Input
2.7M
Output
2k
Steps
40
Tools
23
Latency
2.3m
Cost
$39.98
#2 Ran ls /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/ 55 chars
Command Bash
ls /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/
{
"description": "List agent_memory directory contents"
} Result 5 lines
communications coursework_biology lab lectures meetings
#3 Read /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/ 2,817 chars
Command Grep
{
"pattern": "SOX2",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/",
"output_mode": "files_with_matches"
} Result 9 lines
Found 42 files agent_memory/communications/f177_good_results_sharing.md agent_memory/communications/f200_sox2_question.md agent_memory/lectures/GEN-600/final_paper_proposal.md agent_memory/lectures/GEN-600/20231115_lecture09_notes.md agent_memory/lectures/BIO-510/final_project.md agent_memory/lectures/BIO-510/assignment_02.md agent_memory/lectures/BIO-510/email_20230928_assignment2_help.md agent_m…
#4 Read /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/ 2,167 chars
Command Grep
{
"pattern": "PAX6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/",
"output_mode": "files_with_matches"
} Result 8 lines
Found 33 files agent_memory/communications/f175_gen600_proposal_reminder.md agent_memory/communications/f177_good_results_sharing.md agent_memory/communications/f200_sox2_question.md agent_memory/lectures/GEN-600/final_paper_proposal.md agent_memory/lectures/GEN-600/20231115_lecture09_notes.md agent_memory/lectures/BIO-510/assignment_02.md agent_memory/lectures/BIO-510/email_20230928_assignment2_h…
#6 Edited agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md 28,002 chars
Command Read
{
"file_path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md"
} Result 11 lines
1 # Lab Notebook: LH-EXP-23-014 - Primer Design for Neural Markers 2 3 **Date:** 2023-10-13 4 **Author:** Lena Hansen 5 **Project:** Initial transcriptomic analysis pipeline development 6 **Keywords:** qPCR, primer design, SOX2, PAX6, neural stem cells, bioinformatics, Primer-BLAST 7 8 ## Table of Contents 9 10 1. [Introduction & Objectives](#introduction--objectives) 11 2. [Background: Gene …
#8 Reasoning 74 chars
Now I need to find the courses where Lena first encountered SOX2 and PAX6.
#9 Read agent_memory/coursework_biology/ 1,924 chars
Command Grep
{
"pattern": "SOX2|PAX6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/",
"output_mode": "content",
"-C": 3
} Result 5 lines
<persisted-output> Output too large (28.3KB). Full output saved to: /Users/prasanna/.claude/projects/-Users-prasanna-Documents-supermemoryai-supermemoryfs--scratch-eval-eval-workspace-fs-dp-007/2d0a5acf-d838-48f5-889e-9fb32844062e/tool-results/toolu_01BKuNbQkNRcLR8iMJ6neyGJ.txt Preview (first 2KB): /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_…
#10 Read agent_memory/lectures/ 2,177 chars
Command Grep
{
"pattern": "SOX2|PAX6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/",
"output_mode": "content",
"-C": 2
} Result 5 lines
<persisted-output> Output too large (45.4KB). Full output saved to: /Users/prasanna/.claude/projects/-Users-prasanna-Documents-supermemoryai-supermemoryfs--scratch-eval-eval-workspace-fs-dp-007/2d0a5acf-d838-48f5-889e-9fb32844062e/tool-results/toolu_01A3rozkbPXQM3uzdWJJEo6o.txt Preview (first 2KB): agent_memory/lectures/GEN-600/final_paper_proposal.md-51-* **Signal integrators:** Responding to …
#12 Read agent_memory/coursework_biology/mcb501_lecture04_translation_20230918.md 4,306 chars
Command Grep
{
"pattern": "SOX2|PAX6|first encounter|first heard|first time",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/mcb501_lecture04_translation_20230918.md",
"output_mode": "content",
"-C": 3
} Result 9 lines
4-**Author:** Lena Hansen (MCB Dept., 1st Year PhD Student) 5-**Course:** MCB-501: Molecular Biology of the Cell II 6- 7:[Omitted long matching line] 8- 9-Professor Finch really went into detail on the ribosome's structure and the intricate dance of tRNA molecules. It’s way more complex than I initially thought. I’ll try to capture the key steps: initiation, elongation, and termination. 10- -- 26-…
#13 Read agent_memory/lectures/BIO-510/assignment_02.md 4,096 chars
Command Grep
{
"pattern": "SOX2|PAX6|first|encounter",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/assignment_02.md",
"output_mode": "content",
"-C": 3
} Result 10 lines
62-| ... | ... | ... | ... | 63-| 200 | gene_sox2| 8.90 | Differentiated | 64- 65:[Omitted long matching line] 66- 67-## 3. Methodology: Two-Sample T-Test 68- -- 73-Other tests come to mind, but they aren't suitable here: 74-* **Paired t-test:** This is for situations where the samples are paired (e.g., measuring the same subject before and after …
#15 Read /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/ 2,222 chars
Command Grep
{
"pattern": "first.{0,30}(encounter|heard|learn|met|saw|came across)|encounter.{0,30}(SOX2|PAX6)",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/",
"output_mode": "content",
"-C": 2,
"-i": true
} Result 5 lines
<persisted-output> Output too large (20.8KB). Full output saved to: /Users/prasanna/.claude/projects/-Users-prasanna-Documents-supermemoryai-supermemoryfs--scratch-eval-eval-workspace-fs-dp-007/2d0a5acf-d838-48f5-889e-9fb32844062e/tool-results/toolu_01DMWrUobYoUoveq4JnNQjKr.txt Preview (first 2KB): /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_…
#17 Edited agent_memory/communications/f200_sox2_question.md 39,564 chars
Command Read
{
"file_path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/communications/f200_sox2_question.md"
} Result 8 lines
1 From: Lena Hansen <lena.hansen@northwood.edu> 2 To: Kenji Tanaka <kenji.tanaka@northwood.edu> 3 Date: Wed, 29 Nov 2023 10:15:23 -0500 4 Subject: Quick Question: SOX2 timing and plasmid confirmation 5 6 Hi Dr. Tanaka, 7 8 Hope you're having a good week. I'm working on optimizing the neuronal differentiation protocol for the iPSC line we're using for the SOX2 project, and I had a couple of quick…
#19 Ran cat /Users/prasanna/.claude/projects/-Users-prasanna-Documents-supermemoryai-supermemoryfs--scratch-eval-eval-workspace-fs-dp-007/2d0a5acf-d… 21,283 chars
Command Bash
cat /Users/prasanna/.claude/projects/-Users-prasanna-Documents-supermemoryai-supermemoryfs--scratch-eval-eval-workspace-fs-dp-007/2d0a5acf-d838-48f5-889e-9fb32844062e/tool-results/toolu_01DMWrUobYoUoveq4JnNQjKr.txt | head -200
{
"description": "Read persisted grep output for first-encounter matches"
} Result 3 lines
/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/communications/f159_study_group_formation.md-39-Hi Maria, /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/communications/f159_study_group_formation.md-40- agent_memory/communications/f159_study_group_formation.md:41:Yes, absolutely! I w…
#21 Read agent_memory/coursework_biology/mcb501_midterm_study_guide_20231002.md 1,944 chars
Command Grep
{
"pattern": "SOX2",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/mcb501_midterm_study_guide_20231002.md",
"output_mode": "content",
"-B": 2,
"-A": 5
} Result 5 lines
206-### Questions/Areas to Review 207- 208:[Omitted long matching line] 209-2. **Spliceosome Dynamics:** The assembly and rearrangement of the spliceosome are complex. How do the snRNPs interact and change conformation to become catalytically active? What drives these conformational changes? Is it ATP-dependent? 210-3. **5' Cap vs. 3' Poly(A) Tail:** How do these two modifications *cooperatively…
#22 Read agent_memory/coursework_biology/mcb501_lecture10_stem_cells_20231106.md 5,004 chars
Command Grep
{
"pattern": "PAX6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/mcb501_lecture10_stem_cells_20231106.md",
"output_mode": "content",
"-B": 2,
"-A": 5
} Result 4 lines
137- 138-Dr. Albright specifically mentioned `gene_pax6` as a crucial master regulator in neural development. 139:* **Role of PAX6:** `gene_pax6` encodes a transcription factor that plays a vital role in the development of the eye, brain, and spinal cord. It's often considered a master regulator of **neurogenesis**. 140-* **Expression:** It's expressed in the developing neural tube, the precur…
#24 Ran ls -la /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/ /Users/… 4,452 chars
Command Bash
ls -la /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/ /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/
{
"description": "List coursework and lectures directories"
} Result 6 lines
/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/: total 2776 drwxr-xr-x@ 42 prasanna staff 1344 May 13 03:05 . drwxr-xr-x@ 7 prasanna staff 224 May 13 03:05 .. -rw-r--r--@ 1 prasanna staff 33938 May 13 01:04 cm550_assignment01_organelle_id_20230920.md -rw-r--r--@ 1 prasanna staff 32321 May 13 01:04 cm550_ass…
#26 Ran ls /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/ /Users/prasan… 1,429 chars
Command Bash
ls /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/ /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/GEN-600/
{
"description": "List BIO-510 and GEN-600 lecture files"
} Result 11 lines
/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/: 20230905_lecture02_notes.md 20230912_lecture03_notes.md 20230919_lecture04_notes.md 20230926_lecture05_notes.md 20231017_lecture06_notes.md 20231024_lecture07_notes.md 20231031_lecture08_notes.md 20231107_lecture09_notes.md 20231128_lecture10_notes.md 20231205_lecture11_revi…
#27 Edited agent_memory/lectures/BIO-510/assignment_02.md 9,277 chars
Command Read
{
"file_path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/assignment_02.md",
"offset": 1,
"limit": 80
} Result 12 lines
1 # BIO-510: Assignment 2 - Hypothesis Testing and Data Analysis 2 3 **Student:** Lena Hansen 4 **Course:** BIO-510: Biostatistics for Molecular Biologists 5 **Date:** 2023-09-29 6 **Instructor:** Dr. Evelyn Reed (though this is for Dr. Rossi's section, technically, but Evelyn is my official advisor, so it feels like hers!) 7 8 --- 9 10 ## Table of Contents 11 12 1. [Introduction](#introducti…
#29 Ran grep -l "first" /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology… 870 chars
Command Bash
grep -l "first" /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/*.md /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/*.md 2>/dev/null | head -5
{
"description": "List files that mention 'first'"
} Result 3 lines
/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/cm550_assignment01_organelle_id_20230920.md /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/cm550_assignment02_cytoskeleton_staining_20231004.md /Users/prasanna/Documents/supermemoryai/supermemoryfs…
#30 Read agent_memory/coursework_biology/mcb501_final_exam_study_guide_20231204.md 16 chars
Command Grep
{
"pattern": "first.{0,80}(SOX2|PAX6)|(SOX2|PAX6).{0,80}first|encountered|introduced",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/mcb501_final_exam_study_guide_20231204.md",
"output_mode": "content",
"-B": 1,
"-A": 3
} Result 1 lines
No matches found
#31 Read agent_memory/lectures/ 8,518 chars
Command Grep
{
"pattern": "first.{0,80}(SOX2|PAX6)|(SOX2|PAX6).{0,80}first|encountered|first time",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/",
"output_mode": "content",
"-B": 1,
"-A": 3
} Result 3 lines
/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/GEN-600/email_20231005_GWAS_confusion.md-7- agent_memory/lectures/GEN-600/email_20231005_GWAS_confusion.md:8:[Omitted long matching line] /Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/GEN-600/email_20231005_GWAS_conf…
#33 Reasoning 82 chars
Let me check earlier dates to ensure I find the very first mentions in coursework.
