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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[[Help:Glossary:#|#]]
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[[Help:Glossary:A|A]]
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[[Help:Glossary:B|B]]
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[[Help:Glossary:C|C]]
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[[Help:Glossary:D|D]]
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[[Help:Glossary:E|E]]
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[[Help:Glossary:F|F]]
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[[Help:Glossary:G|G]]
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[[Help:Glossary:H|H]]
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[[Help:Glossary:I|I]]
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[[Help:Glossary:J|J]]
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[[Help:Glossary:K|K]]
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[[Help:Glossary:L|L]]
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[[Help:Glossary:M|M]]
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[[Help:Glossary:N|N]]
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[[Help:Glossary:O|O]]
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[[Help:Glossary:P|P]]
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[[Help:Glossary:Q|Q]]
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[[Help:Glossary:R|R]]
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[[Help:Glossary:S|S]]
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[[Help:Glossary:T|T]]
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[[Help:Glossary:U|U]]
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[[Help:Glossary:V|V]]
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[[Help:Glossary:W|W]]
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[[Help:Glossary:X|X]]
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[[Help:Glossary:Y|Y]]
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[[Help:Glossary:Z|Z]]
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{{Glossary Header}}
  
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This glossary is <b>always under construction!</b> You can contribute by adding entries or simply linking them to relevant information
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==0-9==
 +
; [[3OC6HSL]]
 +
: A small signalling molecule of the [[Acyl-HSLs|acyl-homoserine lactone]] family.
 +
 
 +
==A==
 +
;[[Abstraction Hierarchy]]
 +
: A hierarchy in which individuals work independently at each level.
 +
; [[acyl-HSLs|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==
 +
; [[Help:Protein generators|Generator]]
 +
: A part which produces proteins in reponse to some stimuli.
 +
 
 +
==H==
 +
 
 +
 
 +
==I==
 +
; [[Help:Inverters|Inverter]]
 +
: Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B.
 +
 
 +
==J==
 +
 
 +
 
 +
==K==
 +
 
 +
 
 +
==L==
 +
; [[Tag#LVA Tag|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==
 +
; [[Help:Equipment:PMP| PlateMate Plus]]
 +
: A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates.
 +
; [[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.
 +
; Protein Coding Region
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: 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.
 +
; [[Help:Protein generators|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 [[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==
 +
; 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.
 +
; [[Help:Reporter|Reporter]]
 +
: A gene that helps visualize or quantify the output of a device or part.
 +
; [[Restriction enzymes]]
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: An enzyme that recognizes a particular sequence of bases in DNA, and then cuts the DNA's backbones at that point.
 +
; [[Help:Ribosome Binding Site|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.
 +
 
 +
; [[Help:Signalling|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.
 +
 
 +
==U==
 +
 
 +
 
 +
==V==
 +
 
 +
 
 +
==W==
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 +
 
 +
==X==
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 +
 
 +
==Y==
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==Z==

Latest revision as of 19:37, 12 July 2017

A compedium and index of terms found in the Registry and synthetic biology indexed alphabetically

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.


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.

U

V

W

X

Y

Z