Design of Languages for Systems and Synthetic Biology
Context We propose to encompass context-dependent genomic information and mathematical models in a logical and structured fashion through the use of attribute grammars. Attribute Grammars (AG) provide means to compute a mathematical model (possibly encoding phenotypic traits) from a genetic construct. AGs are a framework for biological Domain Specifi c Languages (DSLs) that, unlike current formalisms …
Research on Language and Biology
The theory: Formal language and Genetic This is related to the work I have done at Peccoud’s synthetic biology lab from 2008 to 2013: Formal languages and DNA molecules Design of Languages for Systems and Synthetic Biology Biological Languages to Design Natural Genomes [Slides] Formal languages to map Genotype to Phenotype in Natural Genomes. Application: …
[OVERVIEW] My BioCAD tools
Design: GenoCAD – 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. Grünberg, J. Hallinan, N. …
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, …
[Slides] Formal languages to map Genotype to Phenotype in Natural Genomes.
Adam, L. Formal languages to map Genotype to Phenotype in Natural Genomes. GBCB seminar, 2012. Speaker: Laura Adam, GBCB Doctoral Candidate Advisor: Jean Peccoud, VBI Title: Formal languages to map Genotype to Phenotype in Natural Genomes Abstract: To formalize Genotype-to-Phenotype mapping and confer predictive powers, missing in current approaches, information from genomic databases and mathematical …
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 …
Modeling structure-function relationships in synthetic DNA sequences using attribute grammars
Authors Yizhi Cai, Matthew W Lux, Laura Adam, Jean Peccoud Publication date 2009/10/9 Journal PLoS computational biology Volume5 Issue10 Pages e1000529 Abstract Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the …