From: A survey of enabling technologies in synthetic biology
Tool, reagent or method | Current use | Past use | Tool, reagent or method | Current use | Past use |
---|---|---|---|---|---|
Physical assembly methods | Â | Â | Genomic database | Â | Â |
  Gateway recombinatorial cloning | 4 | 1 |   GenBank | 10 | 3 |
  de novo DNA synthesis | 3 | 2 |   E!EnsemblGenomes | 7 | 3 |
  Gibson assembly | 3 | 1 |   MicrobesOnline | 3 | 1 |
  Conventional restriction site-based cloning | 2 | 0 |   European Nucleotide Archive | 2 | 2 |
  CPEC | 1 | 2 |   DNA Databank of Japan | 2 | 0 |
  SLIC | 1 | 1 | Sequence tools |  |  |
  PIPE | 1 | 1 |   Search (e.g., BLAST) | 12 | 3 |
  USER | 1 | 1 |   Alignment (e.g., ClustalW2) | 10 | 1 |
  InFusion cloning | 1 | 0 |   Analysis (e.g., OligoCalc) | 7 | 2 |
  RAD assembly | 1 | 0 | Software tools |  |  |
  Transfer PCR | 1 | 0 |   ApE | 6 | 1 |
  Yeast in vivo cloning | 1 | 0 |   Rosetta | 4 | 1 |
  BioBrick assembly standard | 0 | 1 |   Vector NTI | 3 | 5 |
Measurement, functional composition, data exchange |  |  |   Primer3 | 3 | 3 |
  RPU | 0 | 1 |   Mathematica | 2 | 5 |
  Electronic datasheets | 0 | 1 |   Mfold | 1 | 2 |
  Visual datasheets | 0 | 1 |   Gene Designer | 1 | 2 |
DNA synthesis |  |  |   Blast | 1 | 1 |
  Commercial, short oligos | 9 | 4 |   J5 DNA Assembly | 1 | 1 |
  Commercial, gene size (>500bp) | 4 | 3 |   Vector Editor | 1 | 1 |
  In-house, gene-size(>500 bp) | 3 | 2 |   GenoCAD | 1 | 1 |
  In-house, short oligos | 1 | 4 |   Cell Designer | 1 | 0 |
DNA sequencing |  |  |   ClothoCAD | 1 | 0 |
  Commercial | 8 | 3 |   iBioSim | 1 | 0 |
  In-house | 2 | 4 |   Gene Design | 1 | 0 |
Culture technique |  |  |   ProtoBiocompiler | 1 | 0 |
  LB broth or agar | 10 | 3 |   SimBiology | 1 | 0 |
  37°C incubator | 10 | 3 |   SnapGene | 1 | 0 |
  Antibiotic selection | 9 | 4 |   TinkerCell | 1 | 0 |
  Glycerol freezing | 8 | 3 |   GenomeCompiler | 0 | 1 |
  30°C incubator | 7 | 3 |   GEntle | 0 | 1 |
  Colorimetric medium | 4 | 2 |   GLAMM | 0 | 1 |
Other tools, reagents and methods |  |  |   COPASI | 0 | 1 |
  PCR | 9 | 5 |   DeviceEditor | 0 | 1 |
  GFP reporters | 7 | 4 |   Lasegene-DNA Star | 0 | 1 |
  Non-GFP reporters | 6 | 4 |   RBS Calculator | 0 | 1 |
  Directed evolution | 3 | 2 |  |  |  |