Difference between revisions of "Help:Glossary"
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A compedium and index of terms found in the Registry and synthetic biology indexed alphabetically | A compedium and index of terms found in the Registry and synthetic biology indexed alphabetically | ||
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==G== | ==G== | ||
| − | ; [[Generator]] | + | ; [[Help:Protein generators|Generator]] |
: A part which produces proteins in reponse to some stimuli. | : A part which produces proteins in reponse to some stimuli. | ||
| Line 48: | Line 49: | ||
==I== | ==I== | ||
| − | ; [[Inverter]] | + | ; [[Help:Inverters|Inverter]] |
: Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B. | : Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B. | ||
| Line 79: | Line 80: | ||
; [[Help:Equipment:PMP| PlateMate Plus]] | ; [[Help:Equipment:PMP| PlateMate Plus]] | ||
: A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates. | : A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates. | ||
| − | ; [[PoPS]] | + | ; [[Help:PoPS|PoPS]] |
: ''Po''lymerase ''P''er ''S''econd: A measure of number of times that an RNA Polymerase passes out of the regulatory region and into the protein coding region of a BioBrick. | : ''Po''lymerase ''P''er ''S''econd: A measure of number of times that an RNA Polymerase passes out of the regulatory region and into the protein coding region of a BioBrick. | ||
; Protein Coding Region | ; Protein Coding Region | ||
: A section of DNA that can cause the generation of a specific protein. In BioBricks, this includes the BioBrick prefix and suffix, the Ribosome Binding Site (RBS), the codons for the protein's amino acids, and the stop codon. | : A section of DNA that can cause the generation of a specific protein. In BioBricks, this includes the BioBrick prefix and suffix, the Ribosome Binding Site (RBS), the codons for the protein's amino acids, and the stop codon. | ||
| − | ; [[Protein Generator]] | + | ; [[Help:Protein generators|Protein Generator]] |
: A part which is able to produce proteins in response to some stimuli. | : A part which is able to produce proteins in response to some stimuli. | ||
==Q== | ==Q== | ||
;Quad Part Inverter ([[QPI]]) | ;Quad Part Inverter ([[QPI]]) | ||
| − | :QPI refers to a Quad-Part Inverter, that is, a [[Help:PoPS]]-based inverter composed of four sub-parts: a [[Help:Ribosome Binding Site|ribosome binding site]], a [[Help:Protein coding|coding region]] for a repressor protein (ie. cI lambda), a [[Help:Terminators]], and the [[Help:Regulatory|promoter]] (ie. pLamdba) which is regulated by the coded repressor protein | + | :QPI refers to a Quad-Part Inverter, that is, a [[Help:PoPS|PoPS]]-based inverter composed of four sub-parts: a [[Help:Ribosome Binding Site|ribosome binding site]], a [[Help:Protein coding|coding region]] for a repressor protein (ie. cI lambda), a [[Help:Terminators]], and the [[Help:Regulatory|promoter]] (ie. pLamdba) which is regulated by the coded repressor protein |
==R== | ==R== | ||
; Regulatory Region | ; Regulatory Region | ||
: The canonical model of a BioBrick component asserts that proteins generated as a result of other logical or cellular processes (see Protein Coding Region) as well as other active molecules interact with the computational body of a BioBrick component to produce the output signal. The genetic code of the computational body is represented by a Regulatory Region of DNA. | : The canonical model of a BioBrick component asserts that proteins generated as a result of other logical or cellular processes (see Protein Coding Region) as well as other active molecules interact with the computational body of a BioBrick component to produce the output signal. The genetic code of the computational body is represented by a Regulatory Region of DNA. | ||
| − | ; [[Reporter]] | + | ; [[Help:Reporter|Reporter]] |
: A gene that helps visualize or quantify the output of a device or part. | : A gene that helps visualize or quantify the output of a device or part. | ||
; [[Restriction enzymes]] | ; [[Restriction enzymes]] | ||
Latest revision as of 19:37, 12 July 2017
- Registry Help Pages:
- TOC
- At-a-Glance
- FAQ
0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
This glossary is always under construction! You can contribute by adding entries or simply linking them to relevant information. If you write a more comprehensive article, please add a short description on this page in addition to the link.
