{ "slug": "dp_007-q06-codex", "dp": "dp_007", "files": 200, "qid": "q06", "family": "multi_hop", "prompt": "In which courses did Lena first encounter the genes SOX2 and PAX6, and in which lab notebook entry did she design qPCR primers for both genes?", "gold": "Lena first encountered SOX2 in the MCB-501 Lecture 4 notes on Translation (2023-09-18, in the section 'Connecting to Research (SOX2 and my lab work)'). She first encountered PAX6 in the BIO-510 Assignment 2 hypothesis-testing exercise (2023-09-29), which compares gene_pax6 and gene_sox2 expression. qPCR primers for both genes were designed in lab notebook entry LH-EXP-23-014 (2023-10-13).", "agent": "codex", "fs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 1567736, "outputTokens": 7119, "totalTokens": 1574855, "cost": 19.0264, "durationMs": 116999, "answer": "SOX2 first shows up in Lena\u2019s course notes for **MCB-501: Molecular Biology of the Cell II**, in Lecture 04 on translation.\n\nPAX6 first shows up in her course material for **BIO-510: Biostatistics for Molecular Biologists**, in Assignment 2 on hypothesis testing and gene-expression analysis. That BIO-510 assignment is also the first course context I found where **PAX6 and SOX2 appear together**.\n\nShe designed qPCR primers for both genes in **LH-EXP-23-014 - Primer Design for Neural Markers**, dated **2023-10-13**.", "judgeReason": "covers all asked facts", "toolCalls": 24, "trajectory": [ { "step": 1, "inputTokens": 1567736, "outputTokens": 7119, "text": "I\u2019ll search the local `agent_memory` directory first, since the project instructions say the answer is there. I\u2019m looking for mentions of `SOX2`, `PAX6`, Lena, course names, and qPCR primer design.\nThe first pass found a likely primer notebook and several course/lab files, but the output was broad. I\u2019m narrowing this to exact `SOX2` and `PAX6` hits so I can determine the first course encounters rather than just later lab uses.\nThe course trail is now clearer: SOX2 appears earlier in MCB-501 notes, while PAX6 first shows up in BIO-510 assignment material. I\u2019m checking course headers and the primer notebook title so the final answer uses the exact course and entry names.\nSOX2 first shows up in Lena\u2019s course notes for **MCB-501: Molecular Biology of the Cell II**, in Lecture 04 on translation.\n\nPAX6 first shows up in her course material for **BIO-510: Biostatistics for Molecular Biologists**, in Assignment 2 on hypothesis testing and gene-expression analysis. That BIO-510 assignment is also the first course context I found where **PAX6 and SOX2 appear together**.\n\nShe designed qPCR primers for both genes in **LH-EXP-23-014 - Primer Design for Neural Markers**, dated **2023-10-13**.", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg --files agent_memory'\"}", "outputPreview": "agent_memory/communications/f184_end_of_semester_checkin.md\nagent_memory/communications/f198_happy_holidays_email.md\nagent_memory/communications/f167_midterm_cram_session.md\nagent_memory/communications/f196_lecture_correction.md\nagent_memory/communications/f176_proposal_peer_review.md\nagent_memory/communications/f157_first_lab_meeting.md\nagent_memory/communications/f166_bio510_midterm_announcement\u2026", "outputChars": 13068 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"SOX2|PAX6|Lena|qPCR|primer|primers\\\" agent_memory'\"}", "outputPreview": "agent_memory/communications/f178_microscopy_question.md:32:Lena Hansen\nagent_memory/communications/f178_microscopy_question.md:48:Dear Lena,\nagent_memory/communications/f178_microscopy_question.md:135:Lena Hansen\nagent_memory/communications/f178_microscopy_question.md:151:Hi Lena,\nagent_memory/communications/f178_microscopy_question.md:200:Lena Hansen\nagent_memory/communications/f178_microscopy_qu\u2026", "outputChars": 819727 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\bPAX6\\\\\\\\b|\\\\\\\\bPax6\\\\\\\\b|\\\\\\\\bpax6\\\\\\\\b\\\\\\\" agent_memory\\\"\"}", "outputPreview": "agent_memory/communications/f175_gen600_proposal_reminder.md:112:Professor Thorne mentioned my current work \u2013 specifically, some experimental notes related to immunofluorescence and cell differentiation (you can find references to LF-004 and LF-014 in his earlier emails, though these are internal lab notes and not course materials). While my specific experimental details (like the optimization of \u2026", "outputChars": 141041 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\bSOX2\\\\\\\\b|\\\\\\\\bSox2\\\\\\\\b|\\\\\\\\bsox2\\\\\\\\b\\\\\\\" agent_memory\\\"\"}", "outputPreview": "agent_memory/communications/f177_good_results_sharing.md:24:I also spent a ridiculous amount of time trying to get the DAPI staining just right. It\u2019s always such a tricky step \u2013 too much and it overwhelms everything, too little and you can barely see the nuclei. I think I landed on a good concentration this time. I used a 1:10,000 dilution of the DAPI stock solution in PBS, and a 5-minute incubati\u2026", "outputChars": 225529 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"first encounter|first encountered|encountered|course|courses\\\" agent_memory'\"}", "outputPreview": "agent_memory/meetings/mentor_1on1/20231129_tanaka_notes.md:39:The main goal of this meeting was to get me up to speed on the software Kenji and the lab use for image analysis, which is Fiji, an open-source distribution of ImageJ. I've heard of ImageJ before, of course, it's pretty standard in biology labs, but I've never actually used it in any serious capacity. My previous undergrad lab used prop\u2026", "outputChars": 272987 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\b(PAX6|Pax6|pax6)\\\\\\\\b\\\\\\\" agent_memory/coursework_biology agent_memory/lectures\\\"\"}", "outputPreview": "agent_memory/lectures/GEN-600/20231115_lecture09_notes.md:55: * **SOX2 and its network:** Thorne specifically mentioned that SOX2 often interacts with other TFs like PAX6 (another key neurodevelopmental gene) and OCT4 (crucial for pluripotency, less so for committed neural stem cells, but important in early stages). Understanding these co-factors is critical.\nagent_memory/lectures/GEN-600/202\u2026", "outputChars": 13632 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\b(SOX2|Sox2|sox2)\\\\\\\\b\\\\\\\" agent_memory/coursework_biology agent_memory/lectures\\\"\"}", "outputPreview": "agent_memory/lectures/GEN-600/final_paper_proposal.md:53:The sheer diversity of lncRNA functions makes them potent regulators of complex biological processes. Given their roles in epigenetic modification and transcriptional control, it is not surprising that they are increasingly implicated in developmental processes, including cell fate determination and differentiation. The genomics of developme\u2026", "outputChars": 33613 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"qPCR|primer|primers|SOX2|PAX6|Pax6\\\" agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md agent_memory/lab/notebook'\"}", "outputPreview": "agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md:6:**Keywords:** qPCR, primer design, SOX2, PAX6, neural stem cells, bioinformatics, Primer-BLAST\nagent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md:12:3. [Primer Design Strategy](#primer-design-strategy)\nagent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md:15: * [SOX2](#sox2)\nagen\u2026", "outputChars": 258618 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,130p' agent_memory/lectures/BIO-510/email_20230928_assignment2_help.md\\\"\"}", "outputPreview": "From: lena.hansen@northwood.edu\nTo: chloe.davis@northwood.edu\nDate: Thu, 28 Sep 2023 14:11:02 -0400\nSubject: BIO-510 Assignment 2 - R code help needed (!!!)\n\nHi Chloe,\n\nHope you're having a good Thursday! I'm hitting a bit of a wall with Assignment 2 for BIO-510, specifically the R part, and I was wondering if you might have a minute to look at my code? You're like, the R wizard of the Reed lab, a\u2026", "outputChars": 8902 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,130p' agent_memory/coursework_biology/mcb501_lecture04_translation_20230918.md\\\"\"}", "outputPreview": "# MCB 501: Lecture 04 - Translation\n\n**Date:** September 18, 2023\n**Author:** Lena Hansen (MCB Dept., 1st Year PhD Student)\n**Course:** MCB-501: Molecular Biology of the Cell II\n\nThis document contains my notes from today's lecture on **Translation**, the process by which the genetic code encoded in mRNA is used to synthesize proteins. It's building on everything we covered in transcription and RN\u2026", "outputChars": 11222 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"first (encounter|encountered|saw|introduced|learned)|encountered .