{ "slug": "dp_007-q05-codex", "dp": "dp_007", "files": 200, "qid": "q05", "family": "multi_hop", "prompt": "What was the subject of the GEN-600 paper critique assignment, and who did Lena exchange drafts with for feedback?", "gold": "The critique was on the paper 'Epigenetic Landscape Remodeling During Embryonic Stem Cell Fate Decisions' (about epigenetic mechanisms governing cell fate decisions). Lena exchanged drafts with Anika Patel via the GEN-600 email thread on 2023-11-10.", "agent": "codex", "fs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 526716, "outputTokens": 4361, "totalTokens": 531077, "cost": 6.4514, "durationMs": 79979, "answer": "The GEN-600 paper critique assignment was about critiquing a recent paper on epigenetic mechanisms governing cell fate decisions, with emphasis on experimental design and methodology. Lena\u2019s saved critique focused on \u201cEpigenetic Landscape Remodeling During Embryonic Stem Cell Fate Decisions.\u201d\n\nLena exchanged drafts with Anika Patel. In the email thread, Lena reviewed Anika\u2019s Huang et al. critique, and Anika reviewed Lena\u2019s Davies et al. draft for feedback.", "judgeReason": "covers all asked facts", "toolCalls": 14, "trajectory": [ { "step": 1, "inputTokens": 526716, "outputTokens": 4361, "text": "I\u2019ll search the local `agent_memory` first, focusing on the course code, assignment name, and Lena\u2019s draft feedback trail.\nI found the relevant GEN-600 files: the critique assignment itself and an email thread about sharing critique drafts. I\u2019m opening those now to pin down the exact subject and names.\nThere\u2019s one wrinkle: Lena\u2019s saved assignment file names her completed critique as an epigenetics/cell-fate paper, while the draft-exchange email refers to her draft as the \u201cDavies et al.\u201d critique. I\u2019m checking nearby GEN-600 notes so the answer reflects the assignment topic rather than overreading one file name.\nThe GEN-600 paper critique assignment was about critiquing a recent paper on epigenetic mechanisms governing cell fate decisions, with emphasis on experimental design and methodology. Lena\u2019s saved critique focused on \u201cEpigenetic Landscape Remodeling During Embryonic Stem Cell Fate Decisions.\u201d\n\nLena exchanged drafts with Anika Patel. In the email thread, Lena reviewed Anika\u2019s Huang et al. critique, and Anika reviewed Lena\u2019s Davies et al. draft for feedback.", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"GEN-600|paper critique|critique assignment|Lena|draft|feedback\\\" agent_memory'\"}", "outputPreview": "agent_memory/communications/f173_confusing_results_email.md:1:From: Lena Hansen \nagent_memory/communications/f173_confusing_results_email.md:27:Lena\nagent_memory/communications/f173_confusing_results_email.md:29:Lena Hansen\nagent_memory/communications/f173_confusing_results_email.md:41:To: Lena Hansen \nagent_memory/communications/f173_confusing\u2026", "outputChars": 660232 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg --files agent_memory'\"}", "outputPreview": "agent_memory/communications/f173_confusing_results_email.md\nagent_memory/meetings/mentor_1on1/20231129_tanaka_notes.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_su\u2026", "outputChars": 13068 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' agent_memory/lectures/GEN-600/assignment_03_critique.md\\\"\"}", "outputPreview": "# GEN-600: Assignment 03 - Paper Critique\n\n**Author:** Lena Hansen\n**Date:** 2023-11-03\n**Course:** GEN-600: Molecular Mechanisms of Development\n**Assignment:** Paper Critique (Assignment 03)\n**Due Date:** 2023-11-03\n\n---\n\n## Table of Contents\n\n1. **Introduction**\n * Purpose of this Document\n * Selected Paper Overview\n * Course Context (GEN-600)\n2. **Critique of \"Epigenetic Landsc\u2026", "outputChars": 31438 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,240p' agent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md\\\"\"}", "outputPreview": "From: lena.hansen@northwood.edu\nTo: anika.patel@northwood.edu\nDate: Fri, 10 Nov 2023 09:15:23 -0500\nSubject: Re: GEN-600 Paper Critique Drafts\n\nHi Anika,\n\nThanks for sending this over! I've had a chance to read through your critique of the Huang et al. paper. Overall, I think you've done a really thorough job. Your analysis of the experimental design, particularly the control groups and the statis\u2026", "outputChars": 10419 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"critique|draft|feedback|paper|AlSayed|ALSayed|Chen|Park|Patel|Maria|Anika|exchange\\\" agent_memory/lectures/GEN-600 agent_memory/communications'\"}", "outputPreview": "agent_memory/lectures/GEN-600/20230927_lecture04_notes.md:208:Overall, though, I\u2019m feeling much more confident about understanding GWAS papers and the data Kenji and I might be working with. The power of these studies is undeniable, but so are the potential pitfalls. Need to really nail down the statistical concepts for that problem set.\nagent_memory/lectures/GEN-600/20230927_lecture04_notes.md:21\u2026", "outputChars": 411092 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '220,360p' agent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md\\\"\"}", "outputPreview": "Subject: GEN-600 Paper Critique Drafts\nDate: Wed, 08 Nov 2023 13:35:10 -0500\n\nAnika,\n\nThat was a dense GEN-600 lecture today, wasn't it? My brain feels a bit fried trying to keep up with all the new concepts. The paper critique assignment (assignment_03_critique.md) is really intimidating me, especially the part about evaluating experimental design. I'm not sure I'm seeing the subtleties well enou\u2026", "outputChars": 11779 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"Assignment 03|paper critique|critique assignment|Davies|Huang|experimental design|cell fate|epigenetic\\\" agent_memory/lectures/GEN-600/*.md agent_memory/communications/*.md'\"}", "outputPreview": "agent_memory/lectures/GEN-600/20230927_lecture04_notes.md:178:* **No Signal:** A lack of significant peaks doesn't necessarily mean there's no genetic component to the trait. It could mean that the common variants tested don't have strong effects, or that the important genetic effects are due to rare variants (which standard GWAS arrays are not optimized to detect), or structural variants, or ep\u2026", "outputChars": 142078 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,180p' agent_memory/lectures/GEN-600/20231108_lecture08_notes.md\\\"\"}", "outputPreview": "# GEN-600: Molecular Genetics - Lecture 08 Notes\n\n**Date:** 2023-11-08\n**Lecturer:** Dr. Alistair Thorne\n**Topic:** The Genetic Basis of Cancer\n\n***\n\n## Table of Contents\n\n1. Introduction: Cancer as a Genetic Disease\n2. Oncogenes: The Gas Pedal\n * Retroviruses and the Discovery of Oncogenes\n * Proto-oncogenes vs. Oncogenes\n * Examples: Ras, Myc, Her2\n3. Tumor Suppressor Genes: Th\u2026", "outputChars": 14444 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '240,340p' agent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md\\\"\"}", "outputPreview": "**Email Thread Body Start (Most Recent First)**\n\nFrom: lena.hansen@northwood.edu\nTo: anika.patel@northwood.edu\nDate: Fri, 10 Nov 2023 11:45:00 -0500\nSubject: Re: GEN-600 Paper Critique Drafts\n\nHi Anika,\n\nThanks so much for your incredibly thorough feedback on my draft! Your comments are really insightful and exactly the kind of constructive criticism I was hoping for. I appreciate you taking the t\u2026", "outputChars": 10275 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'rg -n \\\"Davies|Bayesian|computational modeling|predicting differentiation|cell fate decisions|Huang\\\" agent_memory/lectures/GEN-600 agent_memory/communications'\"}", "outputPreview": "agent_memory/lectures/GEN-600/20230830_lecture01_notes.md:285:Beyond `GEN-600`, I\u2019m also taking `BIO-510` (Advanced Molecular Biology) and `STA-550` (Statistical Methods in Biology). `BIO-510` is building directly on some of the molecular mechanisms we discussed in my first year, with a deeper dive into gene regulation, epigenetics, and protein-protein interactions. Professor Davies is very thorou\u2026", "outputChars": 35887 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"find agent_memory -iname '*critique*' -o -iname '*davies*' -o -iname '*gen600*'\\\"\"}", "outputPreview": "agent_memory/lectures/GEN-600/assignment_03_critique.md\nagent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md\nagent_memory/communications/f175_gen600_proposal_reminder.md\n", "outputChars": 189 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lectures/GEN-600/assignment_03_critique.md | sed -n '50,70p'\\\"\"}", "outputPreview": " 50\t## 1. Introduction\n 51\t\n 52\t### Purpose of this Document\n 53\t\n 54\tThis document contains my formal critique of a research paper for the GEN-600 Molecular Mechanisms of Development course. The assignment required selecting a recent publication (within the last 3-5 years) that deals with epigenetic mechanisms governing cell fate decisions, analyzing its strengths and weaknesses, w\u2026", "outputChars": 4759 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md | sed -n '280,302p'\\\"\"}", "outputPreview": " 280\tSubject: Re: GEN-600 Paper Critique Drafts\n 281\t\n 282\tHi Lena,\n 283\t\n 284\tThank you for sending your draft over. I've had a chance to review it and provide some comments.\n 285\t\n 286\tOverall, your critique of the Davies et al. paper is very well-structured and insightful. Your points regarding the statistical assumptions of their models and the potential for overfitting are parti\u2026", "outputChars": 3553 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"nl -ba agent_memory/lectures/GEN-600/email_20231110_sharing_critique_drafts.md | sed -n '314,330p'\\\"\"}", "outputPreview": " 314\tDate: Fri, 10 Nov 2023 09:15:23 -0500\n 315\tSubject: Re: GEN-600 Paper Critique Drafts\n 316\t\n 317\tHi Anika,\n 318\t\n 319\tThanks for sending this over! I've had a chance to read through your critique of the Huang et al. paper. Overall, I think you've done a really thorough job. Your analysis of the experimental design, particularly the control groups and the statistical power, is supe\u2026", "outputChars": 2687 } ] } ] }, "smfs": { "agent": "codex", "success": true, "steps": 1, "inputTokens": 329280, "outputTokens": 6601, "totalTokens": 335881, "cost": 4.1494, "durationMs": 86333, "answer": "The GEN-600 paper critique was about epigenetic mechanisms in cell fate decisions, with emphasis on experimental design and methodology. Lena\u2019s draft exchange refers to her critique of the Davies et al. paper.\n\nLena exchanged drafts and feedback with Anika Patel.", "judgeReason": "covers all asked facts", "toolCalls": 21, "trajectory": [ { "step": 1, "inputTokens": 329280, "outputTokens": 6601, "text": "I\u2019ll search the Supermemory mount directly, starting with the profile summary and then semantic grep for the GEN-600 critique details.\nThe semantic search command is failing with a local `401` auth error, so I\u2019m going to inspect the mounted files directly without using text search tools inside the mount.\nThe mount has a GEN-600 lecture area and several relevant communications around the proposal and peer review. I\u2019m narrowing to those files now.\nThe GEN-600 paper critique was about epigenetic mechanisms in cell fate decisions, with emphasis on experimental design and methodology. Lena\u2019s draft exchange refers to her critique of the Davies et al. paper.\n\nLena exchanged drafts and feedback with Anika Patel.", "toolCalls": [ { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'cat /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/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 \\\"GEN-600 paper critique assignment subject Lena exchanged drafts feedback\\\" /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/smfs/dp_007/agent_memory/'\"}", "outputPreview": "Error: auth failed (401)\n", "outputChars": 25 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la'\"}", "outputPreview": "total 1\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 .\ndrwxr-xr-x@ 6 prasanna staff 192 May 26 22:23 ..