You may be familiar with the Microsoft Biology Foundation (opens in new tab) (MBF), an open source bioinformatics .NET library that is designed to provide core functionality for genomics research from commonly-used file parsers to algorithms and web connectors. We’re pleased to announce that we are continuing to invest in the project in the coming year.
We recently posted a preview of MBF v2.0 (opens in new tab), which can be downloaded for development evaluation purposes. (Please note that this release is limited to source code only.) This release resolves a number of previously reported and identified issues. We also implemented-and in some cases, improved-many new features, including:
- BAM extension scenarios and paired end support
- Object model changes to use ISequence : IList
We also optimized some features for MBF v2.0, including:
- Memory profiling and analysis on MBF
- Parallel de Novo Assembler (PaDeNA) memory optimizations
- Sequence optimizations (including non-string and non-character)
- MUMmer optimization based on sequence
- Object model optimizations
- Additional scenarios for the collection of memory and performance profiles
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We are now in the process of implementing additional features. We will discuss those in greater detail at a future date. In the meantime, we invite you to participate in the MBF v2.0 development preview and provide feedback through our community forums (opens in new tab).
For best performance and to avoid any conflicts, we strongly recommend that you completely uninstall MBF v1.0 before you install MBF v2.0. Also, please note that we have identified the following issues that may affect your ability to install the code:
- The DLL version of MBF is incorrectly reported as 1.0.0.0
- The installer installs MBF in a directory named 2.1; it should be 2.0
The recommended (stable) MBF v1.0 code (opens in new tab) and corresponding v1.0 binaries (opens in new tab) are still available for download if you prefer to work with the earlier code. Either way, we encourage you to help us improve MBF by providing feedback in the forums.
For more information:
- MBF Tutorial Webcast (opens in new tab)
- 2010 eScience Workshop (opens in new tab)
- Microsoft Biology Initiative (opens in new tab)
MBF download locations:
- Microsoft Biology Foundation v.2 (source code only) (opens in new tab)
- Microsoft Biology Foundation v.1 (recommended) (opens in new tab)
- Corresponding v.1 Binaries (opens in new tab)
-Beatriz Diaz Acosta, Senior Research Program Manager, Microsoft Research