Difference between revisions of "Catalog"

Latest revision as of 07:08, 6 October 2023

Browse collections
Browse well documented parts • frequently used parts
Browse parts by type • devices by type
Browse parts and devices by function • by chassis • by standard • or by contributor
Browse chassis
Browse user-supplied catalog pages - these pages have not undergone curation by the Registry but have been made by the Registry user community. Please feel free to add new catalog pages to this section.

Browse parts by type

Catalog	List
		Promoters (?): A promoter is a DNA sequence that tends to recruit transcriptional machinery and lead to transcription of the downstream DNA sequence.
		Ribosome Binding Site/about (?): A ribosome binding site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation.
		Protein domains (?): Protein domains are portions of proteins cloned in frame with other proteins domains to make up a protein coding sequence. Some protein domains might change the protein's location, alter its degradation rate, target the protein for cleavage, or enable it to be readily purified.
		Protein coding sequences (?): Protein coding sequences encode the amino acid sequence of a particular protein. Note that some protein coding sequences only encode a protein domain or half a protein. Others encode a full-length protein from start codon to stop codon. Coding sequences for gene expression reporters such as LacZ and GFP are also included here.
		Translational units (?): Translational units are composed of a ribosome binding site and a protein coding sequence. They begin at the site of translational initiation, the RBS, and end at the site of translational termination, the stop codon.
		Terminators (?): A terminator is an RNA sequence that usually occurs at the end of a gene or operon mRNA and causes transcription to stop.
		DNA (?): DNA parts provide functionality to the DNA itself. DNA parts include cloning sites, scars, primer binding sites, spacers, recombination sites, conjugative tranfer elements, transposons, origami, and aptamers.
		Plasmid backbones (?): A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. A plasmid backbone is defined as the plasmid sequence beginning with the BioBrick suffix, including the replication origin and antibiotic resistance marker, and ending with the BioBrick prefix.
		Plasmids (?): A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. If you're looking for a plasmid or vector to propagate or assemble plasmid backbones, please see the set of plasmid backbones. There are a few parts in the Registry that are only available as circular plasmids, not as parts in a plasmid backbone, you can find them here. Note that these plasmids largely do not conform to the BioBrick standard.
		Primers (?): A primer is a short single-stranded DNA sequences used as a starting point for PCR amplification or sequencing. Although primers are not actually available via the Registry distribution, we include commonly used primer sequences here.
		Composite parts (?): Composite parts are combinations of of two or more BioBrick parts.

Browse devices by type

We're in the process of developing new support for the specification of devices in the Registry. For the time being, please see the existing device tables below.

[[1]]	Protein generators (?):
[[2]]	Reporters (?):
[[3]]	Inverters (?):
[[4]]	Receivers and senders (?):
[[5]]	Measurement devices (?):

Browse parts and devices by function

This section replaces the previous Featured parts pages.

	Biosafety: Parts and devices improving biological containment.
	Biosynthesis: Parts involved in the production or degradation of chemicals and metabolites are listed here.
	Cell-cell signaling and quorum sensing: Parts involved in intercellular signaling and quorum sensing between bacteria.
	Cell death: Parts involved in killing cells.
	Coliroid: Parts involved in taking a bacterial photograph.
	Conjugation: Parts involved in DNA conjugation between bacteria.
	Motility and chemotaxis: Parts involved in motility or chemotaxis of cells.
	Odor production and sensing: Parts the produce or sense odorants.
	DNA recombination: Parts involved in DNA recombination.
	Viral vectors: Parts involved in the production and modification of Viral vectors.

Browse parts by curated collection

See more info on Registry collections.

Part Type

Function

Chassis

Interlabs

Interlab 2022 Devices

Toolkit

[http://2012.igem.org/Team:Freiburg|Freiburg 2012 TALE collection]
Genome Integration Toolkit (miniTn7)
JUMP Collection

Award Collections

See parts (and teams!) that have won awards in the iGEM competition

Project Types

Other

Browse parts and devices by chassis

Unless otherwise specified, most parts in the Registry work in Escherichia coli.

Catalog	List
		Escherichia coli (?): Most parts in the Registry function in E. coli.
		Yeast (?): Yeast are simple eukaryotes.
		Bacteriophage T7 (?): Bacteriophage T7 is an obligate lytic phage of E. coli.
		Bacillus subtilis (?): Bacillus subtilis is a model gram-positive bacterium.
		MammoBlocks (?): MammoBlocks are a new category of BioBrick introduced by the MIT iGEM team in 2010 and continued in 2011. There are now dozens of MammoBlocks suitable for rapid expression in mammalian cells.

Browse parts and devices by standard

Unless otherwise specified, most parts in the Registry comply with the original BioBrick assembly standard (also known as Assembly standard 10).

Assembly standard 10 (?): Assembly standard 10, or the original BioBrick assembly standard, was developed by Tom Knight in 2003. Most parts in the Registry comply with this assembly standard.

Assembly standard 23 (?): Assembly standard 23, or the Silver standard, is compatible with original BioBrick assembly standard and allows for in-frame assembly of protein domains.

Assembly standard 25 (?): Assembly standard 25, or the Freiburg standard, extends upon the original BioBrick assembly standard and allows for in-frame assembly of protein domains.

Assembly standard 21 (?): Assembly standard 21, also known as the BglBrick, BBb, or Berkeley standard, is optimized to enable in-frame assembly of protein domains.

Assembly standard 28 (?): Assembly standard 28, also known as the Lim lab standard or AarI cloning, is optimized for assembly of 3 parts into a vector simultaneously. Most parts that comply with Assembly standard 28 function in yeast.

Assembly standard 15 (?): Julie Norville has developed a new set of parts for assembly of fusion proteins.

Assembly standard 65 (?): The MIT iGEM 2010 and 2011 teams have developed a Gateway-based standard for assembly of mammalian promoters, genes, and expression vectors known as MammoBlocks.

Please see [http://hdl.handle.net/1721.1/45137 BBF RFC 29] for naming conventions for standards of physical composition.

Browse parts and devices by contributor

Browse chassis

Looking for a particular strain? You can find it here.

Catalog	List
		Escherichia coli chassis (?): Most parts in the Registry operate in E. coli.
		Bacillus subtilis chassis (?): Bacillus subtilis is a model gram-positive bacterium.
		Cell-free chassis (?): In vitro transcription/translation systems can be useful for some synthetic biological systems.
		Chlamydomonas reinhardtii (?): A unicellular alga with a promising future in synthetic biology.

Browse user-supplied catalog pages

These pages have not undergone curation by the Registry but have been made by the Registry user community. Please feel free to add new catalog pages to this section. Over time, high quality pages will be "promoted" to the primary Registry catalog collection.

	Mesoplasma florum (?): Mesoplasma florum is a particularly simple model organism.
	Genome Integration (?): The miniTn7 BioBrick tool kit is a set of fully BioBrick-compatible vectors based on Tn7 transposon for the integration of parts into microbial genomes.
	Magnetotaxis (?): magnetotactic strain AMB-1 with BioBrick-compatible toolkit enables development of synthetic biology into magnetotaxis and beyond.
	Chlamydomonas reinhardtii Part Collections (?): fitting the MoClo syntax for plants following the Golden Gate cloning standard and therefore the iGEM RFC[1000] Type IIS standard.
	Arthrospira platensis

