Mercurial > repos > tduigou > dnabot
changeset 7:ecb31af4c2f8 draft default tip
planemo upload for repository https://github.com/brsynth/DNA-BOT commit 79f27123846add7020de9cae2912e5289c2b8efd
| author | tduigou |
|---|---|
| date | Tue, 23 Jul 2024 09:55:58 +0000 |
| parents | ec9cef4b5b5a |
| children | |
| files | dnabot.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/dnabot.xml Wed Feb 14 15:25:03 2024 +0000 +++ b/dnabot.xml Tue Jul 23 09:55:58 2024 +0000 @@ -1,7 +1,7 @@ <tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09" license="MIT"> <description>DNA assembly using BASIC on OpenTrons</description> <macros> - <token name="@TOOL_VERSION@">3.1.0</token> + <token name="@TOOL_VERSION@">4.1.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement> @@ -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="150000" 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.