{
  "slug": "dp_007-q04-codex",
  "dp": "dp_007",
  "files": 200,
  "qid": "q04",
  "family": "multi_hop",
  "prompt": "What is the cell line Lena used for her first formal differentiation attempt (per lab notebook LH-EXP-23-003), and what was the date of that attempt? For context, name also the different cell line she had thawed for general hiPSC maintenance six days earlier (per LH-EXP-23-001).",
  "gold": "First differentiation attempt: cell line hESC-NS-12 on 2023-09-11 (lab notebook LH-EXP-23-003). The earlier general-maintenance thaw on 2023-09-05 (LH-EXP-23-001) used a different line, R-H-42b.",
  "agent": "codex",
  "fs": {
    "agent": "codex",
    "success": true,
    "steps": 1,
    "inputTokens": 232371,
    "outputTokens": 1790,
    "totalTokens": 234161,
    "cost": 2.8422,
    "durationMs": 33316,
    "answer": "Lena\u2019s first formal differentiation attempt used hiPSC line `hESC-NS-12`, and the attempt was dated `2023-09-11` in [LH-EXP-23-003](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:3).\n\nSix days earlier, in [LH-EXP-23-001](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md:3), she had thawed a different hiPSC line for general maintenance: `R-H-42b`.",
    "judgeReason": "covers all asked facts",
    "toolCalls": 6,
    "trajectory": [
      {
        "step": 1,
        "inputTokens": 232371,
        "outputTokens": 1790,
        "text": "I\u2019ll search the local `agent_memory` first, since the project instructions say the answer is there, then read the relevant notebook entries for exact dates and cell line names.\nI found the two notebook files directly: `20230911_LH-EXP-23-003_Differentiation-Attempt1.md` and `20230905_LH-EXP-23-001_First-Thaw.md`. I\u2019m opening those now to verify the exact wording rather than inferring from filenames.\nThe notebook confirms the key distinction: the differentiation attempt used `hESC-NS-12`, while the earlier general maintenance thaw used `R-H-42b`. I\u2019m grabbing line numbers so the final answer can point to the exact local entries.\nLena\u2019s first formal differentiation attempt used hiPSC line `hESC-NS-12`, and the attempt was dated `2023-09-11` in [LH-EXP-23-003](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:3).\n\nSix days earlier, in [LH-EXP-23-001](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md:3), she had thawed a different hiPSC line for general maintenance: `R-H-42b`.",
        "toolCalls": [
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc 'rg --files agent_memory'\"}",
            "outputPreview": "agent_memory/communications/f173_confusing_results_email.md\nagent_memory/communications/f156_mcb_orientation_schedule.md\nagent_memory/communications/f178_microscopy_question.md\nagent_memory/communications/f193_it_network_maintenance.md\nagent_memory/communications/f181_lab_lunch_planning.md\nagent_memory/communications/f180_bio510_project_submission.md\nagent_memory/communications/f188_conference_abs\u2026",
            "outputChars": 13068
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"LH-EXP-23-00[13]|formal differentiation|first formal differentiation|thawed|hiPSC|maintenance|cell line|Lena\\\" agent_memory'\"}",
            "outputPreview": "agent_memory/communications/f174_troubleshooting_meeting_sched.md:20:Lena Hansen\nagent_memory/communications/f174_troubleshooting_meeting_sched.md:36:Lena,\nagent_memory/communications/f174_troubleshooting_meeting_sched.md:75:Lena Hansen\nagent_memory/communications/f174_troubleshooting_meeting_sched.md:91:Lena,\nagent_memory/communications/f174_troubleshooting_meeting_sched.md:124:Lena Hansen\nagent_\u2026",
            "outputChars": 728602
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,180p' agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md\\\"\"}",
