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Table 5 Technologies used by survey participants that did not self-identify as synthetic biologists (n = 17)

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    Genomic database   
  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