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