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Created Release: Microsoft Biology Foundation 2.0 - Beta 1 (Apr 21, 2011)

zyskowski — Fri, 22 Apr 2011 04:36:08 GMT

We are pleased to announce the beta 1 release of MBF 2.0. This beta will provide the first significant update since MBF 1.0.

Primary improvements include:

Increased capacity for de novo assembly of human and other large, complex species
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

Please take a look and provide your feedback!

Created Release: MBF v2.0 Development Preview (Dec 03, 2010)

beatriza — Sat, 04 Dec 2010 04:47:18 GMT

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 sugarcane assembly
Object Model changes to use ISequence : IList<byte>
Optomization work:
1. Memory profiling and analysis on MBF
2. PaDeNA memory optimizations
3. Sequence optimizations (including non-string & non-character)
4. MUMmer optimization based on sequence
5. Object Model optimizations
6. 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

Created Release: Microsoft Biology Foundation 1.0 (Jul 09, 2010)

zyskowski — Fri, 09 Jul 2010 16:00:23 GMT

Download Version 1.0 of the Microsoft Biology Foundation here: http://research.microsoft.com/en-us/downloads/304eb276-8ed2-4cf9-ae1d-e48c38ba94b5/.

Updated Release: Microsoft Biology Foundation - Beta 2 (Feb 10, 2010)

zyskowski — Thu, 11 Feb 2010 05:15:34 GMT

We're happy to announce the first CodePlex release of MBF!
Included in this release is a new and improved installer for the Microsoft Biology Foundation, as well as samples, documentation and tools as part of the Software Development Kit (SDK) option:

Microsoft Biology Foundation:
- Core MBF system library (bio.dll).
- Core MBF web service library (WebServicesHandler.dll).
- Advanced algorithms for use in performing Multiple Sequence Alignment as well as whole genome de novo assembly, included both as core library features as well as examples of how to add modular functionality to the core via the Addin auto-registration mechanism (Addin\PaDeNa.dll, Addin\Pamsam.dll).
- Introductory as well as advanced technical documentation to better inform those interested in learning more about the technology and capabilities (Doc).
SDK:
- Complete technical reference documentation explaining all available capabilities of the MBF framework (BioDotNet.chm).
- Trident activity samples for generating genomics workflows using the Trident workflow workbench (bio.workflow.dll).
- IronPython project to show how the MBF library of functional can be used with the Python scripting language (BioDemo.py).
- Sequence Simulator, a small sample application which allows for splitting of large sequences into multiple shorter “reads” – intended to replicate what might come off a next-generation sequencing machine.

Please see the Release Notes download for a more complete description of this release.

Released: Microsoft Biology Foundation - Beta 2 (Feb 10, 2010)

Thu, 11 Feb 2010 05:15:34 GMT

Microsoft Biology Foundation:
- Core MBF system library (bio.dll).
- Core MBF web service library (WebServicesHandler.dll).
- Advanced algorithms for use in performing Multiple Sequence Alignment as well as whole genome de novo assembly, included both as core library features as well as examples of how to add modular functionality to the core via the Addin auto-registration mechanism (Addin\PaDeNa.dll, Addin\Pamsam.dll).
- Introductory as well as advanced technical documentation to better inform those interested in learning more about the technology and capabilities (Doc).
SDK:
- Complete technical reference documentation explaining all available capabilities of the MBF framework (BioDotNet.chm).
- Trident activity samples for generating genomics workflows using the Trident workflow workbench (bio.workflow.dll).
- IronPython project to show how the MBF library of functional can be used with the Python scripting language (BioDemo.py).
- Sequence Simulator, a small sample application which allows for splitting of large sequences into multiple shorter “reads” – intended to replicate what might come off a next-generation sequencing machine.

Please see the Release Notes download for a more complete description of this release.

