Glossary


Adaptation:

The process of becoming adjusted to new conditions.

Antithetic:

To be exactly the opposite of someone or something. This adjective is used to describe the motif used in ADAPTR as it refers to how the sigma-antisigma factors oppose each other and are thus able to cancel each other out.

BioBrick:

A standardised DNA Sequencee that can be used as a modular building block to rapidly create more complex DNA sequences.

Bioengineering:

The application of engineering principles to biology.

Biofuel:

A fuel that is produced through biological processes, such as agriculture and anaerobic digestion, in contrast to fuels produced by geological processes (i.e. those involved in the formation of fossil fuels). Biofuels can be derived directly from plants, or indirectly from agricultural, commercial, domestic, and/or industrial wastes.

Bioreactor:

An apparatus or vessel in which a biological reaction or process is carried out, typically on an industrial scale.

Biosensor:

A biosensor is an analytical device, used for the detection of a chemical substance, that combines a biological component with a physicochemical detector.

Biotechnology:

Technological applicationS that use biological systems or organisms to make or modify products for specific uses.

Bode Plot:

A graph of the frequency response of a system. It is usually a combination of a Bode magnitude plot, expressing the magnitude of the frequency response, and a Bode phase plot, expressing the phase shift.

Chassis:

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology.

Cloning:

The process of insertion of a DNA sequence into a vector for propagation.

Closed Loop:

A system that has a feedback loop or a control system that uses a feedback signal to generate the output.

Control Theory:

Describes the approaches to develop a system that ensures the output is at a desired state through the action of a controller.

Copy Number:

Referring to the number of copies of a particular gene present in the genome of an individual.

Cybergenetics:

Describes the interdisciplinary field of control theory and synthetic biology.

Design of Experiments (DOE):

A systematic method to determine the relationship between factors affecting a process and the output of that process.

Deterministic:

A model that produce an identical result for an identical set of inputs

Eigenvalues:

A scalar associated with a given linear transformation of a vector space and having the property that there is some nonzero vector which when multiplied by the scalar is equal to the vector obtained by letting the transformation operate on the vector.

Eigenvectors:

A vector which when operated on by a given operator gives a scalar multiple of itself.

Expression:

The process in which the product coded for by a gene is made. Genes are expressed.

Feedback:

Feedback is the process by which a fraction of an output signal is used as an input.

Feedforward:

A feedforward is an element or pathway within a control system that passes a controlling signal from a source in its external environment to a load elsewhere in its external environment.

Fermentation:

The chemical breakdown of a substance by bacteria, yeasts, or other microorganisms

Fourier Transform:

A mathematical transform that decomposes functions depending on space or time into functions depending on spatial frequency or temporal frequency.

Gain:

A measure of the ability of a circuit (often an amplifier) to increase the power or amplitude of a signal from the input to the output

Impulse:

The change in momentum, calculated by multiplying force with time.

Integration:

An integral assigns numbers to functions in a way that describes displacement, area, volume, and other concepts that arise by combining infinitesimal data. The process of finding integrals is called integration.

Genome:

The complete set of genes or genetic material present in a cell or organism.

Genetically Modified Organism:

A genetically modified organism (GMO) is an animal, plant, or microbe whose DNA has been altered using genetic engineering techniques.

In vivo:

(of a process) Performed or taking place in a living organism.

In vitro:

(of a process) Performed or taking place in a test tube, culture dish, or elsewhere outside a living organism.

Laplace Transform:

An integral transform that converts a function of a real variable (usually , in the time domain) to a function of a complex variable (in the complex frequency domain, also known as s-domain, or s-plane).

Part:

A sequence of DNA that encodes for a specific biological function.

Pertubation:

A change in conditions of the system in time.

Promoter:

A region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene. The resulting transcription produces an RNA molecule (such as mRNA).

Plasmid:

A circular, double-stranded DNA molecule typically containing a few thousand base pairs that replicates within a cell independently of the chromosomal DNA. Plasmid DNA is easily purified from cells, manipulated using common lab techniques and incorporated into cells

Ribosome Binding Site:

A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation.

Robust Perfect Adaptation (RPA):

the ability of a system to generate an output that returns to a fixed reference level (its ‘set point’) following a persistent change in input stimulus, with no need for tuning of system parameters

Scale-up:

Increase production or capacity.

Stochastic:

A model that produces data to predict the outcome accounting for unpredictability

Transformation:

Transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s).

Vector:

a DNA molecule (often plasmid or virus) that is used as a vehicle to carry a particular DNA segment into a host cell as part of a cloning or recombinant DNA technique. The vector typically assists in replicating and/or expressing the inserted DNA sequence inside the host cell.