DNA-Bot

DNA-Bot tool reads the list of constructs where each row corresponds to one construct and consists of a sequence of BASIC (Biopart Assembly Standard for Idempotent Cloning) linker and DNA part IDs (in an operon format), and the DNA-parts position on the source plates. The tool generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method, as decribed by Storch et al. (10.1021/sb500356d).

These python scripts implement the 4 assembly steps: clip reactions, purification, assembly and strain transformation. In short, the Clip reactions step prepares the mixes for the ligation of the individual DNA parts with the linkers; the Purification step purifies the linker-ligated DNA parts using magnetic beads and the Opentrons magnetic module; the Assembly step mixes the DNA purified parts to build the final constructs; while the Transformation step transforms the chassis micro-organism with the plasmid and inoculates onto agar.

Optional parameters can be set by the user to define the plastic labwares to be used, and set protocol parameters such as washing or incubation times for purification step by providing a YAML settings file. Default settings: https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml