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 …
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 …
ebio·ome: the DNA space explorer.
Talk at SynBioBeta 2017 http://sf2017.synbiobeta.com/speakers/laura-adam/
PACHA.YEAST: Morphogenetic engineering of yeast Microcolonies
Incas regarded space and time as a single concept, referred to as pacha ( Quechua: pacha, Aymara: pacha). A poster of my work on PACHA.YEAST: Highlights: Lab automation with Apprent’yeast: learned patterns to automatically design plasmids from lab data (inferred a probabilistic context-free grammar (PCFG)) Adam, L. & Klavins, E. (2015). archiYEAST: a command-line synthetic yeast …