information-biosecurity.org
http://information-biosecurity.org/ is a website where I compile publications related to biosecurity in the digital world. This is also where the twitter data analysis will available.
Twitter and biosecurity|dual-use (ongoing)
This is an ongoing early stage project in which I get data from twitter into a CouchDB. I am building a website to visualize my compiled data with flask. I do some natural language processing for sentiment analysis. One of my goal is to find dual-use topics… My most frequent words so far… I am …
Low-cost, modular, multi-strain diagnostic (ongoing)
This is the application part of the project I am finishing. We engineered yeast to induce growth arrest using a number of genes/inducers that we then characterized. We then used them as a diagnostic tool. We used nonlinear differential equations. We model our co-culture experiments and made predictions. We used a flow cytometer to collect …
Synthetic control of yeast culture growth rates (ongoing)
I am finishing a project started as a postdoc in the Klavins Lab at UW with Orlando de Lange and Alberto Carignano that we are about to publish. We engineered yeast to induce growth arrest using a number of genes/inducers that we then characterized. We then used it in a cool application. I work both …
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: …
Information Biosecurity: context
Preventing bioterrorism requires innovative solutionsspecific to the nature of the threat. Biotechnology is not like nuclear technology. Soon, tens of thousands of laboratories worldwide will be operating in a multi-billion-dollar industry. Even students working in small laboratories will be able to carry out gene manipulation. The approach to fighting the abuse of biotechnology for terrorist purposes …
Synthetic Biology Behemoth Aims to Police Its Own Industry
IEEE Spectrum July, 3rd 2018 by Elie Dolgin. https://spectrum.ieee.org/the-human-os/biomedical/ethics/synthetic-biology-behemoth-aims-to-police-its-own-industry These algorithmic and machine-learning approaches are what’s needed for biosecurity tools in the industry to move beyond simply matching sequences against known problematic strings of genetic code, says Laura Adam. Adam is cofounder of Ebiosec, a data management platform for synthetic biology, and the developer of GenoTHREAT, an open-source screening tool.
Point of View: A transatlantic perspective on 20 emerging issues in biological engineering
Wintle, B.C. & Boehm, C.R., Rhodes, C., Molloy, J.C., Millett, P., Adam, L., et al.., Sutherland, W.J. (2017) A transatlantic perspective on 20 emerging issues in biological engineering. eLife. Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture …