{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:44:04Z","timestamp":1760708644148},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 structural constraints. As de novo 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.<\/jats:p>\n               <jats:p>Results:\u2003Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii 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.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http:\/\/www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.<\/jats:p>\n               <jats:p>Contact:\u2003peccoud@vt.edu<\/jats:p>\n               <jats:p>Supplementary Information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt646","type":"journal-article","created":{"date-parts":[[2013,11,10]],"date-time":"2013-11-10T01:09:20Z","timestamp":1384045760000},"page":"251-257","source":"Crossref","is-referenced-by-count":5,"title":["Development of a domain-specific genetic language to design <i>Chlamydomonas reinhardtii<\/i> expression vectors"],"prefix":"10.1093","volume":"30","author":[{"given":"Mandy L.","family":"Wilson","sequence":"first","affiliation":[{"name":"1 Virginia Bioinformatics Institute, 2Department of Plant Pathology, Physiology, and Weed Science and 3ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sakiko","family":"Okumoto","sequence":"additional","affiliation":[{"name":"1 Virginia Bioinformatics Institute, 2Department of Plant Pathology, Physiology, and Weed Science and 3ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Adam","sequence":"additional","affiliation":[{"name":"1 Virginia Bioinformatics Institute, 2Department of Plant Pathology, Physiology, and Weed Science and 3ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean","family":"Peccoud","sequence":"additional","affiliation":[{"name":"1 Virginia Bioinformatics Institute, 2Department of Plant Pathology, Physiology, and Weed Science and 3ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA"},{"name":"1 Virginia Bioinformatics Institute, 2Department of Plant Pathology, Physiology, and Weed Science and 3ICTAS Center for Systems Biology of Engineered Tissues, MC 0193, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,11,8]]},"reference":[{"key":"2023012710392106500_btt646-B1","doi-asserted-by":"crossref","first-page":"2760","DOI":"10.1093\/bioinformatics\/btm446","article-title":"A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts","volume":"23","author":"Cai","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012710392106500_btt646-B2","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1093\/nar\/gkq086","article-title":"GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs","volume":"38","author":"Cai","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012710392106500_btt646-B3","doi-asserted-by":"crossref","first-page":"W40","DOI":"10.1093\/nar\/gkp361","article-title":"Writing DNA with GenoCAD","volume":"37","author":"Czar","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012710392106500_btt646-B4","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1104\/pp.117.2.629","article-title":"The chloroplast atpA gene cluster in Chlamydomonas reinhardtii. 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