{"id":1682,"date":"2013-11-11T22:05:07","date_gmt":"2013-11-11T22:05:07","guid":{"rendered":"http:\/\/ladam.info\/?p=1682"},"modified":"2019-01-18T22:06:31","modified_gmt":"2019-01-18T22:06:31","slug":"development-of-a-domain-specific-genetic-language-to-design-chlamydomonas-reinhardtii-expression-vectors","status":"publish","type":"post","link":"https:\/\/ladam.info\/index.php\/2013\/11\/11\/development-of-a-domain-specific-genetic-language-to-design-chlamydomonas-reinhardtii-expression-vectors\/","title":{"rendered":"Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Authors&nbsp;<\/strong>Mandy L Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Publication date<\/strong> 2013\/11\/8<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Journal <\/strong>Bioinformatics Volume30 Issue2 Pages 251-257 <\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"84888905\">Abstract<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Motivation:<\/strong>\u2003Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As&nbsp;<em>de novo<\/em>&nbsp;gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Results:<\/strong>\u2003Using the design of constructs to express genes in the chloroplast of&nbsp;<em>Chlamydomonas reinhardtii<\/em>&nbsp;as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Availability and implementation:<\/strong>\u2003The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at&nbsp;<a href=\"http:\/\/www.genocad.org\/\">http:\/\/www.genocad.org<\/a>. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/2\/251\/222567\">https:\/\/academic.oup.com\/bioinformatics\/article\/30\/2\/251\/222567<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Authors&nbsp;Mandy L Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud Publication date 2013\/11\/8 Journal Bioinformatics Volume30 Issue2 Pages 251-257 Abstract Motivation:\u2003Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific&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":[275,260,272,276,10,265,269,254],"tags":[],"class_list":["post-1682","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-computational-biology","category-genocad","category-java","category-mynews","category-prolog","category-publications-peer-reviewed","category-synthetic-biology"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1682","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=1682"}],"version-history":[{"count":2,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1682\/revisions"}],"predecessor-version":[{"id":1684,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1682\/revisions\/1684"}],"wp:attachment":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media?parent=1682"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/categories?post=1682"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/tags?post=1682"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}