It’s exciting to see that the Microsoft Biology Foundation 1.0 has been released!  You can read more about it here.  From MBF’s Web site:

“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.”

Those of us on the Parallel Extensions team are particularly excited about this release because of MBF’s usage of the parallelism support in .NET 4.  Here are some relevant comments from Michael Zyskowski, a member of the MBF team in Microsoft Research:

“Microsoft Biology Foundation implements some powerful genomic alignment and assembly algorithms, including a novel De novo assembler called PaDeNA (Parallel De Novo Assembler), which employs the use of the latest .NET 4 Parallel Extensions capabilities.  In fact, many of the bioinformatics algorithms included in MBF are pleasingly parallel and take advantage of this great new technology.  Not only does the use of Parallel Extensions greatly improve the runtime performance and hardware utilization, it was also relatively easy to implement and retrofit into existing implementations.

The primary driver in parallel computation for MBF v1.0 is the increased capability of the Windows desktop already available in most research institutions.  We want to offer the researcher the ability to make better use of the computer that normally is dedicated to Office applications like Word, converting it to one that is capable of doing real, human-relevant health care research. This is just the start.”

Exciting stuff.  Congratulations to the MBF team!

The .NET Framework 4 introduces a new mechanism for cancellation of operations, based on new types CancellationToken and CancellationTokenSource. This cancellation mechanism is used across the parallel programming libraries: tasks, concurrent collections, and PLINQ queries.

Using Cancellation Support in .NET Framework 4, written by Mike Liddell, is an in-depth exploration of CancellationToken and CancellationTokenSource, how to make use of the cancellation support, and what are the common usage patterns that arise in practice.

(This paper and many more are available through the Parallel Computing Developer Center on MSDN at http://msdn.microsoft.com/en-us/concurrency/ee851578.aspx.)

Many different kinds of applications can benefit from multi-core parallelism, including add-ins to Microsoft Office.

Donny Amalo wrote a paper, PLINQ and Office Add-ins, where he demonstrates how to implement two parallel Microsoft Office add-ins using PLINQ:

• A parallel Monte Carlo simulation add-in for Excel
• A parallel custom spell checker add-in for Word

(This paper and many more are available through the Parallel Computing Developer Center on MSDN at http://msdn.microsoft.com/en-us/concurrency/ee851578.aspx.)

Despite the similarity in naming, the System.Threading.Tasks.Parallel class and the System.Activities.Statements.Parallel* activities in WF4 are largely orthogonal in the scenarios they address. However, WF4 activities and the new parallel programming types in .NET 4 can be used together to great advantage.

Ling Wo and Cristina Manu wrote a paper, Integrating Parallelism with Windows Workflow Foundation in the .NET Framework 4, that explores the similarities and differences between the two API sets, and demonstrates how to integrate the Task Parallel Library and WF4 to support the development of multi-threaded applications.

(This paper and many more are available through the Parallel Computing Developer Center on MSDN at http://msdn.microsoft.com/en-us/concurrency/ee851578.aspx.)

About six months ago, we posted on this blog to ask for details on if/how you’re using Parallel Extensions, and we got a great number of awesome responses… thanks!!  As that blog post has long since faded into distant memory, we’re asking again :)

Are you using Parallel Extensions, the parallelism support introduced with .NET 4? e.g. Parallel loops, Tasks, PLINQ, ConcurrentDictionary<>, ConcurrentQueue<>, Lazy<>, BlockingCollection<>, ManualResetEventSlim, ThreadLocal<T>, and so on?  Even if you’re using the unsupported .NET 3.5 release of Parallel Extensions, we’d love to hear from you.

Please get in touch by emailing me at stoub at microsoft dot com.  What are you building?  What functionality are you using?  What do you like?  What don’t you like?  What features/additions/changes would you like to see in the future?  etc.  Any and all feedback is welcome and encouraged.

Really looking forward to hearing from you!

Thanks,
Stephen

Boby George and Pooja Nagpal – testers on the Parallel Computing Platform team responsible for the parallel programming support in .NET 4- built a parallel spell checker algorithm and used the Concurrency Visualizer to analyze and improve the performance and scalability of their implementation.

Optimizing Parallel Applications Using Concurrency Visualizer: A Case Study demonstrates how the CPU Utilization view, Threads view, and Cores view can help identify and analyze the scalability bottlenecks in your code.

(This paper and many more are available through the Parallel Computing Developer Center on MSDN at http://msdn.microsoft.com/en-us/concurrency/ee851578.aspx.)