*SOX2|encountered .*PAX6|SOX2.*first|PAX6.*first|first.*SOX2|first.*PAX6\\\" agent_memory'\"}", "outputPreview": "agent_memory/communications/f177_good_results_sharing.md:147:That's fantastic news! Congratulations on the successful PAX6 staining! The image looks beautiful, and the signal-to-noise ratio is excellent. It\u2019s always a huge milestone to get a good IF on the first try (or, in this case, first *successful* try after a few bumps).\nagent_memory/communications/f177_good_results_sharing.md:151:1. **Anti\u2026", "outputChars": 20557 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,45p' agent_memory/lectures/BIO-510/20230905_lecture02_notes.md\\\"\"}", "outputPreview": "# BIO-510: Biostatistics - Lecture 2 Notes\n\n**Date:** 2023-09-05\n**Lecturer:** Dr. Evelyn Reed (Oops, wait, it was Dr. Rossi today, my bad. Evelyn is usually the one for the bio-chem stats, right? Or maybe that's 511. Need to double check the syllabus again. So many courses!)\n**Topic:** Probability Distributions - Normal, Binomial, Poisson\n**Author:** Lena Hansen\n\nOkay, so today's lecture was all \u2026", "outputChars": 3664 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,55p' agent_memory/lectures/BIO-510/assignment_02.md\\\"\"}", "outputPreview": "# BIO-510: Assignment 2 - Hypothesis Testing and Data Analysis\n\n**Student:** Lena Hansen\n**Course:** BIO-510: Biostatistics for Molecular Biologists\n**Date:** 2023-09-29\n**Instructor:** Dr. Evelyn Reed (though this is for Dr. Rossi's section, technically, but Evelyn is my official advisor, so it feels like hers!)\n\n---\n\n## Table of Contents\n\n1. [Introduction](#introduction)\n2. [Dataset Descriptio\u2026", "outputChars": 6295 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,70p' agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md\\\"\"}", "outputPreview": "# Lab Notebook: LH-EXP-23-014 - Primer Design for Neural Markers\n\n**Date:** 2023-10-13\n**Author:** Lena Hansen\n**Project:** Initial transcriptomic analysis pipeline development\n**Keywords:** qPCR, primer design, SOX2, PAX6, neural stem cells, bioinformatics, Primer-BLAST\n\n## Table of Contents\n\n1. [Introduction & Objectives](#introduction--objectives)\n2. [Background: Gene Selection](#background-g\u2026", "outputChars": 5264 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,20p' agent_memory/coursework_biology/mcb501_lecture01_central_dogma_20230828.md\\\"\"}", "outputPreview": "# MCB-501: Lecture 1 - The Central Dogma and DNA Replication (2023-08-28)\n\n**Lecturer:** Dr. Elias Finch\n**Course:** MCB-501: Molecular Biology of the Gene\n**Date:** 2023-08-28\n**Location:** sanger_hall_212\n\n---\n\nOkay, deep breaths. First day of actual grad school lectures. MCB-501. It's supposed to be the foundational course for the whole PhD, so I\u2019m trying not to freak out. Dr. Finch is\u2026 a chara\u2026", "outputChars": 1613 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\*\\\\\\\\*Course:\\\\\\\\*\\\\\\\\*|# MCB ?-?501|Course ID\\\\\\\" agent_memory/coursework_biology/mcb501_*\\\"\"}", "outputPreview": "agent_memory/coursework_biology/mcb501_lecture01_central_dogma_20230828.md:1:# MCB-501: Lecture 1 - The Central Dogma and DNA Replication (2023-08-28)\nagent_memory/coursework_biology/mcb501_lecture01_central_dogma_20230828.md:4:**Course:** MCB-501: Molecular Biology of the Gene\nagent_memory/coursework_biology/mcb501_final_exam_study_guide_20231204.md:1:# MCB-501: Final Exam Study Guide - Second Ha\u2026", "outputChars": 5690 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"BIO-510:|Course ID|\\\\\\\\*\\\\\\\\*Course:\\\\\\\\*\\\\\\\\*\\\\\\\" agent_memory/lectures/BIO-510 agent_memory/communications agent_memory/coursework_biology | head -80\\\"\"}", "outputPreview": "agent_memory/coursework_biology/cm550_lecture05_light_microscopy_20230927.md:4:**Course:** CM550: Molecular and Cellular Biology Techniques\nagent_memory/lectures/BIO-510/20230919_lecture04_notes.md:4:**Course:** BIO-510: Statistical Methods in Biological Research\nagent_memory/coursework_biology/cm550_final_exam_study_guide_20231206.md:3:**Course ID:** course_id_cm_550\nagent_memory/coursework_biolo\u2026", "outputChars": 7119 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\b(PAX6|Pax6|pax6)\\\\\\\\b\\\\\\\" agent_memory | awk -F: '{print \\\"'$1\\\":\\\"$2\\\":\\\"$3}'\\\"' | sort\\\"\"}", "outputPreview": "agent_memory/communications/f175_gen600_proposal_reminder.md:112:Professor Thorne mentioned my current work \u2013 specifically, some experimental notes related to immunofluorescence and cell differentiation (you can find references to LF-004 and LF-014 in his earlier emails, though these are internal lab notes and not course materials). While my specific experimental details (like the optimization of \u2026", "outputChars": 98207 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"rg -n \\\\\\\"\\\\\\\\b(SOX2|Sox2|sox2)\\\\\\\\b\\\\\\\" agent_memory | awk -F: '{print \\\"'$1\\\":\\\"$2\\\":\\\"$3}'\\\"' | sort\\\"\"}", "outputPreview": "agent_memory/communications/f177_good_results_sharing.md:118:I also spent a ridiculous amount of time trying to get the DAPI staining just right. It\u2019s always such a tricky step \u2013 too much and it overwhelms everything, too little and you can barely see the nuclei. I think I landed on a good concentration this time. I need to make sure I document the exact amount I used for future reference, especia\u2026", "outputChars": 147867 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"find agent_memory -maxdepth 3 -type f \\\\\\\\( -iname '*answer*' -o -iname '*summary*' -o -iname '*index*' -o -iname '*map*' \\\\\\\\) -print\\\"\"}", "outputPreview": "agent_memory/lab/notebook/20231218_LH-EXP-23-040_Rotation-Summary-and-Future.md\n", "outputChars": 80 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"Primer Design for Neural Markers|LH-EXP-23-014|f094|course_id_bio_510|course_id_mcb_501|gene_pax6|gene_sox2\\\" agent_memory'\"}", "outputPreview": "agent_memory/lab/notebook/20231214_LH-EXP-23-039_Final-Western-Blot-Test.md:31:SOX2 is a key transcription factor involved in maintaining pluripotency and self-renewal in embryonic stem cells, and it also plays critical roles in neural development and gliogenesis. The successful generation of a cell line with *sustained* overexpression of **gene_sox2** is paramount for dissecting its specific cont\u2026", "outputChars": 32985 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/coursework_biology/mcb501_lecture04_translation_20230918.md | sed -n '1,12p;190,205p'\\\"\"}", "outputPreview": " 1\t# MCB 501: Lecture 04 - Translation\n 2\t\n 3\t**Date:** September 18, 2023\n 4\t**Author:** Lena Hansen (MCB Dept., 1st Year PhD Student)\n 5\t**Course:** MCB-501: Molecular Biology of the Cell II\n 6\t\n 7\tThis document contains my notes from today's lecture on **Translation**, the process by which the genetic code encoded in mRNA is used to synthesize proteins. It's building\u2026", "outputChars": 2702 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lectures/BIO-510/assignment_02.md | sed -n '1,42p'\\\"\"}", "outputPreview": " 1\t# BIO-510: Assignment 2 - Hypothesis Testing and Data Analysis\n 2\t\n 3\t**Student:** Lena Hansen\n 4\t**Course:** BIO-510: Biostatistics for Molecular Biologists\n 5\t**Date:** 2023-09-29\n 6\t**Instructor:** Dr. Evelyn Reed (though this is for Dr. Rossi's section, technically, but Evelyn is my official advisor, so it feels like hers!)\n 7\t\n 8\t---\n 9\t\n 10\t## Table \u2026", "outputChars": 5044 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md | sed -n '1,45p;156,190p;236,242p'\\\"\"}", "outputPreview": " 1\t# Lab Notebook: LH-EXP-23-014 - Primer Design for Neural Markers\n 2\t\n 3\t**Date:** 2023-10-13\n 4\t**Author:** Lena Hansen\n 5\t**Project:** Initial transcriptomic analysis pipeline development\n 6\t**Keywords:** qPCR, primer design, SOX2, PAX6, neural stem cells, bioinformatics, Primer-BLAST\n 7\t\n 8\t## Table of Contents\n 9\t\n 10\t1. [Introduction & Objectives](#in\u2026", "outputChars": 5805 } ] } ] }, "smfs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 1581319, "outputTokens": 8787, "totalTokens": 1590106, "cost": 19.2394, "durationMs": 252647, "answer": "SOX2 first shows up in Lena\u2019s course notes for **MCB-501: Molecular Biology of the Cell II**, in the Sept. 18 translation lecture. PAX6 first shows up in a course context in **BIO-510: Biostatistics for Molecular Biologists**, through Assignment 2 comparing PAX6 and SOX2 expression.