Dataset Open Access

Galaxy Training Data for "Designing plasmids encoding predicted pathways by using the BASIC assembly method"

BAZI KABBAJ Kenza; DUIGOU Thomas

Research group(s)
Joan Herisson; Guillaume Gricourt

This dataset provides the data needed for the Galaxy BASIC assembly workflow training tutorial (https://galaxy-synbiocad.org). This workflow provides a pathway to design plasmids encoding predicted metabolic pathways using the BASIC assembly method (https://doi.org/10.1021/sb500356d). It generates scripts allowing the automatic construction of these plasmids using an Opentrons liquid handling robot. After downloading these scripts on a computer connected to an Opentrons (https://opentrons.com), the user can perform the automatic construction of the plasmids on the bench.

The content of the dataset is as follows:

  • an SBML file modeling a heterologous pathway producing lycopene such as those produced by the Pathway Analysis Workflow (https://galaxy-synbiocad.org).

  • a CSV file listing the parts to be used (linkers, backbone and promoters) in the constructions.

  • two YAML files providing two examples of settings, i.e. providing the identifiers of the laboratory equipment and the parameters of the DNA robot.

Files (38.6 kB)
Name Size
dnabot_london_settings.yaml
md5:42a22f09d181c87900c0499eb0833d57
3.0 kB Download
dnabot_paris_settings.yaml
md5:9c482a9b310a4f71cc07b8fbf1008387
3.0 kB Download
parts_for_lycopene.csv
md5:cd2fd9d51d0efabf0cebba5528c19a80
611 Bytes Download
rp_002_0011.xml
md5:9edb348686bf95421a6f06125152a89b
32.0 kB Download
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