{"id":1654,"date":"2015-01-18T20:14:17","date_gmt":"2015-01-18T20:14:17","guid":{"rendered":"http:\/\/ladam.info\/?p=1654"},"modified":"2019-01-18T21:57:34","modified_gmt":"2019-01-18T21:57:34","slug":"biocad-tools-mapping-genotype-to-phenotype-using-attribute-grammar","status":"publish","type":"post","link":"https:\/\/ladam.info\/index.php\/2015\/01\/18\/biocad-tools-mapping-genotype-to-phenotype-using-attribute-grammar\/","title":{"rendered":"[OVERVIEW] My BioCAD tools"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"><strong>Design: <\/strong>GenoCAD \u2013 Rule-based genetic design tools user-friendly and Domain Specific Language<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. a Rodriguez, N. Roehner, M. L. Wilson, L. Adam, J. C. Anderson, B. a Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Gr\u00fcnberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. a Plahar, E. Sirin, G.-B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro (2014). <strong>The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.<\/strong> <em>Nature Biotechnology, vol. 32, no. 6, pp. 545\u2013550<\/em>.<\/li><li>Galdzicki, M., Wilson, M. L., Rodriguez, C. A., Pocock, M. R., Oberortner, E., Adam, L., \u2026 Sauro, H. M. (2012). <strong>Synthetic Biology Open Language (SBOL)<\/strong> Version 1.1.0, 1\u201326.<\/li><li>Wilson, M. L., Hertzberg, R., Adam, L., &amp; Peccoud, J. (2011). <strong>A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. <\/strong>(C. Voigt, Ed.)Methods in enzymology, 498, 173\u201388. doi:10.1016\/B978-0-12-385120-8.00008-5\n<\/li><li>Wilson, M. L., Okumoto, S., Adam, L., &amp; Peccoud, J. (2013). <strong>Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.<\/strong> <em>Bioinformatics (Oxford, England), 1\u20137. <\/em><\/li><li>Talk: Adam, L. &amp; Peccoud, J. <strong>Formal <\/strong><strong>grammars to protect intellectual properties in <\/strong><strong>synthetic biology<\/strong>. International Conference on Synthetic Biology at Evry, France, December 15-16, 2010.<\/li><li><a href=\"www.openhelix.com\/genocad\" target=\"_blank\" rel=\"noreferrer noopener\">GenoCAD tutorials<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Analyze: <\/strong>Semantic models of DNA sequences<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Cai, Y., Lux, M. W., Adam, L., &amp; Peccoud, J. (2009). <strong>Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. <\/strong>PLoS computational biology, 5(10)<\/li><li>Laura Adam, Matthew W. Lux, Mandy L. Wilson, Tian Hong, Jean Peccoud. <a href=\"https:\/\/ladam.info\/design-of-languages-for-systems-and-synthetic-biology\/\"><strong>Design of Languages for Systems and Synthetic Biology to translate genetic designs into mathematical models<\/strong>. <\/a><\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li>Poster: Adam, L. &amp; Peccoud, J. (2011). <strong>Using user defined semantic languages in synthetic biology: generating DNA compilers. <\/strong>Third International Workshop on BioDesign Automation (IWBDA) at 48th ACM\/EDAC\/IEEE Design Automation Conference (DAC) in San Diego, CA.<\/li><li><a href=\"https:\/\/ladam.info\/adam-l-formal-languages-to-map-genotype-to-phenotype-in-natural-genomes-gbcb-seminar-2012\/\">Talk:. <strong>Formal languages to map Genotype to Phenotype in Natural Genomes. <\/strong>GBCB seminar, 2012.<\/a><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Build: <\/strong>Biosecurity issues and DNA synthesis<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Adam, L., et al. (2011). <strong>Strengths and limitations of the federal guidance on synthetic DNA<\/strong>. Nature Biotechnology, 29(3), 208\u2013210. doi:10.1038\/nbt.1802<\/li><\/ul>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/ladam.info\/cyberbiosecurity\/slides-genothreat-a-biosecurity-software-to-screen-dna-synthesis-orders-against-pathogens\/\">Talk: <strong>GenoTHREAT<\/strong><strong>: A biosecurity software to screen DNA synthesis orders against Pathogens<\/strong>. GBCB seminar, 2011.<\/a><\/li><li>Adam, L.(2011). <a href=\"https:\/\/ladam.info\/essay\/\"><strong>Scientists need to be proactive to foment international biosecurity.<\/strong> <\/a>Runner up essay for the \u201cYoung Scientists\u201d essay contest organized by the Implementation and Support Unit of the Biological Weapon Convention at the United Nations<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">PhD Defense slides: <a href=\"https:\/\/ladam.info\/slides-defense-mapping-genotype-to-phenotype-using-attribute-grammar\/\">HERE<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Design: GenoCAD \u2013 Rule-based genetic design tools user-friendly and Domain Specific Language M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. a Rodriguez, N. Roehner, M. L. Wilson, L. Adam, J. C. Anderson, B. a Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Gr\u00fcnberg, J. Hallinan, N.&nbsp;&hellip;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[275,255,268,272,271,269,254,273,278],"tags":[],"class_list":["post-1654","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-biosecurity","category-communication","category-genocad","category-genothreat","category-publications-peer-reviewed","category-synthetic-biology","category-synthetic-biology-open-language-sbol","category-talks"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1654","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/comments?post=1654"}],"version-history":[{"count":4,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1654\/revisions"}],"predecessor-version":[{"id":1677,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1654\/revisions\/1677"}],"wp:attachment":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media?parent=1654"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/categories?post=1654"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/tags?post=1654"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}