{"id":2903,"date":"2011-01-05T10:30:00","date_gmt":"2011-01-05T10:30:00","guid":{"rendered":"https:\/\/blogs.msdn.microsoft.com\/msr_er\/2011\/01\/05\/join-the-microsoft-biology-foundation-v2-0-development-preview\/"},"modified":"2016-07-20T07:34:11","modified_gmt":"2016-07-20T14:34:11","slug":"join-the-microsoft-biology-foundation-v2-0-development-preview","status":"publish","type":"post","link":"https:\/\/www.microsoft.com\/en-us\/research\/blog\/join-the-microsoft-biology-foundation-v2-0-development-preview\/","title":{"rendered":"Join the Microsoft Biology Foundation v2.0 Development Preview"},"content":{"rendered":"<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><img decoding=\"async\" src=\"https:\/\/msdnshared.blob.core.windows.net\/media\/MSDNBlogsFS\/prod.evol.blogs.msdn.com\/CommunityServer.Blogs.Components.WeblogFiles\/00\/00\/01\/32\/81\/5224.MBFimage.gif\" original-url=\"http:\/\/blogs.msdn.com\/resized-image.ashx\/__size\/160x276\/__key\/CommunityServer-Blogs-Components-WeblogFiles\/00-00-01-32-81\/5224.MBFimage.gif\" alt=\"Microsoft Biology Foundation\" title=\"Microsoft Biology Foundation\" style=\"float: left; border: 0px;\" \/>You may be familiar with the <\/span><\/span><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/en-us\/projects\/bio\/mbf.aspx\"><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">Microsoft Biology Foundation<\/span><\/span><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"> (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&#8217;re pleased to announce that we are continuing to invest in the project in the coming year. <\/span><\/span><\/p>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">We recently posted a preview of <\/span><\/span><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/mbf.codeplex.com\/releases\/view\/56903\"><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">MBF v2.0<\/span><\/span><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">, 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:<\/span><\/span><\/p>\n<ul>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">BAM extension scenarios and paired end support<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Object model changes to use ISequence : IList<byte><\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">We also optimized some features for MBF v2.0, including:<\/span><\/span><\/p>\n<ul>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Memory profiling and analysis on MBF<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Parallel de Novo Assembler (PaDeNA) memory optimizations<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Sequence optimizations (including non-string and non-character)<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">MUMmer optimization based on sequence<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Object model optimizations<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">Additional scenarios for the collection of memory and performance profiles<\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">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 <\/span><\/span><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/www.getsatisfaction.com\/mbi\"><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">community forums<\/span><\/span><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">.<\/span><\/span><\/p>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">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:<\/span><\/span><\/p>\n<ul>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">The DLL version of MBF is incorrectly reported as 1.0.0.0<\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: small;\">The installer installs MBF in a directory named 2.1; it should be 2.0<\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">The recommended (stable) <\/span><\/span><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/mbf.codeplex.com\/releases\/view\/48654\"><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">MBF v1.0 code<\/span><\/span><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"> and <\/span><\/span><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/en-us\/downloads\/304eb276-8ed2-4cf9-ae1d-e48c38ba94b5\/\"><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">corresponding v1.0 binaries<\/span><\/span><span class=\"sr-only\"> (opens in new tab)<\/span><\/a><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"> 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.<\/span><\/span><\/p>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">For more information:<\/span><\/span><\/p>\n<ul>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/apps\/video\/default.aspx?id=142368\">MBF Tutorial Webcast<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<li><span style=\"text-decoration: underline;\"><\/span><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/en-us\/events\/escience2010\/default.aspx\">2010 eScience Workshop<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/bio\">Microsoft Biology Initiative<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\">MBF download locations:<\/span><\/span><\/p>\n<ul>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/mbf.codeplex.com\/releases\/view\/56903\">Microsoft Biology Foundation v.2 (source code only)<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/mbf.codeplex.com\/releases\/view\/48654\">Microsoft Biology Foundation v.1 (recommended)<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<li><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><span style=\"font-size: small;\"><a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" rel=\"noopener noreferrer\" target=\"_blank\" href=\"http:\/\/research.microsoft.com\/en-us\/downloads\/304eb276-8ed2-4cf9-ae1d-e48c38ba94b5\/\">Corresponding v.1 Binaries<span class=\"sr-only\"> (opens in new tab)<\/span><\/a><\/span><\/span><\/span><\/li>\n<\/ul>\n<p><span style=\"font-family: verdana,geneva;\"><span style=\"font-size: medium;\"><i>-Beatriz Diaz Acosta, <\/i><i>Senior Research Program Manager, Microsoft Research<\/i><\/span><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>You may be familiar with the Microsoft Biology Foundation (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&#8217;re pleased to announce that we are continuing to invest in the project in the coming year. We recently posted [&hellip;]<\/p>\n","protected":false},"author":32627,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":[],"msr_hide_image_in_river":0,"footnotes":""},"categories":[1],"tags":[186587,194763,194784,194826,193585,193497,195672,195981,196330,196391,196395,193504,196578,196776,197162],"research-area":[],"msr-region":[],"msr-event-type":[],"msr-locale":[268875],"msr-post-option":[],"msr-impact-theme":[],"msr-promo-type":[],"msr-podcast-series":[],"class_list":["post-2903","post","type-post","status-publish","format-standard","hentry","category-research-blog","tag-net","tag-bam-extension-scenarios","tag-beatriz-diaz-acosta","tag-bioinformatics","tag-escience-workshop","tag-external-research","tag-genomics","tag-isequence","tag-mbf-v2-0","tag-microsoft-biology-foundation-mbf","tag-microsoft-biology-initiative","tag-microsoft-research","tag-mummer","tag-parallel-de-novo-assembler-padena","tag-sequence-optimizations","msr-locale-en_us"],"msr_event_details":{"start":"","end":"","location":""},"podcast_url":"","podcast_episode":"","msr_research_lab":[],"msr_impact_theme":[],"related-publications":[],"related-downloads":[],"related-videos":[],"related-academic-programs":[],"related-groups":[],"related-projects":[],"related-events":[],"related-researchers":[],"msr_type":"Post","byline":"","formattedDate":"January 5, 2011","formattedExcerpt":"You may be familiar with the Microsoft Biology Foundation (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&#039;re pleased to announce that we are continuing to invest&hellip;","locale":{"slug":"en_us","name":"English","native":"","english":"English"},"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/2903","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/users\/32627"}],"replies":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/comments?post=2903"}],"version-history":[{"count":1,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/2903\/revisions"}],"predecessor-version":[{"id":262455,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/posts\/2903\/revisions\/262455"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=2903"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/categories?post=2903"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/tags?post=2903"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=2903"},{"taxonomy":"msr-region","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-region?post=2903"},{"taxonomy":"msr-event-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-event-type?post=2903"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=2903"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=2903"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=2903"},{"taxonomy":"msr-promo-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-promo-type?post=2903"},{"taxonomy":"msr-podcast-series","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-podcast-series?post=2903"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}