\n\nThe lab notebook entry where she designed qPCR primers for both is **LH-EXP-23-014: \u201cPrimer Design for Neural Markers\u201d**, dated **2023-10-13**: [lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md:1).", "judgeReason": "covers all asked facts", "toolCalls": 31, "trajectory": [ { "step": 1, "inputTokens": 1581319, "outputTokens": 8787, "text": "I\u2019ll search the mounted memory for Lena, SOX2/PAX6, and qPCR primer references, then read the matching notes so the course and notebook entry are grounded in the source.\nThe primer-design entry is already surfacing as `LH-EXP-23-014` on 2023-10-13. I\u2019m checking the course notes now for the earliest course-level mentions of each gene so I don\u2019t conflate lab exposure with coursework.\nSOX2 first shows up in Lena\u2019s course notes for **MCB-501: Molecular Biology of the Cell II**, in the Sept. 18 translation lecture. PAX6 first shows up in a course context in **BIO-510: Biostatistics for Molecular Biologists**, through Assignment 2 comparing PAX6 and SOX2 expression.\n\nThe lab notebook entry where she designed qPCR primers for both is **LH-EXP-23-014: \u201cPrimer Design for Neural Markers\u201d**, dated **2023-10-13**: [lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md](/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md:1).", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'pwd && rg --files'\"}", "outputPreview": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory\nprofile.md\nlab/protocols/RL-P-011_confocal_microscopy_LSM880.md\nlab/protocols/RL-P-007_hiPSC_neuronal_diff_v3.2.md\nlab/protocols/RL-P-002_general_cell_culture_v4.md\nmeetings/mentor_1on1/20231129_tanaka_notes.md\nmeetings/mentor_1on1/20231115_tanaka_notes.md\nmeetings/mentor_1on1/20231101_tanak\u2026", "outputChars": 10587 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"Lena SOX2 PAX6 qPCR primers courses lab notebook\\\"'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"Lena SOX2 PAX6 qPCR primers courses lab notebook\"\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 the file)\n\n/lab/notebook/2023101\u2026", "outputChars": 10178 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"Lena first encountered SOX2 PAX6 courses\\\" coursework_biology lectures communications meetings lab'\"}", "outputPreview": "error: unexpected argument 'lectures' found\n\nUsage: smfs grep [OPTIONS] [PATH]\n\nFor more information, try '--help'.\n", "outputChars": 124 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"PAX6 course lecture neural development Lena\\\" coursework_biology lectures communications'\"}", "outputPreview": "error: unexpected argument 'lectures' found\n\nUsage: smfs grep [OPTIONS] [PATH]\n\nFor more information, try '--help'.\n", "outputChars": 124 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"SOX2 course lecture stem cells Lena\\\" coursework_biology lectures communications'\"}", "outputPreview": "error: unexpected argument 'lectures' found\n\nUsage: smfs grep [OPTIONS] [PATH]\n\nFor more information, try '--help'.\n", "outputChars": 124 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"SOX2|PAX6|Lena|first encounter|encountered\\\" .'\"}", "outputPreview": "./communications/f188_conference_abstracts_fwd.md:82:From: Lena Hansen \n./communications/f188_conference_abstracts_fwd.md:90:Lena\n./communications/f188_conference_abstracts_fwd.md:92:Lena Hansen\n./communications/f188_conference_abstracts_fwd.md:199:To: Lena Hansen \n./communications/f188_conference_abstracts_fwd.md:202:Lena, that sounds like a g\u2026", "outputChars": 234934 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -C 3 \\\"SOX2|PAX6\\\" coursework_biology lectures communications | head -n 240'\"}", "outputPreview": "lectures/GEN-600/final_paper_proposal.md-50-* **Guides:** Directing chromatin modifiers to specific genomic locations to alter gene expression epigenetically.