Mercurial > repos > tduigou > dnabot
changeset 8:d016b2051cfd draft default tip
planemo upload for repository https://github.com/brsynth/DNA-BOT commit 79f27123846add7020de9cae2912e5289c2b8efd
| author | tduigou |
|---|---|
| date | Tue, 23 Jul 2024 10:01:37 +0000 |
| parents | a00a395a6edd |
| children | |
| files | dnabot.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/dnabot.xml Fri Sep 29 09:32:24 2023 +0000 +++ b/dnabot.xml Tue Jul 23 10:01:37 2024 +0000 @@ -63,7 +63,7 @@ <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/> <output name="dnabot_scripts" ftype="tar"> <assert_contents> - <has_size value="165900" delta="10000"/> + <has_size value="160000" delta="10000"/> </assert_contents> </output> </test> @@ -72,7 +72,7 @@ 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 in `Storch2015 <https://doi.org/10.1021/sb500356d>`_). +**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.