Design files | TeselaGen's Manual
Introduction
1.
Intro. to BioCAD/CAM
1.1.
From specification, to design, to implementation, to assay
2.
Intro. to DNA Assembly
2.1.
The DNA assembly challenge
2.2.
The traditional multiple cloning site approach
2.3.
The BioBrick approach
2.4.
The SLIC, Gibson, CPEC and SLiCE assembly methods (and GeneArt Seamless Cloning)
2.5.
The Golden Gate assembly method (and MoClo and GoldenBraid)
3.
Synthetic Evolution
3.1.
TeselaGen's Synthetic Evolution Workflow
3.2.
Bioinformatics and BioCAD preliminaries
4.
BioCAD demos
4.1.
DNA Sequence and Part Management
4.2.
Sequence Editing and Part Creation
4.3.
Designing with Device Editor
4.4.
Generating assembly instructions with J5
5.
Managing DNA sequences
5.1.
Importing DNA sequences into your sequence library
5.2.
Creating a sequence
5.3.
Editing a sequence
5.4.
Sequence analysis tools
5.5.
Mapping sequence to parts
6.
Managing columns
6.1.
Adding and removing columns
6.2.
Changing column SBOL Visual icons
6.3.
Changing column assembly orientations
6.4.
Changing column names
6.5.
Controlling column assembly directives for j5
6.6.
Changing the assembly product type (circular-linear)
7.
Managing specific parts
7.1.
Editing a part's name or definition
7.2.
Changing the assembly strategy for a part
7.3.
Creating Eugene design specification rules
7.4.
Importing a set of Eugene design specification rules
7.5.
Cutting, copying, pasting parts
8.
Design files
8.1.
DeviceEditor format (.xml) design files
9.
DNA assembly protocol generator
9.1.
Bioinformatics/BioCAD prerequisites to SLIC/Gibson/CPEC/SLiCE and Golden Gate DNA assembly
9.2.
Process flow for j5 and integration with Registries of Biological Parts and BioCAD tools
9.3.
Brief survey of j5 functionality
10.
Specific examples of using j5
10.1.
SLIC, Gibson, CPEC assembly (and GeneArt® Seamless Cloning)
10.2.
Combinatorial SLIC, Gibson, CPEC assembly
10.3.
Mock assembly
10.4.
Combinatorial Mock assembly
10.5.
Golden Gate assembly
10.6.
Combinatorial Golden Gate assembly
10.7.
Condensation of multiple j5 assembly files
10.8.
Distribution of PCR reactions
10.9.
Conversion of SBOL XML <-> GenBank sequence files
11.
File formats used by j5
11.1.
Comma separated value (.csv); FASTA (.fas) and Genbank (.gb) sequence files
11.2.
jbei-seq format (.xml) sequence files
11.3.
SBOL XML format (.xml) sequence files
12.
j5 input files
12.1.
j5 parameters file
12.2.
Sequences list file and zipped sequences file
12.3.
Parts list file
12.4.
Target part order list file
12.5.
Eugene rules list file
12.6.
Master plasmids list file
12.7.
Master oligos list file
12.8.
Master direct syntheses list file
12.9.
Assembly files to condense list file and zipped assembly files file
12.10.
Downstream automation parameters file
12.11.
Multi-well plate file
12.12.
Source plate list file and zipped source plate files file
13.
j5 output assembly files
13.1.
SLIC/Gibson/CPEC/SLiCE assembly output file
13.2.
Combinatorial SLIC/Gibson/CPEC/SLiCE assembly output file
13.3.
Mock Assembly output file
13.4.
Combinatorial Mock Assembly output file
13.5.
Golden Gate assembly output file
13.6.
Combinatorial Golden Gate assembly output file
13.7.
Condensed multiple j5 assembly files
14.
j5 downstream automation
14.1.
Distribute PCR reactions file
14.2.
NextGen (eXeTek) expression workstation control file
14.3.
PR-PR distribute PCR reactions configuration (.pr) files
15.
j5 error messages
15.1.
j5 input error messages
15.2.
SLIC/Gibson/CPEC/SLiCE or Golden Gate specific error messages
15.3.
Distribute PCR Reactions specific error messages
15.4.
Condense multiple j5 assembly files specific error messages
15.5.
Internal error messages
16.
Experimental protocols
16.1.
SLIC
16.2.
Gibson
16.3.
CPEC
16.4.
SLiCE
16.5.
Golden Gate
16.6.
5' phosphorylation of annealed DNA oligos
17.
Related publications
17.1.
How to cite j5, and publications citing j5
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TeselaGen's Manual
8. Design files
8.1 DeviceEditor format (.xml) design files
