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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

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