#34 Read agent_memory/coursework_biology/ 386 chars
Command Grep
{
"pattern": "SOX2|PAX6|gene_sox2|gene_pax6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/coursework_biology/",
"output_mode": "files_with_matches"
} Result 6 lines
Found 5 files agent_memory/coursework_biology/mcb501_final_exam_study_guide_20231204.md agent_memory/coursework_biology/mcb501_lecture10_stem_cells_20231106.md agent_memory/coursework_biology/mcb501_assignment02_rna_splicing_essay_20231002.md agent_memory/coursework_biology/mcb501_midterm_study_guide_20231002.md agent_memory/coursework_biology/mcb501_lecture04_translation_20230918.md
#35 Read agent_memory/lectures/BIO-510/ 172 chars
Command Grep
{
"pattern": "SOX2|PAX6|gene_sox2|gene_pax6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/",
"output_mode": "files_with_matches"
} Result 4 lines
Found 3 files agent_memory/lectures/BIO-510/final_project.md agent_memory/lectures/BIO-510/assignment_02.md agent_memory/lectures/BIO-510/email_20230928_assignment2_help.md
#36 Read agent_memory/lectures/GEN-600/ 125 chars
Command Grep
{
"pattern": "SOX2|PAX6",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/GEN-600/",
"output_mode": "files_with_matches"
} Result 3 lines
Found 2 files agent_memory/lectures/GEN-600/final_paper_proposal.md agent_memory/lectures/GEN-600/20231115_lecture09_notes.md
#38 Read agent_memory/lectures/BIO-510/email_20230928_assignment2_help.md 436 chars
Command Grep
{
"pattern": "PAX6|SOX2",
"path": "/Users/prasanna/Documents/supermemoryai/supermemoryfs/.scratch/eval/eval/workspace/fs/dp_007/agent_memory/lectures/BIO-510/email_20230928_assignment2_help.md",
"output_mode": "content",
"-B": 1,
"head_limit": 10
} Result 12 lines
9-
10:[Omitted long matching line]
--
52-# The core task is to perform a two-sample t-test. This means comparing the means of two groups.
53:# We need to compare the expression of PAX6 between Condition 1 and Condition 2.
54:# And then do the same for SOX2.
--
57-
58:# Step 1: Filter the data to include only the genes of interest: PAX6 and SOX2.
59:genes_of_interest <- c("PAX6", "SOX2")
[Showing … #40 Reasoning 1,077 chars
Based on the agent_memory files: **Courses where Lena first encountered each gene:** - **SOX2** — first encountered in **MCB-501 (Molecular Biology of the Cell II)** in her notes for Lecture 04 on Translation (2023-09-18, `mcb501_lecture04_translation_20230918.md`), where she wrote Section 7 "Connecting to Research (SOX2 and my lab work)" linking the translation material to her rotation work with Kenji Tanaka. - **PAX6** — first encountered in **BIO-510 (Biostatistics for Molecular Biologists)** in Assignment 2 (2023-09-29, `lectures/BIO-510/assignment_02.md`), a two-sample t-test exercise comparing `gene_pax6` and `gene_sox2` expression between "Stem Cell-Like" and "Differentiated" populations (with the related help-thread email dated 2023-09-28). **qPCR primer design lab notebook entry:** - **LH-EXP-23-014** — "Primer Design for Neural Markers" (2023-10-13, `lab/notebook/20231013_LH-EXP-23-014_Primer-Design-SOX2.md`), where she designed both `LH-EXP-23-SOX2-F/R` and `LH-EXP-23-PAX6-F/R` primer pairs (plus GAPDH/ACTB housekeepers) using NCBI Primer-BLAST.
Answer
Based on the agent_memory files:
**Courses where Lena first encountered each gene:**
- **SOX2** — first encountered in **MCB-501 (Molecular Biology of the Cell II)** in her notes for Lecture 04 on Translation (2023-09-18, `mcb501_lecture04_translation_20230918.md`), where she wrote Section 7 "Connecting to Research (SOX2 and my lab work)" linking the translation material to her rotation work with Kenji Tanaka.
- **PAX6** — first encountered in **BIO-510 (Biostatistics for Molecular Biologists…
Judge: covers all asked facts