{"id":186100,"date":"2011-03-30T00:00:00","date_gmt":"2011-03-31T11:56:01","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/msr-research-item\/executable-knowledge-for-molecular-systems-biology\/"},"modified":"2016-08-22T11:31:08","modified_gmt":"2016-08-22T18:31:08","slug":"executable-knowledge-for-molecular-systems-biology","status":"publish","type":"msr-video","link":"https:\/\/www.microsoft.com\/en-us\/research\/video\/executable-knowledge-for-molecular-systems-biology\/","title":{"rendered":"Executable Knowledge for Molecular Systems Biology"},"content":{"rendered":"<div class=\"asset-content\">\n<p>I will give an overview of an ongoing long-term project aimed at developing a formal yet pragmatic framework for representing and exploring the behavior of complex molecular systems of interaction, such as they occur in cellular signalling. The approach recognizes the convergence of a scientific challenge&#8212;the need for transparent models respectful of the combinatorial complexity of protein-protein interaction networks&#8212;and a knowledge representation challenge&#8212;the formalization, collation, and curation of mechanistic interaction data through which models can become open-source collaborative documents.<\/p>\n<p>This is a &#8220;vision&#8221; talk, more than a technical talk, covering three facets:<\/p>\n<ul>\n<li>A characterization of the problem and associated opportunities, especially the changing role of the notion of &#8220;model&#8221; in systems biology;<\/li>\n<li>A survey of the approach: the definition of a (site-)graph rewriting language along with a suite of tools and web infrastructure;<\/li>\n<li>An outline of the road ahead.<\/li>\n<\/ul>\n<p>This is joint work with Russ Harmer (Harvard, CNRS), Vincent Danos (Edinburgh), Jerome Feret (ENS, Paris), and Jean Krivine (CNRS, Paris).<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>I will give an overview of an ongoing long-term project aimed at developing a formal yet pragmatic framework for representing and exploring the behavior of complex molecular systems of interaction, such as they occur in cellular signalling. The approach recognizes the convergence of a scientific challenge&#8212;the need for transparent models respectful of the combinatorial complexity [&hellip;]<\/p>\n","protected":false},"featured_media":196070,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr_hide_image_in_river":0,"footnotes":""},"research-area":[],"msr-video-type":[],"msr-locale":[268875],"msr-post-option":[],"msr-session-type":[],"msr-impact-theme":[],"msr-pillar":[],"msr-episode":[],"msr-research-theme":[],"class_list":["post-186100","msr-video","type-msr-video","status-publish","has-post-thumbnail","hentry","msr-locale-en_us"],"msr_download_urls":"","msr_external_url":"https:\/\/youtu.be\/iuWWwuXIAp4","msr_secondary_video_url":"","msr_video_file":"","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-video\/186100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-video"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-video"}],"version-history":[{"count":0,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-video\/186100\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media\/196070"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=186100"}],"wp:term":[{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=186100"},{"taxonomy":"msr-video-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-video-type?post=186100"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=186100"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=186100"},{"taxonomy":"msr-session-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-session-type?post=186100"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=186100"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=186100"},{"taxonomy":"msr-episode","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-episode?post=186100"},{"taxonomy":"msr-research-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-theme?post=186100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}