j5 automated DNA assembly
Introduction to DNA assembly
The traditional multiple cloning site approach
The DNA assembly challenge
The BioBrick approach
The SLIC, Gibson, CPEC, and SLiCE assembly methods (and GeneArt® Seamless, In-Fusion® Cloning)
The Golden Gate assembly method (and MoClo and GoldenBraid)
Overview of j5
Bioinformatics/BioCAD prerequisites to SLIC/Gibson/CPEC/SLiCE and Golden Gate DNA assembly
Process flow for j5 and integration with Registries of Biological Parts and BioCAD tools
Brief survey of j5 functionality
Specific examples of how to use j5
SLIC/Gibson/CPEC/SLICE assembly (and GeneArt® Seamless and In-Fusion® Cloning)
Combinatorial SLIC/Gibson/CPEC/SLICE assembly (and GeneArt® Seamless and In-Fusion® Cloning)
Mock assembly
Combinatorial Mock assembly
Golden Gate assembly
Combinatorial Golden Gate assembly
Condensation of multiple j5 assembly files
Distribution of (Split and Pool) PCR reactions
Conversion of SBOL XML <-> GenBank sequence files
Local installation of j5 and DeviceEditor software
Packages required for j5
j5 and DeviceEditor installation
Version change log
In depth guide
Comma separated value (.csv); FASTA (.fas) and Genbank (.gb) sequence files
jbei-seq format (.xml) sequence files
SBOL XML format (.xml) sequence files
j5 input files
j5 parameters file
Sequences list file and zipped sequences file
Parts list file
Target part order list file
Eugene rules list file
Master plasmids list file
Master oligos list file
Master direct syntheses list file
Assembly files to condense list file and zipped assembly files file
Downstream automation parameters file
Multi-well plate file
Source plate list file and zipped source plate files file
j5 output
Assembly files
Combinatorial SLIC/Gibson/CPEC/SLiCE
Mock Assembly
Combinatorial Mock Assembly
Golden Gate
Combinatorial Golden Gate
Condensed multiple j5 assembly files
Downstream automation
Distribute PCR reactions file
PR-PR distribute (split and pool) PCR reactions configuration (.pr) files
Interfaces for using j5
Integration with the JBEI Registry/Vector Editor/DeviceEditor and Clotho BioCAD platforms
XML-RPC web services provider
Simplified j5 web interface
Simplified j5 SBOL XML <-> GenBank conversion utility web interface
Stand alone command line interface
Error messages
List of j5 error messages
Experimental Protocols
One Part CPEC
Golden Gate
5' phosphorylation of annealed DNA oligos
People supporting the development of j5
Research funds supporting the development of j5
Legal documentation
Copyright notice
Non-commercial software license
Commercial software license
Citation of j5
How to cite j5
Publications citing j5
Media coverage of j5
Contact information
The j5 development team