\nlectures/GEN-600/final_paper_proposal.md-51-* **Signal integrators:** Responding to cellular signals and transducing them to downstream effectors.\nlectures/GEN-600/final_paper_proposal.md-52-\nlectures/GEN-600/final_paper_proposal.md:53:T\u2026", "outputChars": 41532 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"which course did Lena first encounter PAX6\\\" coursework_biology'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"which course did Lena first encounter PAX6\"\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 the file)\n\n/coursework_biology/mcb501_\u2026", "outputChars": 7681 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"Lena first encountered SOX2 PAX6 in class lecture course\\\" lectures'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"Lena first encountered SOX2 PAX6 in class lecture course\"\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 the file)\n\n/lectures/GEN\u2026", "outputChars": 8888 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"which course did Lena first encounter SOX2\\\" coursework_biology'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"which course did Lena first encounter SOX2\"\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 the file)\n\n/coursework_biology/mcb501_\u2026", "outputChars": 6715 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba coursework_biology/mcb501_lecture04_translation_20230918.md | sed -n '1,40p;185,235p'\\\"\"}", "outputPreview": " 1\t# MCB 501: Lecture 04 - Translation\n 2\t\n 3\t**Date:** September 18, 2023\n 4\t**Author:** Lena Hansen (MCB Dept., 1st Year PhD Student)\n 5\t**Course:** MCB-501: Molecular Biology of the Cell II\n 6\t\n 7\tThis document contains my notes from today's lecture on **Translation**, the process by which the genetic code encoded in mRNA is used to synthesize proteins. It's building\u2026", "outputChars": 9965 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba coursework_biology/mcb501_lecture10_stem_cells_20231106.md | sed -n '1,30p;120,160p'\\\"\"}", "outputPreview": " 1\t# MCB-501: Lecture 10 - Stem Cells and Differentiation\n 2\t\n 3\t**Date:** 2023-11-06\n 4\t**Author:** Lena Hansen (1st Year PhD Student, MCB Dept)\n 5\t**Course:** `course_id_mcb_501`\n 6\t\n 7\t## Table of Contents\n 8\t\n 9\t1. [Introduction to Stem Cells](#introduction-to-stem-cells)\n 10\t * [What are Stem Cells?](#what-are-stem-cells)\n 11\t * [Key Proper\u2026", "outputChars": 7109 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"PAX6\\\" coursework_biology lectures | cut -d: -f1 | sort -u'\"}", "outputPreview": "coursework_biology/mcb501_final_exam_study_guide_20231204.md\ncoursework_biology/mcb501_lecture10_stem_cells_20231106.md\nlectures/BIO-510/assignment_02.md\nlectures/BIO-510/email_20230928_assignment2_help.md\nlectures/GEN-600/20231115_lecture09_notes.md\nlectures/GEN-600/final_paper_proposal.md\n", "outputChars": 292 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"SOX2\\\" coursework_biology lectures | cut -d: -f1 | sort -u'\"}", "outputPreview": "coursework_biology/mcb501_assignment02_rna_splicing_essay_20231002.md\ncoursework_biology/mcb501_lecture04_translation_20230918.md\ncoursework_biology/mcb501_midterm_study_guide_20231002.md\nlectures/BIO-510/assignment_02.md\nlectures/BIO-510/email_20230928_assignment2_help.md\nlectures/BIO-510/final_project.md\nlectures/GEN-600/20231115_lecture09_notes.md\nlectures/GEN-600/final_paper_proposal.md\n", "outputChars": 394 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lectures/BIO-510/assignment_02.md | sed -n '1,80p;120,180p;220,260p'\\\"\"}", "outputPreview": " 1\t# BIO-510: Assignment 2 - Hypothesis Testing and Data Analysis\n 2\t\n 3\t**Student:** Lena Hansen\n 4\t**Course:** BIO-510: Biostatistics for Molecular Biologists\n 5\t**Date:** 2023-09-29\n 6\t**Instructor:** Dr. Evelyn Reed (though this is for Dr. Rossi's section, technically, but Evelyn is my official advisor, so it feels like hers!)