@@ Line 1: / Line 1: @@
-[[Main Page|< Back to Registry]]
+{{Catalog/MainLinks}}
+* '''Browse''' [[Catalog#Browse_parts_by_curated_collection | '''collections''']]
-----
+*'''Browse''' [[Well Documented Parts | '''well documented parts''']] &bull; [[Frequently_Used_Parts | '''frequently used parts''']]
 *'''Browse''' [[Catalog#Browse_parts_by_type|'''parts by type''']] &bull; [[Catalog#Browse_devices_by_type|'''devices by type''']]
 *'''Browse parts and devices''' [[Catalog#Browse_parts and devices_by_function|'''by function''']] &bull; [[Catalog#Browse_parts and devices_by_chassis|'''by chassis''']] &bull; [[Catalog#Browse_parts and devices_by_standard|'''by standard''']] &bull; '''or''' [[Catalog#Browse_parts and devices_by_contributor|'''by contributor''']]
@@ Line 8: / Line 7: @@
 *'''Browse''' [[Catalog#Browse user-supplied catalog pages|'''user-supplied catalog pages''']] - these pages have not undergone curation by the Registry but have been made by the Registry user community.  Please feel free to add new catalog pages to this section.
 ----
 ===Browse parts by type===
@@ Line 15: / Line 15: @@
 |valign='top'|
 |-
-|valign='top' align='center' width=50px | {{Click || image=Part icon regulatory.png | link=Expression Operating Systems |width=30px | height=30px}}
 |valign='top' align='center' width=50px | {{Click || image=Part icon regulatory.png | link=Promoters |width=30px | height=30px}}
 |valign='top' align='center' |[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Regulatory https://static.igem.org/mediawiki/parts/5/56/RegistryListSmall.png]
 |valign='top'|'''[[Promoters]] [[Help:Promoters|(?)]]''': A promoter is a DNA sequence that tends to recruit transcriptional machinery and lead to transcription of the downstream DNA sequence.
 |-
-|valign='top' align='center' width=50px | {{Click || image=Part icon rbs.png | link=Ribosome Binding Sites |width=30px | height=30px}}
+|valign='top' align='center' width=50px | {{Click || image=Part icon rbs.png | link=Ribosome Binding Site/about |width=30px | height=30px}}
 |valign='top' align='center'|[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=RBS https://static.igem.org/mediawiki/parts/5/56/RegistryListSmall.png]
-|valign='top' |'''[[Ribosome Binding Sites]] [[Help:Ribosome Binding Sites|(?)]]''': A ribosome binding site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation.
+|valign='top' |'''[[Ribosome Binding Site/about]] [[Help:Ribosome Binding Sites|(?)]]''': A ribosome binding site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation.
 |-
 |valign='top' align='center' width=50px | {{Click || image=Part icon protein domain.png | link=Protein domains |width=30px | height=30px}}
@@ Line 60: / Line 59: @@
 |valign='top' |'''[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Composite Composite parts] [[Help:Composite parts|(?)]]''': Composite parts are combinations of of two or more BioBrick parts.
 |}
 ===Browse devices by type===
@@ Line 80: / Line 80: @@
 |valign='top' |'''[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=Measurement Measurement devices] [[Help:Measurement devices|(?)]]''':
 |}
 ===Browse parts and devices by function===
@@ Line 85: / Line 86: @@
 {|
+|align='center' width=80px |{{Click || image=600px-Biohazard.svg.jpg | link=Biosynthesis |width=48px | height=48px }}
+|'''[[Biosafety|Biosafety]]''': Parts and devices improving biological containment.
+|-
 |align='center' width=80px |{{Click || image=Proteincodingregionbiosynthesis.png | link=Biosynthesis |width=48px | height=48px }}
 |'''[[Biosynthesis|Biosynthesis]]''': Parts involved in the production or degradation of chemicals and metabolites are listed here.
@@ Line 112: / Line 116: @@
 |'''[[Viral vectors]]''': Parts involved in the production and modification of Viral vectors.
 |}
+===Browse parts by curated collection===
+See more info on [[Collections | Registry collections]].
+{{Catalog/Collections/List}}
 ===Browse parts and devices by chassis===
@@ Line 137: / Line 147: @@
 |valign='top' align='center' |
 |valign='top' |'''[[Bacillus subtilis]] [[Help:Bacillus subtilis|(?)]]''': Bacillus subtilis is a model gram-positive bacterium.
+|-
+|valign='top' align='center' | {{Click || image=HEK-293.png | link=MammoBlocks |width=30px | height=30px}}
+|valign='top' align='center' |
+|valign='top' |'''[[MammoBlocks]] [[Help:MammoBlocks|(?)]]''': MammoBlocks are a new category of BioBrick introduced by the MIT iGEM team in 2010 and continued in 2011. There are now dozens of MammoBlocks suitable for rapid expression in mammalian cells.
 |}
 ===Browse parts and devices by standard===
@@ Line 148: / Line 163: @@
 |'''[[Assembly standard 23]] [[Help:Assembly standard 23|(?)]]''': Assembly standard 23, or the Silver standard, is compatible with original BioBrick assembly standard and allows for in-frame assembly of protein domains.
 |-
