R08.12.01.02 · 任务小类

液体处理协议设计

Liquid-handler protocol design

Design and simulate pipetting protocols.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。

典型应用: Opentrons Protocol Designer · Opentrons API
小类 GUI 需求标签: HY · 混合

任务提案 · 20

展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。

R08.12.01.02-T01 Design an 8-point serial dilution in Opentrons Protocol Designer

原始指令

In Opentrons Protocol Designer (OT-2, P300 Single GEN2 left, tips in slot 1, NEST 12-well reservoir slot 2, Corning 96-well plate slot 3) design a 1:2 serial dilution across row A: 100 uL diluent to A2-A8, 200 uL stock from reservoir well 1 to A1, then transfer 100 uL A1->A2 ... A7->A8 mixing 3x50 uL after each, new tip each step. Export output/serial.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 drag · 拖放
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 2 / 5

建议验证方式

Checker runs opentrons analyze on the JSON: no errors; liquid tracking gives final volumes (A1-A7 100 uL, A8 200 uL) and stock fraction halving per well within 1%; tip count 15; designerApplication metadata present (hand-written JSON lacks PD step forms and fails). The agent VM has no opentrons package, and serial.json must be the file exported by the Protocol Designer browser session (download history).

建议部分得分

15% deck set up correctly; 25% diluent distribution; 40% dilution chain with mixing; 20% analysis passes

R08.12.01.02-T02 Set up an OT-2 deck with modules and defined liquids in Protocol Designer

原始指令

Create a new Protocol Designer file for OT-2 with: Temperature Module GEN2 in slot 3 with a 96-well aluminum block and NEST PCR plate; magnetic module GEN2 in slot 1 with a deep-well plate; tip racks (20 uL slot 4, 300 uL slot 5); reservoir slot 2; and liquids 'Master mix' (blue, 1.5 mL in reservoir A1) and 'Beads' (brown, 6 mL in A2). Export output/deck.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: drag · 拖放 click · 指向与点击 type · 文字与表单
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 2 / 5

建议验证方式

Parsed JSON: module models and slots exact; labware load names and parents exact; pipettes and tip racks assigned; 2 liquids with names, display colors and initial volumes exact. The VM has no shell, interpreter or text editor, so the JSON can only come from Protocol Designer's export; its designerApplication metadata must name opentrons/protocol-designer.

建议部分得分

35% modules and adapters; 30% labware and slots; 15% pipettes/tips; 20% liquids

R08.12.01.02-T03 Write an Opentrons protocol that normalizes 24 DNA samples

原始指令

Write output/normalize.py (Opentrons Python API v2.20, OT-2) that reads input/concentrations.csv (24 samples in a 96 plate, ng/uL) and normalizes each to 10 ng/uL in 50 uL in a new plate: water first, then sample, using P20 for volumes <20 uL and P300 otherwise, never pipetting below 1 uL (flag such samples in a comment and skip them).

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

opentrons_simulate runs clean; parsed command log gives per-well final concentration within 2% of 10 ng/uL and volume 50 uL; no aspirate below pipette minimum; the 2 too-dilute samples are skipped.

建议部分得分

20% simulates without error; 20% pipette selection rule; 45% final concentrations; 15% skip logic

R08.12.01.02-T04 Build a PCR setup with thermocycler profile in Protocol Designer

原始指令

In Protocol Designer (OT-2 with Thermocycler GEN2) distribute 15 uL master mix from reservoir to all 96 wells with the P20 8-channel, add 5 uL template per input/plate_map.csv with the single channel, then close the lid, run 95 C 3 min, 30 cycles of 95 C 15 s / 60 C 30 s / 72 C 30 s, final 72 C 5 min, hold 4 C. Export output/pcr.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 drag · 拖放
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 4 / 5

建议验证方式

opentrons analyze: no errors; 96 wells receive 15 uL mix then 5 uL of the correct template per map; thermocycler commands: lid closed before profile, step temps/holds/cycles exact, final hold 4 C. PD metadata required. The VM has no shell, interpreter or text editor, so JSON or Python API protocols cannot be hand-written; only a Protocol Designer export with designerApplication metadata is accepted.

