{ "slug": "dp_007-q01-codex", "dp": "dp_007", "files": 200, "qid": "q01", "family": "single_hop", "prompt": "What is the lab protocol ID for general maintenance of human induced pluripotent stem cells in the Reed Lab?", "gold": "RL-P-002", "agent": "codex", "fs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 183435, "outputTokens": 1007, "totalTokens": 184442, "cost": 2.2314, "durationMs": 23525, "answer": "The lab protocol ID is **RL-P-002**.\n\nIt appears in `agent_memory/lab/protocols/RL-P-002_general_cell_culture_v4.md` as the document ID for \u201cGeneral Maintenance of Human Induced Pluripotent Stem Cells (hiPSCs)\u201d in the Reed Lab.", "judgeReason": "covers all asked facts", "toolCalls": 4, "trajectory": [ { "step": 1, "inputTokens": 183435, "outputTokens": 1007, "text": "I\u2019ll search the local `agent_memory` first, since the project instructions say the answer is there.\nThe first pass surfaced multiple references to both `f141` and `protocol_rl_p_002`. I\u2019m narrowing on documents that explicitly describe Reed Lab protocols so I can give the protocol ID rather than a related note ID.\nThe lab protocol ID is **RL-P-002**.\n\nIt appears in `agent_memory/lab/protocols/RL-P-002_general_cell_culture_v4.md` as the document ID for \u201cGeneral Maintenance of Human Induced Pluripotent Stem Cells (hiPSCs)\u201d in the Reed Lab.", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"Reed Lab|induced pluripotent|iPSC|pluripotent|general maintenance|maintenance\\\" agent_memory'\"}", "outputPreview": "agent_memory/meetings/mentor_1on1/20231129_tanaka_notes.md:37:So, the images themselves look pretty good. I managed to get some nice staining for SOX2 (a marker for neural progenitors, which is key for my project) and DAPI (for nuclei, obviously). The hiPSC colonies are generally healthy, though there are a few areas with some minor overgrowth or uneven differentiation, which is normal, I think. K\u2026", "outputChars": 338060 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"protocol_rl_p_002|f141|general maintenance|maintenance of human|human induced pluripotent stem cells|hiPSC Culture\\\" agent_memory'\"}", "outputPreview": "agent_memory/meetings/mentor_1on1/20231129_tanaka_notes.md:37:So, the images themselves look pretty good. I managed to get some nice staining for SOX2 (a marker for neural progenitors, which is key for my project) and DAPI (for nuclei, obviously). The hiPSC colonies are generally healthy, though there are a few areas with some minor overgrowth or uneven differentiation, which is normal, I think. K\u2026", "outputChars": 18995 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg --files agent_memory | rg \\\"f141|protocol|SOP|iPSC|hiPSC|stem\\\"'\"}", "outputPreview": "agent_memory/lab/protocols/RL-P-002_general_cell_culture_v4.md\nagent_memory/lab/protocols/RL-P-007_hiPSC_neuronal_diff_v3.2.md\nagent_memory/lab/protocols/RL-P-011_confocal_microscopy_LSM880.md\nagent_memory/coursework_biology/mcb501_lecture10_stem_cells_20231106.md\n", "outputChars": 265 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' agent_memory/lab/protocols/RL-P-002_general_cell_culture_v4.md\\\"\"}", "outputPreview": "# Reed Lab Standard Operating Procedure: General Maintenance of Human Induced Pluripotent Stem Cells (hiPSCs)\n\n**Document ID:** RL-P-002\n**Version:** 4.0\n**Date Issued:** 2023-09-01\n**Author:** Ben Carter (ben.carter@northwood.edu)\n**Approved By:** Evelyn Reed, PhD\n\n---\n\n## Table of Contents\n\n1. [Scope](#scope)\n2. [Definitions](#definitions)\n3. [Safety Precautions](#safety-precautions)\n4. [Mat\u2026", "outputChars": 17987 } ] } ] }, "smfs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 85070, "outputTokens": 1306, "totalTokens": 86376, "cost": 1.06, "durationMs": 20839, "answer": "The lab protocol ID is `RL-P-002`.\n\nIt\u2019s listed as **\u201cGeneral Maintenance of Human Induced Pluripotent Stem Cells (hiPSCs)\u201d** in the Reed Lab SOP, version 4.0.", "judgeReason": "covers all asked facts", "toolCalls": 2, "trajectory": [ { "step": 1, "inputTokens": 85070, "outputTokens": 1306, "text": "I\u2019ll search the Supermemory mount using its semantic search as instructed, starting with the profile summary to understand what this memory container holds.\nThe profile has no useful summary, so I\u2019m querying the semantic index directly for the protocol title and lab context.\nThe lab protocol ID is `RL-P-002`.\n\nIt\u2019s listed as **\u201cGeneral Maintenance of Human Induced Pluripotent Stem Cells (hiPSCs)\u201d** in the Reed Lab SOP, version 4.0.", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'cat profile.md'\"}", "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 'smfs grep \\\"lab protocol ID general maintenance human induced pluripotent stem cells Reed Lab\\\" /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"lab protocol ID general maintenance human induced pluripotent stem cells Reed Lab\"\n# searches by meaning across files in this container. usage:\n# grep \"natural language query\" search all files\n# grep \"query\" path/to/dir/ search within directory\n# output: :-: (chunk text is verbatim from\u2026", "outputChars": 8365 } ] } ] } }