-
Notifications
You must be signed in to change notification settings - Fork 178
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
fix(opentrons-ai-client): update prompt guide and examples (#15220)
<!-- Thanks for taking the time to open a pull request! Please make sure you've read the "Opening Pull Requests" section of our Contributing Guide: https://github.com/Opentrons/opentrons/blob/edge/CONTRIBUTING.md#opening-pull-requests To ensure your code is reviewed quickly and thoroughly, please fill out the sections below to the best of your ability! --> # Overview Updated prompt guide and template examples. <!-- Use this section to describe your pull-request at a high level. If the PR addresses any open issues, please tag the issues here. --> Closes: AUTH-408 # Test Plan Please run: - `make test-js` <!-- Use this section to describe the steps that you took to test your Pull Request. If you did not perform any testing provide justification why. OT-3 Developers: You should default to testing on actual physical hardware. Once again, if you did not perform testing against hardware, justify why. Note: It can be helpful to write a test plan before doing development Example Test Plan (HTTP API Change) - Verified that new optional argument `dance-party` causes the robot to flash its lights, move the pipettes, then home. - Verified that when you omit the `dance-party` option the robot homes normally - Added protocol that uses `dance-party` argument to G-Code Testing Suite - Ran protocol that did not use `dance-party` argument and everything was successful - Added unit tests to validate that changes to pydantic model are correct --> # Changelog - Changed prompt guide - Changed examples (4) <!-- List out the changes to the code in this PR. Please try your best to categorize your changes and describe what has changed and why. Example changelog: - Fixed app crash when trying to calibrate an illegal pipette - Added state to API to track pipette usage - Updated API docs to mention only two pipettes are supported IMPORTANT: MAKE SURE ANY BREAKING CHANGES ARE PROPERLY COMMUNICATED --> # Review requests Please see the UI and read and try (please read readme how to run dev) <!-- Describe any requests for your reviewers here. --> # Risk assessment Low <!-- Carefully go over your pull request and look at the other parts of the codebase it may affect. Look for the possibility, even if you think it's small, that your change may affect some other part of the system - for instance, changing return tip behavior in protocol may also change the behavior of labware calibration. Identify the other parts of the system your codebase may affect, so that in addition to your own review and testing, other people who may not have the system internalized as much as you can focus their attention and testing there. -->
- Loading branch information
Showing
4 changed files
with
155 additions
and
169 deletions.
There are no files selected for viewing
18 changes: 11 additions & 7 deletions
18
opentrons-ai-client/src/assets/localization/en/protocol_generator.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
218 changes: 101 additions & 117 deletions
218
opentrons-ai-client/src/assets/prompts/prompt-data.ts
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,147 +1,131 @@ | ||
| export const reagentTransfer = ` | ||
| Write a protocol for the Opentrons OT-2 as described below: | ||
| Metadata: | ||
| - Application: Reagent transfer | ||
| - Robot: OT-2 | ||
| - API: 2.15 | ||
| Write a protocol using the Opentrons Python Protocol API v2 for OT-2 robot according to the following description: | ||
| Labware: | ||
| - Source Labware: \`Thermo Scientific Nunc 96 Well Plate 1300 uL\` in slot 9 | ||
| - Destination Labware: \`Opentrons 96 Flat Bottom Adapter with NEST 96 Well Plate 200 uL Flat\` in slot 10 | ||
| - \`Opentrons 96 Filter Tip Rack 1000 uL\` in slot 8 | ||
| - \`Opentrons 96 Tip Rack 1000 uL\` in slot 3 | ||
| Pipette mount: | ||
| - P1000 Single-Channel GEN2 is mounted on left | ||
| - P300 Single-Channel GEN2 is mounted on right | ||
| Labware: | ||
| - Source Labware: Thermo Scientific Nunc 96 Well Plate 2000 µL on slot 7 | ||
| - Destination Labware: Opentrons 24 Well Aluminum Block with NEST 0.5 mL Screwcap on slot 3 | ||
| - Tiprack: Opentrons 96 Filter Tip Rack 1000 µL on slot 4 | ||
| - P1000 Single-Channel GEN2 is mounted on the left | ||
| - P1000 Single-Channel GEN2 is mounted on the right | ||
| Commands: | ||