建议部分得分

25% master mix distribution; 30% template map; 35% thermocycler profile; 10% clean analysis

R08.12.01.02-T05 Design ELISA wash steps on Flex with the 8-channel and waste chute

原始指令

In Protocol Designer for Opentrons Flex (Flex 8-Channel 1000 uL, waste chute), design 3 wash cycles for a 96-well ELISA plate: dispense 300 uL wash buffer per well from the reservoir, delay 30 s, aspirate to waste at 1 mm from bottom with 5 uL/s, reusing one tip set across cycles. Export output/elisa_wash.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Analysis clean on Flex; 3 cycles x 12 columns of 300 uL dispense, 30 s delays, aspirate offsets 1 mm and flow rate 5 uL/s; waste chute as trash; tip count 12 (one set). The VM has no shell, interpreter or text editor, so the protocol can only come from a Protocol Designer export (designerApplication metadata checked).

建议部分得分

30% dispense steps; 15% delays; 30% aspirate offset and rate; 25% tip reuse and waste chute (3:2)

R08.12.01.02-T06 Cherry-pick 96 hits from four source plates with the Opentrons API

原始指令

Write output/hitpick.py (OT-2, P20 single) that reads input/picks.csv (96 rows: source_plate 1-4, source_well, dest_well, volume 2-10 uL) and transfers each pick to a destination plate with a fresh tip per pick, ordering transfers by source plate to minimize head travel. Plates in slots 1-4, destination slot 5.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

opentrons_simulate on picks.csv and a hidden second CSV: every transfer matches source, destination and volume exactly; new tip per pick; transfers grouped by source plate; tip racks replaced via pause when exhausted.

建议部分得分

50% transfers exact; 15% tip policy; 15% ordering; 20% handles hidden CSV and tip exhaustion

R08.12.01.02-T07 Modify transfer settings in an existing Protocol Designer file

原始指令

Import input/protocol.json into Protocol Designer. In step 'Add reagent' change tip use to 'per source well', add a 10 uL air gap, touch tip after dispense, and mix 5 times instead of 3; in step 'Transfer samples' set aspirate height to 2 mm. Leave everything else unchanged and export output/protocol_v2.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 2 / 5

建议验证方式

JSON diff of step forms vs input: only the listed fields changed in the two steps; opentrons analyze still clean; command log reflects air gaps, touch tips and 5 mixes. The VM has no shell, interpreter or text editor, so the JSON cannot be hand-edited; only a Protocol Designer re-export with designerApplication metadata is accepted.

建议部分得分

60% five settings changed (equal share each); 25% nothing else changed; 15% analysis clean

R08.12.01.02-T08 Write a Flex SPRI bead cleanup with gripper moves and magnetic block

原始指令

Write output/spri.py (Flex, 8-channel 1000 uL and 50 uL) for a 1.8x SPRI cleanup of 24 samples (50 uL): add 90 uL beads with mixing, incubate 5 min, gripper-move the plate to the magnetic block, wait 3 min, remove supernatant at 1 mm, two 150 uL 80% ethanol washes, air-dry 4 min, move off magnet, elute in 25 uL and transfer 22 uL to a fresh plate.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 5 / 5

建议验证方式

Simulation clean on Flex; parsed command sequence: bead volume 90 uL per sample, moveLabware with gripper to and from the magnetic block, delay durations exact, supernatant aspirate heights <=1.5 mm, 2 washes, elution 25 uL and 22 uL transfer to the right wells.

建议部分得分

15% bead addition; 25% gripper moves and incubations; 25% supernatant and washes; 35% elution transfer and clean simulation (5:2)

R08.12.01.02-T09 Debug an Opentrons protocol that fails simulation

原始指令

input/broken.py fails opentrons_simulate with three errors: it runs out of tips, aspirates 250 uL with a P20, and loads a labware incompatible with the temperature module adapter. Fix it so it simulates cleanly while performing the same intended transfers described in its docstring. Save output/fixed.py.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Simulation clean; command log transfer set (source, dest, total volume) equals the docstring intent; P20 never above 20 uL per aspirate; adapter/labware pair compatible; tips sufficient.

建议部分得分

75% three errors fixed (equal share each); 25% intended transfers preserved

R08.12.01.02-T10 Tune flow rates and offsets for viscous glycerol transfers in Protocol Designer

原始指令

Edit input/glycerol.json in Protocol Designer so the 'Transfer 50% glycerol' step uses aspirate flow 10 uL/s, dispense 10 uL/s, a 2 s delay after aspirate, aspirate 1 mm and dispense 3 mm from well bottom, blowout into destination well, and withdrawal speed reduced via touch-tip off. Export output/glycerol_v2.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Parsed step form and analyzed command params: flow rates, delay, well-bottom offsets and blowout location exact; other steps unchanged; analysis clean. The VM has no shell, interpreter or text editor, so the JSON cannot be hand-edited; only a Protocol Designer re-export with designerApplication metadata is accepted.

