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This document discusses the Microsoft Biology Foundation (MBF), an open source bioinformatics toolkit built on the .NET Framework. MBF provides components for working with biological data formats, sequences, and algorithms. It is intended as a foundation for other tools and applications to build upon, rather than an application itself. The community around MBF consists of scientific programmers with a range of expertise. MBF is cross-platform, with new features in version 2 including advanced math functions, comparative assembly, command line tools, and visualization capabilities. The source code and community are hosted on Codeplex to encourage open source development of the toolkit.
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This document describes Bio-NGS, a BioRuby plugin for conducting programmable workflows for Next Generation Sequencing (NGS) data. Bio-NGS provides a software development framework, application, and project environment for analyzing NGS data. It integrates third-party bioinformatics tools as wrappers or bindings and allows for modular, reusable plugins. The document outlines features of the Bio-NGS application, software development framework, and project environment.
F07-Cloud-Hadoop-BAM
Hadoop-BAM is a small Java library that allows Binary Alignment Map (BAM) files, a common format for storing aligned DNA sequencing reads, to be directly manipulated and processed on Hadoop. It handles challenges like BAM's binary format and compression by detecting record boundaries and providing access to the files through the Picard SAM API. The library was used to build tools for preprocessing large BAM files for interactive browsing of genome data on Hadoop, demonstrating good scaling on a test of over 50GB of sequencing data from 1000 Genomes Project. Future work involves developing more BAM analysis tools that can leverage Hadoop-BAM.
C03-Visualization-Webapollo
WebApollo is a web-based genome annotation editor that allows multiple users to collaboratively edit annotations in real-time. It uses a client-server model where the web-based client communicates with an annotation editing engine and data server through a framework called Trellis. This allows annotations to be accessed and edited without installing software by running in a web browser.
F01-Cloud-Mygene.info
This document describes MyGene.Info, a gene annotation service that provides gene data through a RESTful API. It discusses how gene data is stored and queried from a CouchDB document-oriented database. Users can search for genes and retrieve full or filtered annotation objects for specific genes in JSON format through HTTP requests to the MyGene.Info website. The service aims to allow quick development of gene-centric websites and applications without needing to maintain a local gene annotation database.
A01-Openness in knowledge-based systems
This document discusses the potential for open source artificial intelligence to help understand molecular biology data. It argues that capturing common sense knowledge computationally has been challenging, but knowledge about molecular biology exists explicitly. An open source AI focused on molecular biology could help explain genomic data by developing a comprehensive knowledge base and using abductive inference. However, explaining biological phenomena is difficult and requires judgment. The document advocates for open source development to gain productivity advantages and build trust through transparency. It outlines challenges and opportunities for facilitating an open source AI community focused on understanding life.
F03-Cloud-Obiwee
OBIWEE is an open source bioinformatics cloud environment for running intensive workflows. It uses SLICEE as a workflow authoring tool and runs jobs on a scalable virtual cluster deployed on private or public clouds using OpenNebula or EC2. Workflows are authored by describing command lines and OBIWEE handles parallelization and job submission to the cluster. It provides tools for deployment, data management, and client access via command line or GUI interfaces like Kepler.
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Bosc mercer
- 1. A Framework for Bioinformatics on the Microsoft PlatformSimon MercerDirector, Health & WellbeingMicrosoft Research Connections 2/25/2011
- 3. May be wet-bench scientists themselves
- 4. Frequently support the lab and analyze the data
- 6. open source under the Apache 2.0 license
- 8. support for DNA, RNA and protein sequences
- 9. algorithm framework for analysis and transformation
- 11. it provides the basis for visualizations to be built on top ofYour Application MBF .NET Framework 4.0
- 12. Cross-Platform Capabilities Possible to target non-Windows platforms using Silverlight / Mono / Moonlight
- 13. New in v2 Advanced Math functions Available free to academics via the Intel MKL library and Sho Comparative DNA sequence assembly Assemble to reference of a related strain or species Command line tools Exposing MBF features on the command line Discovery via Visualization Natural navigation and annotation of assembled genomes Delight the Developer Ability to easily and efficiently create, extend and debug applications Grow the Community Provide training, easy on-ramps and incentives for contributing to the library
- 14. Open Source Development Source Code Community Support MBF.codeplex.com
- 16. Installers and tools available from:http://research.microsoft.com/bio/
- 17. Source Code and developer community support available from:http://mbf.codeplex.comThe name is going to change The MBF project is NOT guided by Microsoft alone The MBF project will NOT be owned by Microsoft:
Editor's Notes
- Extensibilitycore concepts mapped as interfacescan easily provide alternative implementations or add any missing features you needLanguage Neutralitybuilt on top of .NET – use any supported languagesupports dynamic languages such as IronPythonDesigned and implemented using best practicescommented source code provided so nothing is a black box algorithms all cite publications
- To use MBF in other environments, you will use Silverlight as your application style and then rely on Mono/Moonlight or the Silverlight plug-in on the OSX platform to run your code. You can still use Visual Studio for your IDE on the Windows platform, or if you are willing to work with the source code, you can use a Mono-based IDE such as MonoDevelop or SharpDevelop. MBF v2 will also support a Silverlight version with a subset of functionality but capable of running wherever Silverlight is supported