| - Using P1000 Single-Channel GEN2 pipette on left mount, transfer 195.0 uL of reagent | ||
| from H10, F12, D7, B1, C8 wells in source labware | ||
| to first well in the destination labware. | ||
| Use new tip for each transfer. | ||
| 1. Use the left-mounted P1000 Single-Channel GEN2 pipette to transfer 196 uL of reagent from wells A7, A6, A5, A2, A3 | ||
| of the source labware to the corresponding wells A5, A9, A1, A10, A2 of the destination labware. Use a new tip for each transfer. | ||
| 2. Use the right-mounted P1000 Single-Channel GEN2 pipette to transfer 8 uL of liquid from wells A9, A12, A6, A10, A3 | ||
| of the source labware to the corresponding wells A7, A11, A6, A3, A9 of the destination labware. Use the same tip for all transfers. | ||
| ` | ||
|
|
||
| export const flexReagentTransfer = ` | ||
| Write a protocol for the Opentrons Flex as described below: | ||
| Metadata and requirements: | ||
| - Application: Reagent transfer | ||
| - Robot: Flex | ||
| - API: 2.15 | ||
| Write a protocol using the Opentrons Python Protocol API v2 for Flex robot according to the following description: | ||
| Labware: | ||
| - Source Labware: \`Opentrons 96 PCR Heater-Shaker Adapter with NEST Well Plate 100 ul\`, in slot D1 | ||
| - Destination Labware: \`Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 uL\`, in slot C2 | ||
| - Tiprack: \`Opentrons Flex 96 Filter Tip Rack 1000 uL\`, in slot C1 | ||
| Pipette Mount: | ||
| - Flex 1-Channel 1000 µL Pipette is mounted on the left side | ||
| - Flex 1-Channel 50 µL Pipette is mounted on the right side | ||
| - Flex 1-Channel 1000 uL Pipette is mounted on the left side | ||
| Labware: | ||
| - Source Labware 1: NEST 1 Well Reservoir 195 mL is positioned on slot B1 | ||
| - Source Labware 2: Bio-Rad 384 Well Plate 50 µL is positioned on slot B2 | ||
| - Source Labware 3: Bio-Rad 96 Well Plate 200 µL is positioned on slot B3 | ||
| - Destination Labware 1: Corning 384 Well Plate 112 µL Flat is positioned on slot D1 | ||
| - Destination Labware 2: Corning 96 Well Plate 360 µL Flat is positioned on slot D2 | ||
| - Tiprack 1: Opentrons Flex 96 Filter Tip Rack 200 µL is used on slot A1 | ||
| - Tiprack 2: Opentrons Flex 96 Filter Tip Rack 50 µL is used on slot A2 | ||
| Commands | ||
| - Using Flex 1-Channel 50 µL Pipette on right mount, transfer 15 µL from first of source labware 1 to each well | ||
| in destination labware 1 and destination labware 2. Reuse the same tip. | ||
| - Again using Flex 1-Channel 50 µL Pipette, transfer 20 µL from each well in source labware 2 to | ||
| each well in the destination labware 1. Reuse the same tip. | ||
| - Using Flex 1-Channel 1000 µL Pipette on left mount, transfer 100µL liquid from each well in source labware 3 | ||
| to each well in destination labware 2. Use a new tip each time. | ||
| Commands: | ||
| 1. Using Flex 1-Channel 1000 uL Pipette on left mount, transfer 117.0 uL of reagent from the first well in source labware | ||
| to E12, G12, B9, A6, D7 wells in the destination labware. Use a new tip for each transfer. | ||
| ` | ||
|
|
||
| export const pcr = ` | ||
| Write a protocol for the Opentrons OT-2 as described below: | ||
| Metadata: | ||
| - Application: ThermoPrime Taq DNA Polymerase, with 10x buffer and separate vial of 25 mM MgCl2Thermo Scientific kit PCR amplification | ||
| - Robot: OT-2 | ||
| - API: 2.15 | ||
| Pipette mount: | ||
| - P20 Single Channel is mounted on the right side | ||
| Write a protocol using the Opentrons Python Protocol API v2 for the OT-2 robot according to the following description: | ||
| Modules: | ||
| - Thermocycler module is present on slot 7 | ||
| - Temperature module is place on slot 3 | ||
| - The thermocycler module is located in slot 7. | ||
| - The sample temperature module is positioned in slot 1. | ||
| - The mastermix temperature module is positioned in slot 3. | ||
| Labware: | ||
| - Source sample labware is Opentrons 96 Well Aluminum Block with NEST Well Plate 100 µL plate placed on slot 1 | ||
| - Source mastermix labware is Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap, placed on temperature module on slot 3 | ||
| - Destination Labware is an Opentrons Tough 96 Well Plate 200 µL PCR Full Skirt placed on thermocycler module on slot 7 | ||
| - 20 ul Filter tiprack is used on slot 4 | ||
| - The source sample labware, an Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt, is placed on the temperature module in slot 1. | ||