建议部分得分

30% flow rates; 20% delay; 30% offsets; 20% blowout

R08.12.01.02-T11 Reformat four 96-well plates into one 384-well plate by quadrant

原始指令

Write output/reformat.py (OT-2, P20 8-channel GEN2) that transfers 5 uL from each of four 96-well plates (slots 1-4) into a 384-well plate (slot 5) using standard quadrant mapping: plate 1 -> A1 offset, plate 2 -> A2, plate 3 -> B1, plate 4 -> B2. New tips per column.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Simulation clean; liquid tracking per source well lands in the gold 384 well for all 384 positions; 48 column transfers with fresh tips; volume 5 uL each.

建议部分得分

70% mapping correct (proportional); 15% tip policy; 15% volumes and clean run

R08.12.01.02-T12 Set up a 384-well qPCR plate in triplicate with Protocol Designer

原始指令

Design in Protocol Designer (OT-2, P20 8-channel and single) a qPCR setup for 3 assays x 8 samples x triplicate on a 384-well plate: 8 uL assay master mix then 2 uL sample per well following input/qpcr_layout.xlsx, NTCs in the last 3 wells of each assay block. Export output/qpcr384.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 type · 文字与表单
工作产物: WP06 · 代码 / 工程
条件: long · 长流程
提案难度: 4 / 5

建议验证方式

opentrons analyze: per-well final composition (assay, sample or NTC, 10 uL) equals layout for all 81 used wells; no sample enters NTC wells; tips changed between samples. The VM has no shell, interpreter or text editor, so the protocol can only come from a Protocol Designer export (designerApplication metadata checked).

建议部分得分

35% master mix per assay block; 40% samples per layout; 15% NTC integrity; 10% clean analysis

R08.12.01.02-T13 Add runtime parameters to handle variable sample counts

原始指令

Extend input/extraction.py into output/extraction_rtp.py with Opentrons runtime parameters: sample_count (int 1-96, default 24) and elution_volume (choice 30/50/100 uL). The protocol must use the 8-channel for full columns and the single-channel for the remainder of a partial column.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 4 / 5

建议验证方式

Checker simulates with 5 parameter combos (e.g. 1, 13, 24, 95, 96 samples x volumes): only the first N wells receive liquid with the chosen elution volume; full columns use the 8-channel; no extra wells touched.

建议部分得分

20% parameters declared correctly; 50% correct wells for 5 combos (equal share each); 30% channel usage rule

R08.12.01.02-T14 Convert a Protocol Designer JSON into an equivalent Python protocol

原始指令

Translate input/pd_protocol.json (a 6-step reagent addition protocol made in Protocol Designer) into output/translated.py using the Python API, preserving deck layout, pipettes, liquid handling parameters and step order, so both produce the same command sequence.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API · Opentrons Protocol Designer
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

opentrons analyze on both files; normalized command lists (labware, wells, volumes, flow rates, offsets, tip actions) compared: >=98% of commands identical in order.

建议部分得分

20% deck and pipettes; 50% command sequence match (scaled); 30% liquid-handling params

R08.12.01.02-T15 Program heater-shaker incubation steps in an Opentrons protocol

原始指令

Write output/shake.py (Flex) that adds 200 uL media to a 24-well plate on the Heater-Shaker, closes the labware latch, heats to 37 C, shakes at 300 rpm for 20 min, stops shaking, opens the latch, and only then moves the plate with the gripper to slot C2. Pipetting must not occur while shaking.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Simulation clean; command order checked: latch close before shake, temperature wait before shake, shake duration 20 min, deactivate shaker before latch open and gripper move; no pipetting commands during shaking.

建议部分得分

20% media addition; 40% heater-shaker command order; 20% durations and setpoints; 20% safe gripper move

R08.12.01.02-T16 Redesign a protocol to fit within two tip racks without cross-contamination

原始指令

input/assay.json (Protocol Designer) uses 310 tips but only two 300 uL racks fit on the deck. Redesign the steps in Protocol Designer to use at most 192 tips: reuse tips where the same reagent goes to multiple wells (distribute), but always change tips between different samples. Export output/assay_v2.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 4 / 5

建议验证方式

Analysis: <=192 tips used; final per-well contents identical to the original protocol; contamination check: no tip touches two different sample liquids (liquid tracking per tip). The VM has no shell, interpreter or text editor, so the JSON cannot be hand-edited; only a Protocol Designer re-export with designerApplication metadata is accepted.