Updated Release: Microsoft Biology Foundation - Beta 2 (Feb 10, 2010)

zyskowski — Thu, 11 Feb 2010 05:13:36 GMT

Microsoft Biology Foundation:
- Core MBF system library (bio.dll).
- Core MBF web service library (WebServicesHandler.dll).
- Advanced algorithms for use in performing Multiple Sequence Alignment as well as whole genome de novo assembly, included both as core library features as well as examples of how to add modular functionality to the core via the Addin auto-registration mechanism (Addin\PaDeNa.dll, Addin\Pamsam.dll).
- Introductory as well as advanced technical documentation to better inform those interested in learning more about the technology and capabilities (Doc).
SDK:
- Complete technical reference documentation explaining all available capabilities of the MBF framework (BioDotNet.chm).
- Trident activity samples for generating genomics workflows using the Trident workflow workbench (bio.workflow.dll).
- IronPython project to show how the MBF library of functional can be used with the Python scripting language (BioDemo.py).
- Sequence Simulator, a small sample application which allows for splitting of large sequences into multiple shorter “reads” – intended to replicate what might come off a next-generation sequencing machine.

Please see the "Documentation" section for a more complete set of release notes.

Updated Release: Microsoft Biology Foundation - Beta 2 (Feb 10, 2010)

zyskowski — Wed, 10 Feb 2010 21:28:23 GMT

Microsoft Biology Foundation:
- Core MBF system library (bio.dll).
- Core MBF web service library (WebServicesHandler.dll).
- Advanced algorithms for use in performing Multiple Sequence Alignment as well as whole genome de novo assembly, included both as core library features as well as examples of how to add modular functionality to the core via the Addin auto-registration mechanism (Addin\PaDeNa.dll, Addin\Pamsam.dll).
- Introductory as well as advanced technical documentation to better inform those interested in learning more about the technology and capabilities (Doc).
SDK:
- Complete technical reference documentation explaining all available capabilities of the MBF framework (BioDotNet.chm).
- Trident activity samples for generating genomics workflows using the Trident workflow workbench (bio.workflow.dll).
- IronPython project to show how the MBF library of functional can be used with the Python scripting language (BioDemo.py).
- Sequence Simulator, a small sample application which allows for splitting of large sequences into multiple shorter “reads” – intended to replicate what might come off a next-generation sequencing machine.

Please see the "Documentation" section for a more complete set of release notes.

Created Release: Sequence Assembler - Beta 2 (Feb 10, 2010)

zyskowski — Wed, 10 Feb 2010 21:26:50 GMT

As part of the Microsoft Biology Foundation project, we are also offering a tool called the Sequence Assembler, a Solution Accelerator application built on MBF to demonstrate the value of the platform as well as provide a useful tool for genomics research.

A WPF application provided as a sample/example of how to expose the MBF library features in a dedicated genomics program.
Integration of the MBF parsers, algorithms and web services in an easy to explore GUI.
Inclusion of the SilverMap BLAST visualization tool built in SilverLight.

Released: Sequence Assembler - Beta 2 (Feb 10, 2010)

Wed, 10 Feb 2010 21:26:50 GMT

A WPF application provided as a sample/example of how to expose the MBF library features in a dedicated genomics program.
Integration of the MBF parsers, algorithms and web services in an easy to explore GUI.
Inclusion of the SilverMap BLAST visualization tool built in SilverLight.

Created Release: Beta 2 (Feb 10, 2010)

zyskowski — Wed, 10 Feb 2010 21:21:22 GMT

Microsoft Biology Foundation:
- Core MBF system library (bio.dll).
- Core MBF web service library (WebServicesHandler.dll).
- Advanced algorithms for use in performing Multiple Sequence Alignment as well as whole genome de novo assembly, included both as core library features as well as examples of how to add modular functionality to the core via the Addin auto-registration mechanism (Addin\PaDeNa.dll, Addin\Pamsam.dll).
- Introductory as well as advanced technical documentation to better inform those interested in learning more about the technology and capabilities (Doc).
SDK:
- Complete technical reference documentation explaining all available capabilities of the MBF framework (BioDotNet.chm).
- Trident activity samples for generating genomics workflows using the Trident workflow workbench (bio.workflow.dll).
- IronPython project to show how the MBF library of functional can be used with the Python scripting language (BioDemo.py).
- Sequence Simulator, a small sample application which allows for splitting of large sequences into multiple shorter “reads” – intended to replicate what might come off a next-generation sequencing machine.

Please see the "Documentation" section for a more complete set of release notes.