{"id":161019,"date":"2011-07-01T00:00:00","date_gmt":"2011-07-01T00:00:00","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/msr-research-item\/synthesizing-biological-theories\/"},"modified":"2018-10-16T21:05:10","modified_gmt":"2018-10-17T04:05:10","slug":"synthesizing-biological-theories","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/synthesizing-biological-theories\/","title":{"rendered":"Synthesizing Biological Theories"},"content":{"rendered":"<div class=\"asset-content\">\n<p>Studies of biological systems are often facilitated by diagram models that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of biology necessitates computational models that can extend these representations to include their dynamic behavior. We present here a new tool we call Synthesizing Biological Theories which enables biologists and modelers to construct high-level theories and models of biological systems, capturing biological hypotheses, inferred mechanisms, and experimental results within the same framework. Among the key features of the tool are convenient ways to represent several competing theories and the interactive nature of building and running the models using an intuitive, rigorous scenario-based visual language. The defnition of the modeling language is geared towards enabling formal verifcation and analysis.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Studies of biological systems are often facilitated by diagram models that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of biology necessitates computational models that can extend these representations to include their dynamic behavior. We present here a new tool we call Synthesizing Biological Theories which enables biologists and modelers [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":null,"msr_publishername":"Springer Verlag","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"Computer Aided Verification (CAV'11)","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"","msr_number":"","msr_organization":"","msr_pages_string":"579\u2013584","msr_page_range_start":"579","msr_page_range_end":"584","msr_series":"LNCS","msr_volume":"6806","msr_copyright":"","msr_conference_name":"Computer Aided Verification (CAV'11)","msr_doi":"","msr_arxiv_id":"","msr_s2_paper_id":"","msr_mag_id":"","msr_pubmed_id":"","msr_other_authors":"","msr_other_contributors":"","msr_speaker":"","msr_award":"","msr_affiliation":"","msr_institution":"","msr_host":"","msr_version":"","msr_duration":"","msr_original_fields_of_study":"","msr_release_tracker_id":"","msr_s2_match_type":"","msr_citation_count_updated":"","msr_published_date":"2011-07-01","msr_highlight_text":"","msr_notes":"","msr_longbiography":"","msr_publicationurl":"","msr_external_url":"","msr_secondary_video_url":"","msr_conference_url":"","msr_journal_url":"","msr_s2_pdf_url":"","msr_year":2011,"msr_citation_count":0,"msr_influential_citations":0,"msr_reference_count":0,"msr_s2_match_confidence":0,"msr_microsoftintellectualproperty":true,"msr_s2_open_access":false,"msr_s2_author_ids":[],"msr_pub_ids":[],"msr_hide_image_in_river":0,"footnotes":""},"msr-research-highlight":[],"research-area":[13553],"msr-publication-type":[193716],"msr-publisher":[],"msr-focus-area":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[],"msr-conference":[],"msr-journal":[],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-161019","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-medical-health-genomics","msr-locale-en_us"],"msr_publishername":"Springer Verlag","msr_edition":"Computer Aided Verification (CAV'11)","msr_affiliation":"","msr_published_date":"2011-07-01","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"579\u2013584","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"6806","msr_number":"","msr_editors":"","msr_series":"LNCS","msr_issue":"","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":1,"msr_main_download":"220210","msr_publicationurl":"","msr_doi":"","msr_publication_uploader":[{"type":"file","title":"sbt.pdf","viewUrl":"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2011\/07\/sbt.pdf","id":220210,"label_id":0}],"msr_related_uploader":"","msr_citation_count":0,"msr_citation_count_updated":"","msr_s2_paper_id":"","msr_influential_citations":0,"msr_reference_count":0,"msr_arxiv_id":"","msr_s2_author_ids":[],"msr_s2_open_access":false,"msr_s2_pdf_url":null,"msr_attachments":[],"msr-author-ordering":[{"type":"user_nicename","value":"hkugler","user_id":32012,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=hkugler"},{"type":"text","value":"Cory Plock","user_id":0,"rest_url":false},{"type":"text","value":"Andy Roberts","user_id":0,"rest_url":false}],"msr_impact_theme":[],"msr_research_lab":[],"msr_event":[],"msr_group":[],"msr_project":[544545],"publication":[],"video":[],"msr-tool":[169164],"msr_publication_type":"inproceedings","related_content":{"projects":[{"ID":544545,"post_title":"Station B","post_name":"stationb","post_type":"msr-project","post_date":"2019-03-11 15:56:07","post_modified":"2021-09-28 09:10:36","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/stationb\/","post_excerpt":"Our work on the Station B project has now been retired. We continue to actively explore the exciting intersection of computing and life sciences, with other projects located on\u00a0www.microsoft.com\/research. Building a platform for programming biology The ability to program biology could enable fundamental breakthroughs across a broad range of industries, including medicine, agriculture, food, construction, textiles, materials and chemicals. It could also help lay the foundation for a future bioeconomy based on sustainable technology. 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