            "outputPreview": "# Lab Notebook: LH-EXP-23-003 - Neuronal Differentiation - Attempt 1\n\n**Date:** 2023-09-11\n**Author:** Lena Hansen\n**Project:** Core Project - hiPSC Neuronal Differentiation\n**Experiment Series:** experiment_series_lh_23\n\n## Overview\n\nThis marks the beginning of the first formal attempt at inducing neuronal differentiation from the established human induced pluripotent stem cell (hiPSC) line, hESC\u2026",
            "outputChars": 17513
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,180p' agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md\\\"\"}",
            "outputPreview": "# Lab Notebook Entry: LH-EXP-23-001 - First Thaw\n\n**Date:** 2023-09-05\n**Author:** Lena Hansen\n**Project:** Rotation Project - hiPSC Maintenance and Differentiation\n**Location:** Maple Creek Lab, Cell Culture Suite 2B\n\n## Objective\n\nThis entry details the first successful thaw and plating of human induced pluripotent stem cells (hiPSCs), specifically line R-H-42b. The primary goal was to re-establ\u2026",
            "outputChars": 27617
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md | sed -n '1,35p'\\\"\"}",
            "outputPreview": "     1\t# Lab Notebook: LH-EXP-23-003 - Neuronal Differentiation - Attempt 1\n     2\t\n     3\t**Date:** 2023-09-11\n     4\t**Author:** Lena Hansen\n     5\t**Project:** Core Project - hiPSC Neuronal Differentiation\n     6\t**Experiment Series:** experiment_series_lh_23\n     7\t\n     8\t## Overview\n     9\t\n    10\tThis marks the beginning of the first formal attempt at inducing neuronal differentiation from \u2026",
            "outputChars": 2607
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md | sed -n '1,40p'\\\"\"}",
            "outputPreview": "     1\t# Lab Notebook Entry: LH-EXP-23-001 - First Thaw\n     2\t\n     3\t**Date:** 2023-09-05\n     4\t**Author:** Lena Hansen\n     5\t**Project:** Rotation Project - hiPSC Maintenance and Differentiation\n     6\t**Location:** Maple Creek Lab, Cell Culture Suite 2B\n     7\t\n     8\t## Objective\n     9\t\n    10\tThis entry details the first successful thaw and plating of human induced pluripotent stem cells \u2026",
            "outputChars": 4241
          }
        ]
      }
    ]
  },
  "smfs": {
    "agent": "codex",
    "success": true,
    "steps": 1,
    "inputTokens": 213940,
    "outputTokens": 2713,
    "totalTokens": 216653,
    "cost": 2.6487,
    "durationMs": 81282,
    "answer": "Lena\u2019s first formal differentiation attempt used **hESC-NS-12** and was dated **2023-09-11** in [LH-EXP-23-003](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:3).\n\nSix days earlier, on **2023-09-05**, she had thawed **R-H-42b** for general hiPSC maintenance in [LH-EXP-23-001](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md:3).",
    "judgeReason": "covers all asked facts",
    "toolCalls": 8,
    "trajectory": [
      {
        "step": 1,
        "inputTokens": 213940,
        "outputTokens": 2713,
        "text": "I\u2019ll search the mounted memory first, then open the lab notebook entries around the relevant lines so the answer is grounded in the files.\nThe relevant notebook files are present: `LH-EXP-23-003` for the first differentiation attempt and `LH-EXP-23-001` six days earlier. I\u2019m opening those entries now to confirm the exact cell line names and dates.\nI found the matching evidence: the differentiation notebook names `hESC-NS-12`, while the earlier thaw notebook names a different line, `R-H-42b`. I\u2019m grabbing line numbers so the final answer can point to the exact entries.\nLena\u2019s first formal differentiation attempt used **hESC-NS-12** and was dated **2023-09-11** in [LH-EXP-23-003](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:3).\n\nSix days earlier, on **2023-09-05**, she had thawed **R-H-42b** for general hiPSC maintenance in [LH-EXP-23-001](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md:3).",
        "toolCalls": [
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc pwd\"}",
            "outputPreview": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory\n",
            "outputChars": 108
