to code contributions from the community, extending the range of available functionality to researchers and life scientists everywhere.
To learn more, please visit the documentation tab:
http://mbf.codeplex.com/documentation
Discussions
Please feel free to provide your comments in the Discussion section, submit bugs via the Issue Tracker, or contact the folks associated with the project if you wish to take on a contributary role in this effort. We are extrememly excited to be breaking new ground for Microsoft in the area of Open Source, but more importantly are looking forward to helping the scientific community become better equiped for solving the complex challenges they fact in the area of genomics and healthcare.