-|'''[[Assembly standard 25]] [[Help:Assembly standard 25|(?)]]''': Assembly standard 25, or the Freiburg standard, extends upon the original BioBrick assembly standard and allows for in-frame assembly of protein domains.
+|'''[[RFC25 "Freiburg standard" parts|Assembly standard 25]] [[Help:Assembly standard 25|(?)]]''': Assembly standard 25, or the Freiburg standard, extends upon the original BioBrick assembly standard and allows for in-frame assembly of protein domains.
 |-
 |'''[[Assembly standard 21]] [[Help:Assembly standard 21|(?)]]''': Assembly standard 21, also known as the BglBrick, BBb, or Berkeley standard, is optimized to enable in-frame assembly of protein domains.
@@ Line 155: / Line 170: @@
 |-
 |'''[[Assembly standard 15]] [[Help:Assembly standard 15|(?)]]''': Julie Norville has developed a new set of parts for assembly of fusion proteins.
+|-
+|'''[[Assembly standard 65]] [[Help:Assembly standard 65|(?)]]''': The MIT iGEM 2010 and 2011 teams have developed a Gateway-based standard for assembly of mammalian promoters, genes, and expression vectors known as MammoBlocks.
 |}
 ''Please see [http://hdl.handle.net/1721.1/45137 BBF RFC 29] for naming conventions for standards of physical composition.''
 ===Browse parts and devices by contributor===
-'''[https://igem.org/Team_Parts?year=2010 iGEM 2010]''' | '''[https://igem.org/Team_Parts?year=2009 iGEM 2009]''' | '''[https://igem.org/Team_Parts?year=2008 iGEM 2008]''' | '''[https://igem.org/Team_Parts?year=2007 iGEM 2007]''' | '''[https://igem.org/Team_Parts?year=2006 iGEM 2006]''' |
+'''[https://igem.org/Team_Parts?year=2023 iGEM 2023]''' |
+'''[https://igem.org/Team_Parts?year=2022 iGEM 2022]''' | '''[https://igem.org/Team_Parts?year=2021 iGEM 2021]''' |
+'''[https://igem.org/Team_Parts?year=2020 iGEM 2020]''' | '''[https://igem.org/Team_Parts?year=2019 iGEM 2019]''' |
+'''[https://igem.org/Team_Parts?year=2018 iGEM 2018]''' | '''[https://igem.org/Team_Parts?year=2017 iGEM 2017]''' |
+'''[https://igem.org/Team_Parts?year=2016 iGEM 2016]''' | '''[https://igem.org/Team_Parts?year=2015 iGEM 2015]''' | '''[https://igem.org/Team_Parts?year=2014 iGEM 2014]''' | '''[https://igem.org/Team_Parts?year=2013 iGEM 2013]''' | '''[https://igem.org/Team_Parts?year=2012 iGEM 2012]''' | '''[https://igem.org/Team_Parts?year=2011 iGEM 2011]''' | '''[https://igem.org/Team_Parts?year=2010 iGEM 2010]''' | '''[https://igem.org/Team_Parts?year=2009 iGEM 2009]''' | '''[https://igem.org/Team_Parts?year=2008 iGEM 2008]''' | '''[https://igem.org/Team_Parts?year=2007 iGEM 2007]''' | '''[https://igem.org/Team_Parts?year=2006 iGEM 2006]''' |
 '''[https://igem.org/Team_Parts?year=2005 iGEM 2005]''' | '''[https://igem.org/Lab_Parts Labs]''' | '''[https://igem.org/Course_Parts Courses]'''
 ===Browse chassis===
@@ Line 183: / Line 206: @@
 |
 |valign='top' |'''[[Cell-free chassis]] [[Help:Cell-free chassis|(?)]]''': ''In vitro'' transcription/translation systems can be useful for some synthetic biological systems.
+|-
+|valign='top' align='center' width=50px | {{Click || image=algae_icon.png | link=Chlamydomonas reinhardtii chassis |width=30px | height=30px}}
+|
+|valign='top' |'''[[Chlamydomonas reinhardtii]] [[Help:Chlamydomonas reinhardtii chassis|(?)]]''': A unicellular alga with a promising future in synthetic biology.
 |}
 ===Browse user-supplied catalog pages===
@@ Line 191: / Line 219: @@
 |valign='top' align='center' width=50px | {{Click || image=Part_icon_cell.png | link=Mesoplasma florum |width=30px | height=30px}}
 |valign='top' |'''[[Mesoplasma florum]] [[Help:Mesoplasma florum|(?)]]''': Mesoplasma florum is a particularly simple model organism.
-|}
+|-
+|valign='top' align='center' width=50px | {{Click || image=logo_Tn7.png | link=Genome Integration |width=30px | height=30px}}
+|valign='top' |'''[[Genome Integration]] [[Help:Genome Integration|(?)]]''': The miniTn7 BioBrick tool kit is a set of fully BioBrick-compatible vectors based on Tn7 transposon for the integration of parts into microbial genomes.
+|-
+|valign='top' align='center' width=50px | {{Click || image=bacteria_mtb.gif | link=''Magnetospirillum magneticum'' AMB-1 |width=30px | height=30px}}
+|valign='top' |'''[[Magnetotaxis]] [[Help:Magnetotaxis|(?)]]''': magnetotactic strain AMB-1 with BioBrick-compatible toolkit enables development of synthetic biology into magnetotaxis and beyond.
+|-
+|valign='top' align='center' width=50px | {{Click || image=algae_icon.png | link=Chlamydomonas reinhardtii |width=30px | height=30px}}
+|valign='top' |'''[[Chlamydomonas_reinhardtii_parts | Chlamydomonas reinhardtii Part Collections ]] [[Help:Chlamydomonas reinhardtii|(?)]]''': fitting the MoClo syntax for plants following the Golden Gate cloning standard and therefore the iGEM RFC[1000] Type IIS standard.
+|-
+|valign='top' align='center' width=50px | {{Click || image=Part_icon_cell.png | link=Arthrospira platensis |width=30px | height=30px}}
+|valign='top' |'''[[Arthrospira_platensis | Arthrospira platensis ]]'''
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