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Timeline

  • October 2011 - .NET Bio 1.0 is being released by its new owners, The Outercurve Foundation. This version is based on the Microsoft Biology Foundation version 2.0 beta 1, plus additional bug fixes generated during the beta feedback period. Listed below are some of the changes/updates since MBF version 1.0.
  • Increased capacity and speed for de novo assembly
  • Core object model improvements for smaller memory footprint and increased parallel processing
  • Silverlight implementation to facilitate cross-platform development
  • Support for the ‘Wiggle’ (.wgl) format commonly used in genome browsers.
  • New command line utilities also accessible via bio.dll:
1. Comparative Assembly – allows re-sequencing and comparative assembly of genomes of same or similar species
2. Comparative utility – assembles reads using comparative assembly algorithm
3. Consensus utility – generates consensus sequence from overlapping reads
4. Layout Refinement utility – refines reference layout between target and reference genome
5. Repeat Resolution utility – resolves ambiguity around ambiguously placed reads
6. Scaffold utility – uses mate pair information to create larger contigs aka scaffolds
7. NUCMER utility - .NET re-implementation of MUMmer 3.0 – aligns multiple reference and multiple query sequences in many vs. many fashion
8. LIS utility – finds longest increasing sub-sequence from a list of maximal unique matches (MUMS)
For a full list of changes please see the Getting Started Guide
  • September 2011 - Microsoft Biology Foundation is renamed to be .NET Bio. As part of the project ownership transition the OuterCurve Foundation. has renamed the project from the Microsoft Biology Foundation to .NET Bio. This new name provides emphasis on the capabilities inherit in the Microsoft .NET technology and fits more with the ongoing direction of the project.
  • August 2011 - Microsoft Biology Foundation Project ownership is transferred from Microsoft Corporation to the OuterCurve Foundation.
  • April 2011 - Microsoft Biology Foundation Version 2.0 Beta 1
    • Increased capacity for de novo assembly of larger and more complex species than version 1.0
    • 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
    • Documentation updates
Simon Mercer, director in the Microsoft Research Connections group, provides an overview of the improvements and features of the beta release of MBF version 2.0.



December 2010 - Microsoft Biology Foundation V2 Developer Preview
This release is intended as development evaluation and is limited to source code only.
In addition to bug fixes some of the below features have been implemented or improved:
  • BAM extension scenarios and paired end support
  • MUMmer optimizations to support sugarcane assembly
  • Object Model changes to use ISequence : IList<byte>
  • Optimization work:
    • Memory profiling and analysis on MBF
    • PaDeNA memory utilization
    • Sequence optimizations (including non-string & non-character)
    • MUMmer algorithm based on sequence
    • Object Model optimizations
    • More scenarios for collection of memory & perf profiles
  • July 2010 - Microsoft Biology Foundation 1.0
This initial version included parsers for common bioinformatics file formats; algorithms for manipulating DNA, RNA, and protein sequences; and connectors to biological web services, such as NCBI BLAST.
  • Month Year - Project Origin
The Microsoft Biology Foundation project was conceived and initiated at Microsoft by Simon Mercer.








Last edited Jan 3, 2012 at 7:59 PM by Rickbe, version 30

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