\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 communications\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 coursework_biology\ndrwxr-xr-x 6 root wheel 0 May 26 22:23 lab\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 lectures\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 meet\u2026", "outputChars": 464 }, { "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 'smfs --help'\"}", "outputPreview": "supermemoryfs (smfs) \u2014 exposes a Supermemory container as a real local directory. Typically invoked indirectly via `supermemory mount`, but can also be used directly.\n\nUsage: smfs \n\nCommands:\n login Authenticate with Supermemory (prefer `supermemory login` from the TS CLI)\n whoami Show the currently-authenticated user, org, and API endpoint\n mount Mount a Supermemory container \u2026", "outputChars": 1056 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la communications'\"}", "outputPreview": "total 3085\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 36658 May 26 22:23 f156_mcb_orientation_schedule.md\n-rw-r--r-- 1 root wheel 35616 May 26 22:23 f157_first_lab_meeting.md\n-rw-r--r-- 1 root wheel 38381 May 26 22:23 f158_project_kickoff_scheduling.md\n-rw-r--r-- 1 root wheel 37666 May 26 22:23 f159_study_gro\u2026", "outputChars": 3530 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la coursework_biology'\"}", "outputPreview": "total 2629\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 33938 May 26 22:23 cm550_assignment01_organelle_id_20230920.md\n-rw-r--r-- 1 root wheel 32321 May 26 22:23 cm550_assignment02_cytoskeleton_staining_20231004.md\n-rw-r--r-- 1 root wheel 30557 May 26 22:23 cm550_assignment03_experimental_design_20231030.md\n-rw-r-\u2026", "outputChars": 3773 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la meetings'\"}", "outputPreview": "total 0\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 ..\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 advisor_1on1\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 mentor_1on1\n", "outputChars": 206 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la lab'\"}", "outputPreview": "total 0\ndrwxr-xr-x 6 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 ..\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 meetings\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 notebook\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 operations\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 protocols\n", "outputChars": 304 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la lectures'\"}", "outputPreview": "total 0\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 7 root wheel 0 May 26 22:23 ..\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 BIO-510\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 GEN-600\n", "outputChars": 197 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la lectures/GEN-600'\"}", "outputPreview": "total 1348\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 40477 May 26 22:23 20230830_lecture01_notes.md\n-rw-r--r-- 1 root wheel 30557 May 26 22:23 20230906_lecture02_notes.md\n-rw-r--r-- 1 root wheel 30839 May 26 22:23 20230920_lecture03_notes.md\n-rw-r--r-- 1 root wheel 34805 May 26 22:23 20230927_lecture04_notes\u2026", "outputChars": 1624 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la meetings/advisor_1on1'\"}", "outputPreview": "total 432\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 29410 May 26 22:23 20230901_reed_notes.md\n-rw-r--r-- 1 root wheel 29020 May 26 22:23 20230915_reed_notes.md\n-rw-r--r-- 1 root wheel 29787 May 26 22:23 20230929_reed_notes.md\n-rw-r--r-- 1 root wheel 30602 May 26 22:23 20231013_reed_notes.md\n-rw-r--r-- 1 roo\u2026", "outputChars": 590 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la meetings/mentor_1on1'\"}", "outputPreview": "total 453\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 4 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 26127 May 26 22:23 20230906_tanaka_notes.md\n-rw-r--r-- 1 root wheel 34666 May 26 22:23 20230920_tanaka_notes.md\n-rw-r--r-- 1 root wheel 36619 May 26 22:23 20231004_tanaka_notes.md\n-rw-r--r-- 1 root wheel 28148 May 26 22:23 20231018_tanaka_notes.md\n-rw-r--r-\u2026", "outputChars": 604 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc 'ls -la lab/meetings'\"}", "outputPreview": "total 933\ndrwxr-xr-x 2 root wheel 0 May 26 22:23 .\ndrwxr-xr-x 6 root wheel 0 May 26 22:23 ..\n-rw-r--r-- 1 root wheel 31183 May 26 22:23 20230829_lab_meeting_notes.md\n-rw-r--r-- 1 root wheel 30968 May 26 22:23 20230905_lab_meeting_notes.md\n-rw-r--r-- 1 root wheel 29066 May 26 22:23 20230912_lab_meeting_notes.md\n-rw-r--r-- 1 root wheel 30989 May 26 22:23 20230919_lab_meetin\u2026", "outputChars": 1185 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' lectures/GEN-600/email_20231110_sharing_critique_drafts.md\\\"\"}", "outputPreview": "From: lena.hansen@northwood.edu\nTo: anika.patel@northwood.edu\nDate: Fri, 10 Nov 2023 09:15:23 -0500\nSubject: Re: GEN-600 Paper Critique Drafts\n\nHi Anika,\n\nThanks for sending this over! I've had a chance to read through your critique of the Huang et al. paper. Overall, I think you've done a really thorough job. Your analysis of the experimental design, particularly the control groups and the statis\u2026", "outputChars": 9721 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' lectures/GEN-600/assignment_03_critique.md\\\"\"}", "outputPreview": "# GEN-600: Assignment 03 - Paper Critique\n\n**Author:** Lena Hansen\n**Date:** 2023-11-03\n**Course:** GEN-600: Molecular Mechanisms of Development\n**Assignment:** Paper Critique (Assignment 03)\n**Due Date:** 2023-11-03\n\n---\n\n## Table of Contents\n\n1. **Introduction**\n * Purpose of this Document\n * Selected Paper Overview\n * Course Context (GEN-600)\n2. **Critique of \"Epigenetic Landsc\u2026", "outputChars": 31438 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' communications/f175_gen600_proposal_reminder.md\\\"\"}", "outputPreview": "From: marcus.thorne@northwood.edu\nTo: gen600-students@northwood.edu\nDate: Wed, 15 Nov 2023 09:15:37 -0500\nSubject: Reminder: Final Paper Proposal Deadline - November 20th\n\nDear GEN-600 Students,\n\nThis is a gentle reminder that the deadline for your final paper proposals is fast approaching. Please ensure that your proposals are submitted by **Monday, November 20th**.\n\nAs previously detailed in the\u2026", "outputChars": 26117 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' communications/f176_proposal_peer_review.md\\\"\"}", "outputPreview": "From: anika.patel@northwood.edu\nTo: lena.hansen@northwood.edu, maria.rodriguez@northwood.edu, james.williams@northwood.edu\nDate: Sat, 18 Nov 2023 10:02:15 -0500\nSubject: GEN-600 Proposal Drafts - For Peer Review\n\nHi everyone,\n\nHope you're all having a good weekend so far!\n\nAs per our study group chat, I've attached my draft proposal for the GEN-600 paper. I'm really trying to nail down the specifi\u2026", "outputChars": 14998 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '220,420p' lectures/GEN-600/email_20231110_sharing_critique_drafts.md\\\"\"}", "outputPreview": "Subject: GEN-600 Paper Critique Drafts\nDate: Wed, 08 Nov 2023 13:35:10 -0500\n\nAnika,\n\nThat was a dense GEN-600 lecture today, wasn't it? My brain feels a bit fried trying to keep up with all the new concepts. The paper critique assignment (assignment_03_critique.md) is really intimidating me, especially the part about evaluating experimental design. I'm not sure I'm seeing the subtleties well enou\u2026", "outputChars": 14005 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,180p' lectures/GEN-600/20231108_lecture08_notes.md\\\"\"}", "outputPreview": "# GEN-600: Molecular Genetics - Lecture 08 Notes\n\n**Date:** 2023-11-08\n**Lecturer:** Dr. Alistair Thorne\n**Topic:** The Genetic Basis of Cancer\n\n***\n\n## Table of Contents\n\n1. Introduction: Cancer as a Genetic Disease\n2. Oncogenes: The Gas Pedal\n * Retroviruses and the Discovery of Oncogenes\n * Proto-oncogenes vs. Oncogenes\n * Examples: Ras, Myc, Her2\n3. Tumor Suppressor Genes: Th\u2026", "outputChars": 14444 }, { "name": "command_execution", "input": "{\"command\": \"/bin/zsh -lc \\\"sed -n '1,220p' lectures/GEN-600/20231115_lecture09_notes.md\\\"\"}", "outputPreview": "# GEN-600 Lecture 09: Genomics of Development - Notes & Reflections\n\n**Date:** 2023-11-15\n**Author:** Lena Hansen\n**Course:** course_id_gen_600\n\nThis 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 embryogenesis to the more complex regulatory networ\u2026", "outputChars": 36535 } ] } ] } }