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optrn_simulator's Introduction

optrn_simulator

GUI for Opentrons Simulator

packages the app is using

  • tkinter
  • request
  • pyinstaller

how to run the app

git clone https://github.com/koji/optrn_simulator.git
cd optrn_simulator
pip install -r requirements.txt
python app.py

2023-12-11 09_29_19-tk (Ubuntu-22 04)

tkinter_simulator.mp4

This app is using the following simple API server.
https://github.com/koji/api-for-simulator

create the app

pyinstaller --onefile app.py

sample protocol

from opentrons import protocol_api
# Metadata
metadata = {
    'protocolName': 'DNA Extraction Prep',
    'author': 'Your Name <[email protected]>',
    'description': 'Simple transfer of reagents for DNA extraction preparation',
    'apiLevel': '2.13'
}
def run(protocol: protocol_api.ProtocolContext):
    # Labware Setup
    tiprack_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', '1')
    tiprack_300ul = protocol.load_labware('opentrons_96_tiprack_300ul', '2')
    source_rack_50ml = protocol.load_labware('opentrons_6_tuberack_falcon_50ml_conical', '7')
    source_rack_1_5ml = protocol.load_labware('opentrons_24_tuberack_nest_1.5ml_snapcap', '5')
    destination_rack_1_5ml = protocol.load_labware('opentrons_24_tuberack_nest_1.5ml_snapcap', '3')
    # Pipette Setup
    p20_single = protocol.load_instrument('p20_single_gen2', 'left', tip_racks=[tiprack_20ul])
    p300_single = protocol.load_instrument('p300_single_gen2', 'right', tip_racks=[tiprack_300ul])
    # Commands
    # Transfer 50 uL of reagent from source 50ml tube to destination 1.5ml tubes
    for column in destination_rack_1_5ml.columns()[:2]:  # First 2 columns
        p300_single.pick_up_tip()
        p300_single.aspirate(50, source_rack_50ml.wells_by_name()['A1'])
        for well in column:
            p300_single.dispense(50, well)
        p300_single.drop_tip()
    # Transfer 10 uL of reagent from source 1.5ml tubes to destination 1.5ml tubes
    for source_well, dest_well in zip(source_rack_1_5ml.columns()[:2], destination_rack_1_5ml.columns()[:2]):
        for s_well, d_well in zip(source_well, dest_well):
            p20_single.pick_up_tip()
            p20_single.aspirate(10, s_well)
            p20_single.dispense(10, d_well)
            p20_single.drop_tip()

optrn_simulator's People

Contributors

koji avatar renovate[bot] avatar

Stargazers

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Watchers

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optrn_simulator's Issues

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

This repository currently has no open or pending branches.

Detected dependencies

pip_requirements
requirements.txt

  • Check this box to trigger a request for Renovate to run again on this repository

clean up code

  • clean up app.py
  • clean up utils.py (after adding line numbers to text box)

Use Docker

Currently calling the endpoint that is hosted on hf spaces.
Introduce Docker to allow to exec the app locally

Add line number

Add line number to the upper text box to display line numbers of the code to make result more understandable

update ui

when clicking send button clear the previous result

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