\n 7\t\n 8\t---\n 9\t\n 10\t## Table \u2026", "outputChars": 14860 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lectures/BIO-510/email_20230928_assignment2_help.md | sed -n '1,120p'\\\"\"}", "outputPreview": " 1\tFrom: lena.hansen@northwood.edu\n 2\tTo: chloe.davis@northwood.edu\n 3\tDate: Thu, 28 Sep 2023 14:11:02 -0400\n 4\tSubject: BIO-510 Assignment 2 - R code help needed (!!!)\n 5\t\n 6\tHi Chloe,\n 7\t\n 8\tHope you're having a good Thursday! I'm hitting a bit of a wall with Assignment 2 for BIO-510, specifically the R part, and I was wondering if you might have a minute to look \u2026", "outputChars": 9254 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba coursework_biology/mcb501_assignment02_rna_splicing_essay_20231002.md | sed -n '1,80p;120,190p'\\\"\"}", "outputPreview": " 1\t# MCB-501: Advanced Molecular Biology - Assignment 2\n 2\t\n 3\t## The Multifaceted Role of Alternative Splicing in Generating Proteomic Diversity\n 4\t\n 5\t**Student Name:** Lena Hansen\n 6\t**Student ID:** student_id_lena_hansen\n 7\t**Course:** MCB-501\n 8\t**Date:** October 2, 2023\n 9\t\n 10\t***\n 11\t\n 12\t### Table of Contents\n 13\t\n 14\t1. [Introduction](#\u2026", "outputChars": 21482 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba coursework_biology/mcb501_midterm_study_guide_20231002.md | sed -n '1,80p;160,230p'\\\"\"}", "outputPreview": " 1\t# MCB-501 Midterm Study Guide - Fall 2023\n 2\t\n 3\t**Author:** Lena Hansen\n 4\t**Date:** October 2, 2023\n 5\t**Course:** MCB-501: Molecular and Cellular Biology I\n 6\t**Author's Note:** This is my personal study guide for the upcoming midterm. I've compiled notes from the first five lectures, trying to synthesize the key concepts and identify areas where I need to focus more \u2026", "outputChars": 15530 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba profile.md | sed -n '1,200p'\\\"\"}", "outputPreview": " 1\t# Memory Profile\n 2\t# This file is auto-generated from your memories.\n 3\t# It is not editable. To update, modify the source files\n 4\t# that contain this information.\n 5\t\n", "outputChars": 193 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md | sed -n '1,130p'\\\"\"}", "outputPreview": " 1\t# Lab Notebook: LH-EXP-23-014 - Primer Design for Neural Markers\n 2\t\n 3\t**Date:** 2023-10-13\n 4\t**Author:** Lena Hansen\n 5\t**Project:** Initial transcriptomic analysis pipeline development\n 6\t**Keywords:** qPCR, primer design, SOX2, PAX6, neural stem cells, bioinformatics, Primer-BLAST\n 7\t\n 8\t## Table of Contents\n 9\t\n 10\t1. [Introduction & Objectives](#in\u2026", "outputChars": 9426 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"PAX6 first mention course BIO 510 assignment Lena\\\"'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"PAX6 first mention course BIO 510 assignment Lena\"\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 the file)\n\n/coursework_biology/\u2026", "outputChars": 7362 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"SOX2 first mention course MCB BIO assignment Lena\\\"'\"}", "outputPreview": "/lab/notebook/20231207_LH-EXP-23-036_Cell-Line-Infection.md:32-34:## 2. Background\\n\\nPrevious work in the lab (and indeed, the wider field) has demonstrated that SOX2 is a crucial transcription factor for maintaining pluripotency. Overexpression of SOX2 can enhance reprogramming efficiency and potentially impact downstream differentiation trajectories. The goal here is to create a cellular model \u2026", "outputChars": 8221 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lectures/BIO-510/assignment_02.md | sed -n '300,380p'\\\"\"}", "outputPreview": " 300\t95 percent confidence interval:\n 301\t 0.8571234 1.9834766\n 302\tsample estimates:\n 303\t mean in group Stem Cell-Like mean in group Differentiated\n 304\t 5.452100 4.072100\n 305\t```\n 306\t\n 307\t**T-test results for gene_sox2:**\n 308\t\n 309\t```\n 310\t Welch Two Sample t-test\n 311\t\n 312\tdata: expression_level by c\u2026", "outputChars": 9493 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lectures/BIO-510/email_20230928_assignment2_help.md | sed -n '117,220p'\\\"\"}", "outputPreview": " 117\t# Step 4: Perform the actual t-test for each gene.\n 118\t# The assignment (f051) specifically asks for a two-sample t-test for PAX6 and SOX2 *separately*.