Contents
0-9
- 3OC6HSL
- A small signalling molecule of the acyl-homoserine lactone family.
A
- Abstraction Hierarchy
- A hierarchy in which individuals work independently at each level.
- acyl-homoserine lactones (acyl-HSLs)
- Small signalling molecules
B
- BioBrick Component
- A portion of a Biobrick device that is available as a BioBrick product. A protein coding region is a BioBrick device if it is available as a BioBrick product and documented in the BioBrick Data Book.
- BioBrick Device
- A BioBrick system consisting of one or more BioBrick components that together instantiate a full logical or functional process. Normally, this consists of input protein coding regions that code for the input proteins and a BioBrick computational body that processes the input proteins and generates TIPS at the output sites.
C
- canonical model
- a simplified model that adequately represents the components and interactions under study (the actual system may or may not be structured like the canonical model).
- cell-to-cell signalling
- communication between an individual cell and its neighbors in culture or on a plate.
- chassis
- the cell that contains and supports a synthetic biology system
- composable
- capable of combining to make a larger whole. In the context of BioBricks, the assembly of two BioBricks creates a new, single BioBrick that can, in turn, be used in downstream assemblies.
D
E
F
G
- Generator
- A part which produces proteins in reponse to some stimuli.
H
I
- Inverter
- Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B.
J
K
L
- LVA Tag
- A tag for degradation.
- Lux
- An operon for self-regulation production of luminescent proteins.
M
- [http
- //openwetware.org/wiki/Miniprep/Kit-free_high-throughput_protocol Miniprep]
- A process for isolating small amounts of plasmid DNA from bacteria by lysing the cells and precipitating chromosomal DNA and other cell structures.
N
O
- Output High (O_H)
- This is an output characteristic from a transfer function (see "output curve" entry below)
- Output Curve
- The current formula idealizing the output curve for <math>(a*c)/(1 + ((i/b)^n)</math>
P
- PlateMate Plus
- A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates.
- PoPS
- Polymerase Per Second: A measure of number of times that an RNA Polymerase passes out of the regulatory region and into the protein coding region of a BioBrick.
- Protein Coding Region
- A section of DNA that can cause the generation of a specific protein. In BioBricks, this includes the BioBrick prefix and suffix, the Ribosome Binding Site (RBS), the codons for the protein's amino acids, and the stop codon.
- Protein Generator
- A part which is able to produce proteins in response to some stimuli.
Q
- Quad Part Inverter (QPI)
- QPI refers to a Quad-Part Inverter, that is, a PoPS-based inverter composed of four sub-parts: a ribosome binding site, a coding region for a repressor protein (ie. cI lambda), a Help:Terminators, and the promoter (ie. pLamdba) which is regulated by the coded repressor protein
R
- Regulatory Region
- The canonical model of a BioBrick component asserts that proteins generated as a result of other logical or cellular processes (see Protein Coding Region) as well as other active molecules interact with the computational body of a BioBrick component to produce the output signal. The genetic code of the computational body is represented by a Regulatory Region of DNA.
- Reporter
- A gene that helps visualize or quantify the output of a device or part.
- Restriction enzymes
- An enzyme that recognizes a particular sequence of bases in DNA, and then cuts the DNA's backbones at that point.
- Ribosome Binding Site
S
- Small Molecule Sensors
- A small molecule sensor can trigger gene expression when a small molecule becomes present in a cell's environment. Generally, each sensor is specific only to one or a range of small molecules. These sensors are generally surface proteins that can bind to a small molecule ligand. Upon binding, the surfact protein changes conformation, causing one or more intra-cell signals to induce gene expression. A common method of creating a small molecule sensor is to find (discover or literature research) a cellular pathway that is induced by a certain molecule. The surface protein(s) and intial promotors of the mechanism can be isolated from the wild type cellular pathway and made into a BioBrick part. The isolated surface protein + promotor can be put upstream of a new expression gene and inserted into a cell.
- Signalling Molecules
- A molecules involved in (generally) intercellular signalling methods
T
- Tag
- Small functional sequences of amino acids.
- Transfer function
- The ratio of output and input in a system.