SUMMARY.md

Summary

• Intro. to BioCAD/CAM
  • From specification, to design, to implementation, to assay
• Intro. to DNA Assembly
  • The DNA assembly challenge
  • The traditional multiple cloning site approach
  • The BioBrick approach
  • The SLIC, Gibson, CPEC and SLiCE assembly methods (and GeneArt Seamless Cloning)
  • The Golden Gate assembly method (and MoClo and GoldenBraid)
• Synthetic Evolution
  • TeselaGen's Synthetic Evolution Workflow
  • Bioinformatics and BioCAD preliminaries
• BioCAD demos
  • DNA Sequence and Part Management
  • Sequence Editing and Part Creation
  • Designing with Device Editor
  • Generating assembly instructions with J5
• Managing DNA sequences
  • Importing DNA sequences into your sequence library
  • Creating a sequence
  • Editing a sequence
  • Sequence analysis tools
  • Mapping sequence to parts
• Managing columns
  • Adding and removing columns
  • Changing column SBOL Visual icons
  • Changing column assembly orientations
  • Changing column names
  • Controlling column assembly directives for j5
  • Changing the assembly product type (circular-linear)
• Managing specific parts
  • Editing a part's name or definition
  • Changing the assembly strategy for a part
  • Creating Eugene design specification rules
  • Importing a set of Eugene design specification rules
  • Cutting, copying, pasting parts
• Design files
  • DeviceEditor format (.xml) design files
• DNA assembly protocol generator
  • 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 using j5
  • SLIC, Gibson, CPEC assembly (and GeneArt® Seamless Cloning)
  • Combinatorial SLIC, Gibson, CPEC assembly
  • Mock assembly
  • Combinatorial Mock assembly
  • Golden Gate assembly
  • Combinatorial Golden Gate assembly
  • Condensation of multiple j5 assembly files
  • Distribution of PCR reactions
  • Conversion of SBOL XML <-> GenBank sequence files
• File formats used by j5
  • 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
  • SLIC/Gibson/CPEC/SLiCE assembly output file
  • Combinatorial SLIC/Gibson/CPEC/SLiCE assembly output file
  • Mock Assembly output file
  • Combinatorial Mock Assembly output file
  • Golden Gate assembly output file
  • Combinatorial Golden Gate assembly output file
  • Condensed multiple j5 assembly files
• j5 downstream automation
  • Distribute PCR reactions file
  • NextGen (eXeTek) expression workstation control file
  • PR-PR distribute PCR reactions configuration (.pr) files
• j5 error messages
  • j5 input error messages
  • SLIC/Gibson/CPEC/SLiCE or Golden Gate specific error messages
  • Distribute PCR Reactions specific error messages
  • Condense multiple j5 assembly files specific error messages
  • Internal error messages
• Experimental protocols
  • SLIC
  • Gibson
  • CPEC
  • SLiCE
  • Golden Gate
  • 5' phosphorylation of annealed DNA oligos
• Related publications
  • How to cite j5, and publications citing j5