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"test -f profile.md && sed -n '1,120p' profile.md || true\\\"\"}",
            "outputPreview": "# Memory Profile\n# This file is auto-generated from your memories.\n# It is not editable. To update, modify the source files\n# that contain this information.\n\n",
            "outputChars": 158
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc 'rg --files'\"}",
            "outputPreview": "profile.md\nmeetings/mentor_1on1/20231129_tanaka_notes.md\nmeetings/mentor_1on1/20231115_tanaka_notes.md\nmeetings/mentor_1on1/20231101_tanaka_notes.md\nmeetings/mentor_1on1/20231018_tanaka_notes.md\nmeetings/mentor_1on1/20231004_tanaka_notes.md\nmeetings/mentor_1on1/20230920_tanaka_notes.md\nmeetings/mentor_1on1/20230906_tanaka_notes.md\nmeetings/advisor_1on1/20231201_reed_notes.md\nmeetings/advisor_1on1/\u2026",
            "outputChars": 10479
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md\\\"\"}",
            "outputPreview": "# Lab Notebook: LH-EXP-23-003 - Neuronal Differentiation - Attempt 1\n\n**Date:** 2023-09-11\n**Author:** Lena Hansen\n**Project:** Core Project - hiPSC Neuronal Differentiation\n**Experiment Series:** experiment_series_lh_23\n\n## Overview\n\nThis marks the beginning of the first formal attempt at inducing neuronal differentiation from the established human induced pluripotent stem cell (hiPSC) line, hESC\u2026",
            "outputChars": 20736
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md\\\"\"}",
            "outputPreview": "# Lab Notebook Entry: LH-EXP-23-001 - First Thaw\n\n**Date:** 2023-09-05\n**Author:** Lena Hansen\n**Project:** Rotation Project - hiPSC Maintenance and Differentiation\n**Location:** Maple Creek Lab, Cell Culture Suite 2B\n\n## Objective\n\nThis entry details the first successful thaw and plating of human induced pluripotent stem cells (hiPSCs), specifically line R-H-42b. The primary goal was to re-establ\u2026",
            "outputChars": 28609
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"cell line|Cell line|line|thaw|differentiation|formal|attempt|Date|date\\\" lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md'\"}",
            "outputPreview": "lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:3:**Date:** 2023-09-11\nlab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md:10:This marks the beginning of the first formal attempt at inducing neuronal differentiation from the established human induced pluripotent stem cell (hiPSC) line, hESC-NS-12, using the **Reed Lab hiPSC Neuronal Differentiation Protocol v3.2** (inte\u2026",
            "outputChars": 20685
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lab/notebook/20230911_LH-EXP-23-003_Differentiation-Attempt1.md | sed -n '1,35p;130,140p'\\\"\"}",
            "outputPreview": "     1\t# Lab Notebook: LH-EXP-23-003 - Neuronal Differentiation - Attempt 1\n     2\t\n     3\t**Date:** 2023-09-11\n     4\t**Author:** Lena Hansen\n     5\t**Project:** Core Project - hiPSC Neuronal Differentiation\n     6\t**Experiment Series:** experiment_series_lh_23\n     7\t\n     8\t## Overview\n     9\t\n    10\tThis marks the beginning of the first formal attempt at inducing neuronal differentiation from \u2026",
            "outputChars": 3284
          },
          {
            "name": "command_execution",
            "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lab/notebook/20230905_LH-EXP-23-001_First-Thaw.md | sed -n '1,45p;54,62p'\\\"\"}",
            "outputPreview": "     1\t# Lab Notebook Entry: LH-EXP-23-001 - First Thaw\n     2\t\n     3\t**Date:** 2023-09-05\n     4\t**Author:** Lena Hansen\n     5\t**Project:** Rotation Project - hiPSC Maintenance and Differentiation\n     6\t**Location:** Maple Creek Lab, Cell Culture Suite 2B\n     7\t\n     8\t## Objective\n     9\t\n    10\tThis entry details the first successful thaw and plating of human induced pluripotent stem cells \u2026",
            "outputChars": 6700
          }
        ]
      }
    ]
  }
}