Feb 2022 - DNA-BOT has now been updated to produce scripts that run on the Opentrons OT2 in APIv2. It also incorporates options for different hardware configurations by producing multiple scripts for each of the 4 steps. The Thermocycler module can now be optionally used in the step 1 clip reactions as well as the step 4 transformations. In addition, different labware inputs are available through the Graphical User Interface (GUI) or Command Line Interface (CLI).
This work was originally published in OUP Synthetic Biology
Users looking to implement the DNA-BOT workflow are encouraged to consult the instructions. If you are looking to contribute to this project, please raise an issue or pull request. Otherwise, feel free to reach out to geoffbaldwin.
dnabot can be run in 2 modes:
- with a graphical interface: see
Running the dnabot appsection in instructions. dnabot was developed using Python v3.7. Refer to requirements.txt. - without a graphical interface: you need to specify all settings through the command line, you can see the instructions in the sections below.
conda create --name <myenv>
conda activate <myenv>
conda install -c conda-forge -c brsynth dnabot<myenv> has to be replaced by whatever meaningful name that will pleased the user.
conda activate <myenv>
python -m dnabot.dnabot_app --help
python -m dnabot.dnabot_appconda activate <myenv>
python -m dnabot.dnabot_app nogui --help
python -m dnabot.dnabot_app nogui \
--construct_path /path/to/constructs.csv \
--source_paths /path/to/linker_parts_coord.csv /path/to/user_parts_coord.csv \
--output_dir /path/to/output/dirusage: dnabot_app.py [-h] [--default_settings_file DEFAULT_SETTINGS_FILE] {nogui} ...
DNA assembly using BASIC on OpenTrons.
positional arguments:
{nogui} Optional, to define settings from the terminal instead of the graphical interface. Type
"python dnabot_app.py nogui -h" for more info.
optional arguments:
-h, --help show this help message and exit
--default_settings_file DEFAULT_SETTINGS_FILE
Optional, file providing labware IDs and parameter to be used. Default:
/Users/tduigou/code/test/dnabot/dnabot/default_settings.yaml.usage: dnabot_app.py nogui [-h] --construct_path CONSTRUCT_PATH --source_paths SOURCE_PATHS [SOURCE_PATHS ...]
[--etoh_well ETOH_WELL] [--soc_column SOC_COLUMN] [--output_dir OUTPUT_DIR]
[--template_dir TEMPLATE_DIR]
optional arguments:
-h, --help show this help message and exit
--construct_path CONSTRUCT_PATH
Construct CSV file.
--source_paths SOURCE_PATHS [SOURCE_PATHS ...]
Source CSV files.
--etoh_well ETOH_WELL
Well coordinate for Ethanol. Default: A11
--soc_column SOC_COLUMN
Column coordinate for SOC. Default: 1
--output_dir OUTPUT_DIR
Output directory. Default: same directory than the one containing the "construct_path" file
--template_dir TEMPLATE_DIR
Template directory. Default: "template_ot2_scripts" located next to the present script.
Use the --default_settings_file argument to set different default values. This option is
available either using the GUI or the CLI interface.
conda activate <myenv>
python -m dnabot.dnabot_app --default_settings_file /path/to/custom/default_settings.yaml.The default settings file should follow the structure below (yaml file). The
labware IDs to be used can be updated with the labwares section, while the
parameters for the seperation step are listed in the parameters section.
labwares:
# Pipettes #############################################
# Opentrons P20 Single-Channel Electronic Pipette
p20_single:
id: p20_single_gen2
# Opentrons P300 8-Channel Electronic Pipette
p300_multi:
id: p300_multi_gen2
# Modules ###############################################
# Opentrons magnetic module
mag_deck:
id: magdeck
# id: magnetic module gen2 # BRS script 2
# Tip racks #############################################
# Opentrons 20μL tips rack
96_tiprack_20ul:
id: opentrons_96_tiprack_20ul
# id: tipone_3dprinted_96_tiprack_20ul # BRS
# Opentrons 300μL tips rack
96_tiprack_300ul:
id: opentrons_96_tiprack_300ul
# id: tipone_yellow_3dprinted_96_tiprack_300ul # BRS
# Plates ################################################
# Opentrons 4-in-1 tubes rack for 1.5 ml eppendorf tubes
24_tuberack_1500ul:
id: e14151500starlab_24_tuberack_1500ul
# id: opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap # BRS scripts 1, 3, 4
# 96 well rigid PCR plate (clip and transformation steps)
96_wellplate_200ul_pcr_step_14:
id: 4ti0960rig_96_wellplate_200ul
# id: green_96_wellplate_200ul_pcr # BRS scripts 1, 4
# 96 well rigid PCR plate (purification and assembly steps)
96_wellplate_200ul_pcr_step_23:
id: 4ti0960rig_96_wellplate_200ul
# id: black_96_wellplate_200ul_pcr # BRS script 2, 3
# Agar plate (transformation step)
agar_plate_step_4:
id: 4ti0960rig_96_wellplate_200ul
# id: thermoomnitrayfor96spots_96_wellplate_50ul # BRS script 4
# Reservoir plate 21 mL 12 channels
12_reservoir_21000ul:
id: 4ti0131_12_reservoir_21000ul
# id: citadel_12_wellplate_22000ul # BRS script 2
# 96 deep well plate 2 mL wells
96_deepwellplate_2ml:
id: 4ti0136_96_wellplate_2200ul
# id: transparent_96_wellplate_2ml_deep # BRS scripts 2, 4
# Corning 12 Well Plate 6.9 mL Flat
12_corning_wellplate:
id: corning_12_wellplate_6.9ml_flat
parameters:
# Purification step #####################################
# Magnetic module height (mm) - purification step
purif_magdeck_height:
value: 20.0
# value: 10.8 # BRS
# Washing time (min) - purification step
purif_wash_time:
value: 0.5
# Bead ratio - purification step
purif_bead_ratio:
value: 1.8
# Incubation time (min) - purification step
purif_incubation_time:
value: 5.0
# Settling time (min) - purification step
purif_settling_time:
value: 2.0
# value: 6 # BRS
# Drying time (min) - purification step
purif_drying_time:
value: 5.0
# value: 15 # BRS
# Elution time (min) - purif step
purif_elution_time:
value: 2.0
# value: 5 # BRS
# Transformation step ###################################
# Incubation temperature
transfo_incubation_temp:
value: 4
# value: 8 # BRS
# Incubation time (min)
transfo_incubation_time:
value: 20
# value: 30 # BRSAfter a git clone:
conda env create -f environment.yaml -n <dev_env>
conda develop -n <dev_env> .You may be prompted to install conda-build in your base environment (conda install conda-build).
The default conda environment name will be dnabot-dev if not specified by -n <dev-env>.
Test your installation with:
conda activate <dev_env>
python -m dnabot.dnabot_app nogui --help
python -m pytest testsTo uninstall:
conda deactivate
conda env remove -n <dev_env>You need to install pytest if it's not done yet (conda install pytest).
conda install pytest
python -m pytest testsThe update of DNABOT to APIv2 and improvements to the front end involved the work of several people:
- Thomas Duigou - tduigou
- Geoff Baldwin - geoffbaldwin
- Gizem Buldum - gizembuldum
Initial work revising the template scripts to run in Opentrons APIv2 was done by a team of Masters students from the MRes in Systems and Synthetic Biology at Imperial College London, thanks to:
- Xin Luo
- Ruihan Bai
- Zhenhua Wu
- Lianne Wu
- Ting An Lee
- Xiangming Xu
The original code for DNABOT produced OT2 scripts that ran in APIv1 and was authored by:
- Matthew C Haines - hainesm6
This project is licensed under the MIT License - see the LICENSE file for details
- Marko Storch for all his help with instructions and DNA-BOT manuscript.
- Geoff Baldwin for all his help with the DNA-BOT manuscript.