Titlebook: Computational Methods in Synthetic Biology; Mario Andrea Marchisio Book 2015 Springer Science+Business Media New York 2015 CAD programs.DN

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Computational Design of RNA Parts, Devices, and Transcripts with Kinetic Folding Algorithms Implemenme- and dynamic aptazyme-regulated expression devices with quantitatively predictable functions (rREDs and aREDs, respectively) have been described (Carothers et al., Science 334:1716–1719, 2011). Here, we provide a detailed practical procedure for computational transcript design by illustrating a h

ECG769

Kappa Rule-Based Modeling in Synthetic Biologycan model biological interactions both at the genetic and the protein–protein interaction level, resulting in detailed stochastic models accounting naturally for transcriptional and translational resource usage. We also hope to impart the intuitively modular nature of the modeling processes involved

Compatriot

Chemical Master Equation Closure for Computer-Aided Synthetic Biology over 70 years. With the first complete solution of chemical master equations, a wide range of experimental observations of biomolecular interactions may be mathematically conceptualized. We anticipate that models based on the closure scheme described herein may assist in rationally designing synthe

commensurate

CT-angiography

https://doi.org/10.1007/978-1-4842-6461-4thetic biology devices including biosensors, bioproduction, or regulation circuits. To that end, a rational workflow for computational protein design is described here consisting of (a) searching in the sequence, structure or chemical spaces for the desired function and associated protein templates;

GRUEL

https://doi.org/10.1007/978-1-4842-6461-4urable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter

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https://doi.org/10.1007/978-1-4842-6461-4devices with predictable behaviors continues to increase. By combining engineered transcript components, such as ribosome binding sites, transcriptional terminators, ligand-binding aptamers, catalytic ribozymes, and aptamer-controlled ribozymes (aptazymes), gene expression in bacteria can be fine-tu

AWL

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https://doi.org/10.1007/978-3-658-29889-0h level of abstraction through constraints on otherwise unspecified DNA parts. The GEC compiler then selects parts which satisfy the constraints from a given parts database. GEC further provides more conventional programming language constructs for abstraction, e.g., through modularity. The GEC lang

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