| - The source mastermix labware, an Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt, is placed on the temperature module in slot 3. | ||
| - The destination labware, an Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt, is placed on the thermocycler module in slot 7. | ||
| - A 20 uL filter tip rack is used in slot 4. | ||
| Well allocation: | ||
| - source wells are first 41 wells column wise in both master mix and sample source plates | ||
| - destination wells: first 41 wells column wise on thermocycler | ||
| Pipette Mount: | ||
| - A P20 Multi-Channel Gen2 pipette is mounted on the left side. | ||
| Well Allocation: | ||
| - Sample source wells: the first 64 wells column-wise in the sample source plate. | ||
| - Mastermix source wells: the first 64 wells column-wise in the mastermix plate. | ||
| - Destination wells: the first 64 wells column-wise in the thermocycler. | ||
| Commands: | ||
| Note that every step is a single entity. Do not combine. Also, every step should be performed in order. | ||
| 1. The total number of samples is 41 | ||
| 2. Set the thermocycler such that: | ||
| - block temperature is 6 degree C | ||
| - lid temperature to 90 degree C | ||
| - lid open | ||
| 3. Set the master mix temperature module at 10 C. The temperature module wait time is 50 seconds. | ||
| 4. Transfer 10 uL of mastermix from source well to destination well. Use the same pipette tip for all transfers. | ||
| 5. Transfer 3 ul of sample to destination well reusing tip everytime. After dispensing, mix the sample and mastermix | ||
| of 13 ul total volume 4 times and then perform blowout before dropping tip. | ||
| 6. Close the lid of the thermocycler. | ||
| 7. Set the thermocycle to following parameters (**note that each step is independent**): | ||
| Step 1: 66 degree C for 47 seconds for 1 cycles | ||
| Step 2: 88 degree C for 28 seconds, 82 degree C for 14 seconds, 68 degree C for 68 seconds for 15 cycles | ||
| Step 3: 70 degree C for 240 seconds for 1 cycles | ||
| Then, execute thermocycler profile for each step. | ||
| 8. After the above three steps are completed, hold thermocycler block at 4 C | ||
| 9. Open thermocycler lid | ||
| 10. Deactivate the temperature modules | ||
| 1. Set the total number of samples to 64. | ||
| 2. Open the thermocycler lid. | ||
| 3. Set the thermocycler block temperature to 6C. | ||
| 4. Set the thermocycler lid temperature to 55C. | ||
| 5. Set the sample temperature module to 4C. | ||
| 6. Set the mastermix temperature module to 10C. | ||
| 7. Transfer 7 uL of mastermix from the mastermix source wells to the destination wells. Use the same pipette tip for all transfers. | ||
| 8. Transfer 5 uL of the sample from the source to the destination. Mix the sample and mastermix for a total volume of 12 uL 9 times. | ||
| Blow out to \`destination well\` after each transfer. Use a new tip for each transfer. | ||
| 9. Close the thermocycler lid. | ||
| 10. Execute the thermocycler with the following profile: | ||
| - 74C for 65 seconds for 1 cycle, block max volume is sample and mastermix volume | ||
| 11. Execute the thermocycler with the following profile: | ||
| - 60C for 7 seconds, 84C for 19 seconds, 57C for 44 seconds for 13 cycles, block max volume is sample and mastermix volume | ||
| 12. Execute the thermocycler with the following profile: | ||
| - 75C for 480 seconds for 1 cycle, block max volume is sample and mastermix volume | ||
| 13. Hold the thermocycler block at 4C. | ||
| 14. Open the thermocycler lid. | ||
| 15. Deactivate the mastermix temperature module. | ||
| 16. Deactivate the sample temperature module. | ||
| ` | ||
|
|
||
| export const flexPcr = ` | ||
| Write a protocol for the Opentrons Flex as described below: | ||
| Metadata and requirements: | ||
| - Application: GeneAmp2x PCR amplification | ||
| - Robot: Flex | ||
| - API: 2.15 | ||
| Pipette mount: | ||
| - Flex 1-Channel 50 µL Pipette is mounted on the right side | ||
| Write a protocol using the Opentrons Python Protocol API v2 for Flex robot according to the following description: | ||
| Modules: | ||
| - Thermocycler module GEN 2 | ||
| - Sample temperature module GEN 2 is placed in slot D1 | ||
| - Mastermix temperature module GEN 2 is placed in slot D3 | ||
| Modules and adapters: | ||
| - Thermocycler GEN 2 module is present on slot A1+B1 | ||
| - Temperature module GEN 2 is place on slot D3 | ||
| Adapter: | ||
| - Opentrons 96 Well Aluminum Block adapter is placed on the sample temperature module GEN 2 | ||
| - Opentrons 96 Well Aluminum Block adapter is placed on the mastermix temperature module GEN 2 | ||
