{"id":162141,"date":"2011-11-01T00:00:00","date_gmt":"2011-11-01T00:00:00","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/msr-research-item\/visual-dsd-a-design-and-analysis-tool-for-dna-strand-displacement-systems\/"},"modified":"2019-03-06T03:39:48","modified_gmt":"2019-03-06T11:39:48","slug":"visual-dsd-a-design-and-analysis-tool-for-dna-strand-displacement-systems","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/visual-dsd-a-design-and-analysis-tool-for-dna-strand-displacement-systems\/","title":{"rendered":"Visual DSD: a design and analysis tool for DNA strand displacement systems"},"content":{"rendered":"<div class=\"asset-content\">\n<p id=\"__p2\" class=\"p p-first\"><strong>Summary:<\/strong> The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation of the DSD programming language and compiler described by <a id=\"__tag_328854803\" class=\" bibr popnode tag_hotlink tag_tooltip\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3208393\/#B7\">Lakin <em>et al.<\/em> (2011<\/a>) with additional features such as support for polymers of unbounded length. It also supports stochastic and deterministic simulation, construction of continuous-time Markov chains and various export formats which allow models to be analysed using third-party tools.<\/p>\n<p id=\"__p3\"><strong>Availability:<\/strong> Visual DSD is available as a web-based Silverlight application for most major browsers on Windows and Mac OS X at <a class=\"msr-external-link glyph-append glyph-append-open-in-new-tab glyph-append-xsmall\" href=\"http:\/\/research.microsoft.com\/dna\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/research.microsoft.com\/dna<span class=\"sr-only\"> (opens in new tab)<\/span><\/a>. It can be installed locally for offline use. Command-line versions for Windows, Mac OS X and Linux are also available from the web page.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Summary: The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and analysis of computational devices implemented using DNA strand displacement, in a convenient web-based graphical interface. It is an implementation of the DSD programming language and compiler described by Lakin et al. (2011) with additional features such as support for polymers of unbounded length. [&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":"","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"Bioinformatics","msr_number":"","msr_organization":"","msr_pages_string":"","msr_page_range_start":"3211","msr_page_range_end":"3213","msr_series":"","msr_volume":"27","msr_copyright":"","msr_conference_name":"","msr_doi":"","msr_arxiv_id":"","msr_s2_paper_id":"","msr_mag_id":"","msr_pubmed_id":"","msr_other_authors":"Simon Youssef","msr_other_contributors":"","msr_speaker":"","msr_award":"","msr_affiliation":"","msr_institution":"Biological Computation Group, Microsoft Research, Cambridge CB3 0FB, UK.","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":"2011-11-15","msr_highlight_text":"","msr_notes":"","msr_longbiography":"","msr_publicationurl":"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr543","msr_external_url":"","msr_secondary_video_url":"","msr_conference_url":"","msr_journal_url":"","msr_s2_pdf_url":"","msr_year":0,"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":[13546],"msr-publication-type":[193715],"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-162141","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-computational-sciences-mathematics","msr-locale-en_us"],"msr_publishername":"","msr_edition":"","msr_affiliation":"","msr_published_date":"2011-11-15","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"","msr_chapter":"","msr_isbn":"","msr_journal":"Bioinformatics","msr_volume":"27","msr_number":"","msr_editors":"","msr_series":"","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":"","msr_publicationurl":"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr543","msr_doi":"","msr_publication_uploader":[{"type":"url","viewUrl":"false","id":"false","title":"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr543","label_id":"243109","label":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":[{"id":0,"url":"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr543"}],"msr-author-ordering":[{"type":"text","value":"Matthew R Lakin","user_id":0,"rest_url":false},{"type":"text","value":"Simon Youssef","user_id":0,"rest_url":false},{"type":"text","value":"Filippo Polo","user_id":0,"rest_url":false},{"type":"user_nicename","value":"Stephen Emmott","user_id":33572,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Stephen Emmott"},{"type":"user_nicename","value":"Andrew Phillips","user_id":31075,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Andrew Phillips"}],"msr_impact_theme":[],"msr_research_lab":[],"msr_event":[],"msr_group":[],"msr_project":[544545,170217],"publication":[],"video":[],"msr-tool":[],"msr_publication_type":"article","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. Despite&hellip;","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/544545"}]}},{"ID":170217,"post_title":"Programming DNA Circuits","post_name":"programming-dna-circuits","post_type":"msr-project","post_date":"2009-02-07 13:36:42","post_modified":"2020-03-06 10:49:40","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/programming-dna-circuits\/","post_excerpt":"Molecular devices made of nucleic acids show great potential for applications ranging from bio-sensing to intelligent nanomedicine. They allow computation to be performed at the molecular scale, while also interfacing directly with the molecular components of living systems. They form structures that are stable inside cells, and their interactions can be precisely controlled by modifying their nucleotide sequences. 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