建议部分得分

35% tip budget met; 40% final contents unchanged; 25% no cross-sample contamination

R08.12.01.02-T17 Create a custom tube-rack labware definition and use it in a protocol

原始指令

Use Opentrons Labware Creator to define a 24-position 2 mL tube rack from the datasheet input/rack_datasheet.pdf (footprint, well spacing, depth, diameter), export output/custom_rack.json, then use it in output/aliquot.py to distribute 1.5 mL of buffer from a reservoir into all 24 tubes.

平台: web · 任意系统（网页） lin · Linux mac · macOS
应用: Opentrons Labware Creator · Opentrons API
交互表面: brow · 浏览器 term · 终端
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: type · 文字与表单 click · 指向与点击 code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: multiapp · 多应用
提案难度: 4 / 5

建议验证方式

Labware JSON validates against schema v2; dimensions within 0.1 mm of datasheet; well grid A1-D6 positions correct; protocol simulates with the custom labware and delivers 1.5 mL to each tube.

建议部分得分

40% labware geometry; 20% schema-valid; 30% distribution protocol; 10% clean simulation

R08.12.01.02-T18 Lay out an ELISA standard curve and samples from an assay spec

原始指令

From input/assay_spec.pdf (8-point standard curve 0-1000 pg/mL in duplicate, 40 samples in duplicate diluted 1:4, blanks), write output/elisa_setup.py (OT-2) that prepares the standard dilution series in tubes, then plates standards, diluted samples and blanks into a 96-well plate per the spec layout, 100 uL per well.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 3 / 5

建议验证方式

Liquid tracking: standards concentrations within 2% of the 8 targets; plate wells contain the specified standard/sample/blank at 100 uL with 1:4 dilution; layout matches spec map.

建议部分得分

35% standard series; 35% plate layout; 20% sample dilution; 10% clean simulation

R08.12.01.02-T19 Pool 48 sequencing libraries equimolarly with volume constraints

原始指令

Write output/pool.py (OT-2, P20 single) that pools the 48 libraries in input/libs.csv (concentration nM per well) equimolarly into one 1.5 mL tube: each library contributes 2 fmol, volumes 1-20 uL; libraries needing <1 uL are first diluted 1:10 in a dilution plate; total pool volume must not exceed 600 uL.

平台: lin · Linux mac · macOS win · Windows
应用: Opentrons API
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP06 · 代码 / 工程
条件: 未声明
提案难度: 5 / 5

建议验证方式

Simulated liquid tracking: each library's molar contribution within 5% of 2 fmol; no aspirate <1 uL; dilution performed for the 6 concentrated libraries; pooled volume <=600 uL; also passes a hidden libs CSV.

建议部分得分

45% molar contributions; 20% dilution logic; 15% volume constraints; 20% hidden CSV

R08.12.01.02-T20 Build an end-repair and ligation library prep in Protocol Designer

原始指令

Implement the end-repair and adapter-ligation section of input/library_prep_manual.pdf for 16 samples in Protocol Designer (OT-2, thermocycler, magnetic module, temperature module at 4 C): reagent additions, mixing, thermocycler incubations, bead cleanup, and pause steps where the manual requires manual handling. Export output/libprep.json.

平台: web · 任意系统（网页）
应用: Opentrons Protocol Designer
交互表面: brow · 浏览器
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 type · 文字与表单 drag · 拖放
工作产物: WP06 · 代码 / 工程
条件: long · 长流程 tutorial · 阅读文档 / 教程
提案难度: 5 / 5

建议验证方式

opentrons analyze clean; checker compares step sequence to a gold outline of 22 operations: reagent volumes per sample within 0.5 uL, incubation temps/times exact, magnet engage heights and durations, pause messages at the 3 manual points. The VM has no shell, interpreter or text editor, so the protocol can only come from a Protocol Designer export (designerApplication metadata checked).

建议部分得分

25% reagent additions; 25% thermocycler incubations; 25% bead cleanup; 25% pauses and clean analysis (3:2)

已有研究映射

当前映射未给此小类指定基准参考。

液体处理协议设计

任务提案 · 20

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建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

原始指令

建议验证方式

建议部分得分

已有研究映射

同工作流族的小类