Welcome to Teselagen's Manual.

We strive to provide a design-build-test-evolve platform for automated combinatorial DNA assembly; with sequence viewing and editing, combinatorial design, and j5 scarless genetic assembly, all at the least possible cost. Please use the menu on the left to learn more about our platform.

Contact Info

For business inquiries or other questions, please contact: Contact [at] Teselagen [dot] com

Table of Contents

  1. Intro. to BioCAD/CAM
    • From specification, to design, to implementation, to assay
  2. 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)
  3. Synthetic Evolution
    • TeselaGen's Synthetic Evolution Workflow
    • Bioinformatics and BioCAD preliminaries
  4. BioCAD demos
    • DNA Sequence and Part Management
    • Sequence Editing and Part Creation
    • Designing with Device Editor
    • Generating assembly instructions with J5
  5. Managing DNA sequences
    • Importing DNA sequences into your sequence library
    • Creating a sequence
    • Editing a sequence
    • Sequence analysis tools
    • Mapping sequence to parts
  6. 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)
  7. 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
  8. Design files
    • DeviceEditor format (.xml) design files
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. j5 downstream automation
    • Distribute PCR reactions file
    • NextGen (eXeTek) expression workstation control file
    • PR-PR distribute PCR reactions configuration (.pr) files
  15. 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
  16. Experimental protocols
    • SLIC
    • Gibson
    • CPEC
    • SLiCE
    • Golden Gate
    • 5' phosphorylation of annealed DNA oligos
  17. Related publications
    • How to cite j5, and publications citing j5