Abstract: The present invention relates to a method for determining one or more intrinsic properties of a DNA component from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component, wherein the DNA component is involved in transcription of one or more target signals, wherein the plurality of measurements comprises measurements relating to the density of the cell culture over the time period and measurements relating to the amount of the one or more target signals in the cell culture over the time period.

Abstract: The present invention relates to a method for determining one or more intrinsic properties of a DNA component from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component, wherein the DNA component is involved in transcription of one or more target signals, wherein the plurality of measurements comprises measurements relating to the density of the cell culture over the time period and measurements relating to the amount of the one or more target signals in the cell culture over the time period.

Abstract: Creating genetic devices for use in micro-organisms or other biological systems is described. In an embodiment a computer system receives at a program editor, input specifying a plurality of part designs, at least some of which comprise part properties expressed as logical variables; and the input also specifies constraints on the logical variables. For example, the input is a computer program which specifies constraints on the logical variables which, for example, relate to properties of the DNA sequences such as reactions and biological behaviors. In an example, a compiler resolves the constraints using a database of genetic parts in order to generate candidate parts for the proposed genetic device. In examples the sequences of genetic parts are translated into reactions and simulated using an automated simulator and/or implemented in a living cell or other biological system. In embodiments the compiler also uses a database of reactions.

Abstract: The present invention relates to a method for determining one or more intrinsic properties of a DNA component from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component, wherein the DNA component is involved in transcription of one or more target signals, wherein the plurality of measurements comprises measurements relating to the density of the cell culture over the time period and measurements relating to the amount of the one or more target signals in the cell culture over the time period.

Abstract: A common framework provides for concurrently simulating a broad range of modeling languages with an arbitrary stochastic simulation method. The common framework is instantiated to each modeling language by defining a species function and a reactions function. The species function converts a model of the modeling language to a set of species, and the reactions function computes a set of possible reactions from a given set of species. The common framework is instantiated to a particular simulation method by defining three functions: one for computing the next reaction, another for computing the reaction activity from an initial set of reactions and species populations, and another for updating the reaction activity as the species populations change over time. Accordingly, the common framework compiles a set of species and possible reactions, dynamically updates the set of possible reactions, and selects the next reaction in an iterative cycle.

Abstract: Creating genetic devices for use in micro-organisms or other biological systems is described. In an embodiment a computer system receives at a program editor, input specifying a plurality of part designs, at least some of which comprise part properties expressed as logical variables; and the input also specifies constraints on the logical variables. For example, the input is a computer program which specifies constraints on the logical variables which, for example, relate to properties of the DNA sequences such as reactions and biological behaviors. In an example, a compiler resolves the constraints using a database of genetic parts in order to generate candidate parts for the proposed genetic device. In examples the sequences of genetic parts are translated into reactions and simulated using an automated simulator and/or implemented in a living cell or other biological system. In embodiments the compiler also uses a database of reactions.