\n 119\t# So, for PAX6, I need to compare the expression values between samples in Condition 1 and samples in Condition 2.\n 120\t# And similarly for SOX2.\n 121\t\n 122\t# This is the part where I get stuck or encounter errors.\n 123\t# \u2026", "outputChars": 6141 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -C 2 \\\"SOX2|PAX6\\\" lectures/BIO-510/assignment_02.md lectures/BIO-510/email_20230928_assignment2_help.md coursework_biology/mcb501_lecture04_translation_20230918.md coursework_biology/mcb501_lecture10_stem_cells_20231106.md'\"}", "outputPreview": "coursework_biology/mcb501_lecture04_translation_20230918.md-5-**Course:** MCB-501: Molecular Biology of the Cell II\ncoursework_biology/mcb501_lecture04_translation_20230918.md-6-\ncoursework_biology/mcb501_lecture04_translation_20230918.md:7:This document contains my notes from today's lecture on **Translation**, the process by which the genetic code encoded in mRNA is used to synthesize proteins. \u2026", "outputChars": 38426 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -i \\\"first (saw|see|seen|encounter|encountered)|encountered|first mention|first time|remember seeing\\\" .'\"}", "outputPreview": "./lab/notebook/20231010_LH-EXP-23-013_Differentiation-Attempt2.md:25:This document details the commencement of the second attempt at inducing neuronal differentiation from human induced pluripotent stem cells (hiPSCs) for experiment **LH-EXP-23-013**. The primary goal remains to establish a reproducible protocol for generating functional neuronal populations suitable for downstream electrophysiolo\u2026", "outputChars": 17569 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba lectures/GEN-600/20231115_lecture09_notes.md | sed -n '1,110p;220,260p'\\\"\"}", "outputPreview": " 1\t# GEN-600 Lecture 09: Genomics of Development - Notes & Reflections\n 2\t\n 3\t**Date:** 2023-11-15\n 4\t**Author:** Lena Hansen\n 5\t**Course:** course_id_gen_600\n 6\t\n 7\tThis is a record of my notes from Dr. Thorne\u2019s lecture on developmental genomics, held on November 15th, 2023. He covered a lot of ground, from the basic principles of differential gene expression during em\u2026", "outputChars": 18248 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -i \\\"sox2\\\" coursework_biology lectures | cut -d: -f1 | sort -u'\"}", "outputPreview": "coursework_biology/mcb501_assignment02_rna_splicing_essay_20231002.md\ncoursework_biology/mcb501_final_exam_study_guide_20231204.md\ncoursework_biology/mcb501_lecture04_translation_20230918.md\ncoursework_biology/mcb501_lecture10_stem_cells_20231106.md\ncoursework_biology/mcb501_midterm_study_guide_20231002.md\nlectures/BIO-510/assignment_02.md\nlectures/BIO-510/email_20230928_assignment2_help.md\nlectur\u2026", "outputChars": 514 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -i \\\"pax6\\\" coursework_biology lectures | cut -d: -f1 | sort -u'\"}", "outputPreview": "coursework_biology/mcb501_final_exam_study_guide_20231204.md\ncoursework_biology/mcb501_lecture10_stem_cells_20231106.md\nlectures/BIO-510/assignment_02.md\nlectures/BIO-510/email_20230928_assignment2_help.md\nlectures/GEN-600/20231115_lecture09_notes.md\nlectures/GEN-600/final_paper_proposal.md\n", "outputChars": 292 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n -i \\\"course.*(SOX2|sox2)|(SOX2|sox2).*course|course.*(PAX6|pax6)|(PAX6|pax6).*course\\\" .'\"}", "outputPreview": "./communications/f177_good_results_sharing.md:22:I\u2019m going to repeat the staining on a different batch of cells just to be sure it\u2019s reproducible, but I\u2019m feeling really confident now. I still need to optimize the secondary antibody concentration for the GFP channel (which is going to be for my reporter gene expression later, so not in this image), but for the PAX6 marker itself, this looks pretty\u2026", "outputChars": 1003 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'smfs grep \\\"In which courses did Lena first encounter the genes SOX2 and PAX6\\\"'\"}", "outputPreview": "# supermemory semantic search \u2014 10 results for \"In which courses did Lena first encounter the genes SOX2 and PAX6\"\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 the file)\n\n/lab\u2026", "outputChars": 9457 } ] } ] } }