| Labware: | ||
| - Source sample labware is Opentrons 96 Well Aluminum Block with NEST Well Plate 100 µL plate placed on slot D1 | ||
| - Source mastermix labware is Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap, placed on temperature module on slot D3 | ||
| - Destination Labware is an Opentrons Tough 96 Well Plate 200 µL PCR Full Skirt placed on thermocycler GEN 2 module | ||
| - Opentrons Flex 96 Filter Tip Rack 50 µL is used on slot C1 | ||
| - Source sample labware is Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt placed on the adapter on the sample temperature module in slot 1 | ||
| - Source mastermix labware is Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt placed on the adapter on the mastermix temperature module in slot 3 | ||
| - Destination Labware is an Opentrons Tough 96 Well Plate 200 uL PCR Full Skirt placed on thermocycler module in slot 7 | ||
| - Opentrons Flex 96 Filter Tip Rack 1000 uL is used in slot C1 | ||
| - Opentrons Flex 96 Filter Tip Rack 50 uL is used in slot C2 | ||
| Sample position: | ||
| - source wells are first 64 wells column wise in both master mix and sample source plates | ||
| - destination wells: first 64 wells column wise on thermocycler | ||
| Pipette mount: | ||
| - Flex 8-Channel 1000 uL Pipette is mounted on the left side | ||
| - Flex 8-channel 50 ul pipette is mounted on the right side | ||
| Well allocation: | ||
| - mastermix source wells: the first 9 columns in the mastermix plate | ||
| - sample source wells: the first 9 columns of the sample plate | ||
| - destination wells: first 9 columns on thermocycler | ||
| Commands: | ||
| Note that every step is a single entity. Do not combine. Also, every step should be performed in order. | ||
| 1. The total number of samples is 64 | ||
| 2. Set the thermocycler such that | ||
| - block temperature is 6 degree C | ||
| - lid temperature to 90 degree C | ||
| - lid open | ||
| 3. Set the master mix temperature module at 10 C. The temperature module wait time is 50 seconds. | ||
| 4. Transfer 10 uL of mastermix from source well to destination well. Use the same pipette tip for all transfers. | ||
| 5. Transfer 3 ul of sample to destination well reusing tip everytime. After dispensing, mix the sample and mastermix | ||
| of 13 ul total volume 4 times and then perform blowout before dropping tip. | ||
| 6. Close the lid of the thermocycler. | ||
| 7. Set the thermocycle to following parameters (**note that each step is independent**): | ||
| Step 1: 66 degree C for 47 seconds for 1 cycles | ||
| Step 2: 88 degree C for 28 seconds, 82 degree C for 14 seconds, 68 degree C for 68 seconds for 15 cycles | ||
| Step 3: 70 degree C for 240 seconds for 1 cycles | ||
| Then, execute thermocycler profile for each step. | ||
| 8. After the above three steps are completed, hold thermocycler block at 4 C | ||
| 9. Open thermocycler lid | ||
| 10. Deactivate the temperature modules | ||
| 1. Set the total number of samples to 72. | ||
| 2. Set the thermocycler block temperature to 6 degree C. | ||
| 3. Set the thermocycler lid temperature to 55 degree C. | ||
| 4. Open the thermocycler lid. | ||
| 5. Set the sample temperature module to 37 degree C. | ||
| 6. Set the master mix temperature module to 10 C. | ||
| 7. Use right pipette to transfer 15 uL of mastermix from source well to destination well. Use the same pipette tip for all transfers. | ||
| 8. Use left pipette to transfer 10 ul of sample from the source to destination well. Mix the sample and mastermix of | ||
| 25 ul total volume 9 times. Blow out to \`destination well\`. Use a new tip for each transfer. | ||
| 9. Close the thermocycler lid. | ||
| 10. Execute the thermocycle with the following profile: | ||
| - 74 degree C for 65 seconds for 1 cycle, block max volume is sample and mastermix volume | ||
| 11. Execute the thermocycle with the following profile: | ||
| - 60 degree C for 7 seconds, 84 degree C for 19 seconds, 57 degree C for 44 seconds for 25 cycles, block max volume is sample and mastermix volume | ||
| 12. Execute the thermocycle with the following profile: | ||
| - 75 degree C for 480 seconds for 1 cycle, block max volume is sample and mastermix volume | ||
| 13. Hold thermocycler block at 4 C. | ||
| 14. Open thermocycler lid. | ||
| 15. Deactivate the master mix temperature module. | ||
| 16. Deactivate the sample temperature module. | ||
| ` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.