[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. 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). The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology, vol. 32, no. 6, pp. 545–550.
- Galdzicki, M., Wilson, M. L., Rodriguez, C. A., Pocock, M. R., Oberortner, E., Adam, L., … Sauro, H. M. (2012). Synthetic Biology Open Language (SBOL) Version 1.1.0, 1–26.
- Wilson, M. L., Hertzberg, R., Adam, L., & Peccoud, J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. (C. Voigt, Ed.)Methods in enzymology, 498, 173–88. doi:10.1016/B978-0-12-385120-8.00008-5
- Wilson, M. L., Okumoto, S., Adam, L., & Peccoud, J. (2013). Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. Bioinformatics (Oxford, England), 1–7.
- Talk: Adam, L. & Peccoud, J. Formal grammars to protect intellectual properties in synthetic biology. International Conference on Synthetic Biology at Evry, France, December 15-16, 2010.
- GenoCAD tutorials
Analyze: Semantic models of DNA sequences
- Cai, Y., Lux, M. W., Adam, L., & Peccoud, J. (2009). Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS computational biology, 5(10)
- Laura Adam, Matthew W. Lux, Mandy L. Wilson, Tian Hong, Jean Peccoud. Design of Languages for Systems and Synthetic Biology to translate genetic designs into mathematical models.
- Poster: Adam, L. & Peccoud, J. (2011). Using user defined semantic languages in synthetic biology: generating DNA compilers. Third International Workshop on BioDesign Automation (IWBDA) at 48th ACM/EDAC/IEEE Design Automation Conference (DAC) in San Diego, CA.
- Talk:. Formal languages to map Genotype to Phenotype in Natural Genomes. GBCB seminar, 2012.
Build: Biosecurity issues and DNA synthesis
- Adam, L., et al. (2011). Strengths and limitations of the federal guidance on synthetic DNA. Nature Biotechnology, 29(3), 208–210. doi:10.1038/nbt.1802
- Talk: GenoTHREAT: A biosecurity software to screen DNA synthesis orders against Pathogens. GBCB seminar, 2011.
- Adam, L.(2011). 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
PhD Defense slides: HERE