The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
Authors: Michal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, …
News coverage GenoCAD
Languages written to design synthetic living systems useful for new products, health care. March 13, 2014 by Emily Kale. https://www.sciencedaily.com/releases/2014/03/140313164524.htm 50 Awesome Open Source Apps You’ve (Probably) Never Heard Of.25 October 2010 by Cynthia Harvey. Originally on datamation.com http://www.freerepublic.com/focus/chat/2615454/posts
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors
Authors Mandy L Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud Publication date 2013/11/8 Journal Bioinformatics Volume30 Issue2 Pages 251-257 Abstract Motivation: Expression 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 …
[Slides DEFENSE] Mapping Genotype to Phenotype using Attribute Grammar
MAPPING GENOTYPE TO PHENOTYPE USING ATTRIBUTE GRAMMAR Doctoral Dissertation Defense Thursday, July 25th, 2013 – 1:00PM Virginia Bioinformatics Institute – Room 325LAURA ADAM Genetics, Bioinformatics and Computational Biology Program ADVISORY COMMITTEE: Jean Peccoud (Chair) David Bevan, Harold Garner, François Képès, Naren Ramakrishnan, John Tyson Abstract Over the past 10 years, several synthetic biology research groups …
GenoCAD tutorials
We developed tutorial material on GenoCAD which I used on several occasions. Adam, L. & Peccoud, J. Tutorial : GenoCAD I&II. Modelling Complex Biological Systems in the Context of Genomics in Nice, France, March, 2013. (invited) Adam, L. & Peccoud, J. Tutorial : GenoCAD I&II. Modelling Complex Biological Systems in the Context of Genomics at Evry, France, May 21-25, 2012 and La-Colle-sur-Loup, France, …
News coverage GenoTHREAT
Biosecurity for the Age of Redesigned Life.November 8, 2013 by JOHN DANKOSKY. NPR Science Friday (http://www.sciencefriday.com/segments/biosecurity-for-the-age-of-redesigned-life/) iGEM Team Developing Biosecurity Software for Synthetic Genomics.Jul 23, 2010 by Uduak Grace Thomas. (https://www.genomeweb.com/informatics/igem-team-developing-biosecurity-software-synthetic-genomics) Bioinformatics used to detect rogue use of synthetic biology. July 19-20, 2010 by Barry Whyte, Virginia Tech (PR). Biotechniques, Science Blog, e! Science News, R&D Mag, Eurekalert, ScienceDaily, …
Scientists need to be proactive to foment international biosecurity.
Runner-up essay for the “Young Scientists” essay contest organized by the Implementation and Support Unit of the Biological Weapon Convention at the United Nations
Strengths and limitations of the federal guidance on synthetic DNA
Adam, L., Kozar, M., Letort, G., Mirat, O., Srivastava, A., Stewart, T., Wilson, M.L., Peccoud, J. (2011). Strengths and limitations of the federal guidance on synthetic DNA. Nature Biotechnology.
A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD
Authors Mandy L Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud Publication date 2011/1/1 Book Methods in enzymology Volume 498 Pages 173-188 GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific …
Formal grammars to protect intellectual properties in synthetic biology.
International Conference on Synthetic Biology at Evry, France, December 15-16, 2010. (invited talk+poster)