Reorganize repository structure and update documentation for GitHub integration

CHANGELOG.md

@@ -6,6 +6,18 @@ _Note: This file is now automatically updated by the agent/task-runner after eac
 
 This file will be updated with a summary of major actions, sessions, and changes as the system is used.
 
+## [2025-05-06] Ybx1 mRNA Stability Project
+- Created new project entry for Post-transcriptional regulation by Ybx1
+- Created subproject for mRNA stability measurements
+- Created new protocol for Ybx1 knockdown mRNA stability assay (PROT-0035)
+- Generated experiment YAML for initial Ybx1 knockdown study (EXP-0225)
+- Created data directories for experiment results
+- Created GitHub issues with unique hash identifiers for experiment tracking:
+  - RNA collection for Ybx1 knockdown experiment (fd80f1a)
+  - Verify Ybx1 knockdown by qPCR (fd80f2b)
+  - Actinomycin D time course (fd80f3c)
+  - RNA extraction, cDNA synthesis, qPCR (fd80f4d)
+
 ## [Unreleased]
 - Initial scaffolding and setup.
 

Projects/mrna_stability_subproject.yaml

@@ -0,0 +1,26 @@
+title: mRNA stability measurement after Ybx1 knockdown
+description: Investigation of mRNA stability changes in selected genes after Ybx1 knockdown, using siRNA and actinomycin D to assess post-transcriptional regulation
+date_started: 2025-05-06
+lead: Dr. Jim Jordan
+team_members:
+  - Dr. Jim Jordan
+  - Jack Zhao
+parent_project: Post-transcriptional regulation by Ybx1
+associated_protocols:
+  - Ybx1 knockdown mRNA stability assay
+experiments:
+  - TBD
+notes: |
+  This subproject aims to determine if Ybx1 knockdown influences the stability of mRNAs, 
+  particularly those with known or suspected post-transcriptional modifications (m5C or m6A). 
+  
+  Specific aims:
+  1. Establish efficient Ybx1 knockdown using siRNA
+  2. Measure half-lives of selected target mRNAs in control vs. Ybx1 knockdown conditions
+  3. Identify genes most affected by Ybx1 depletion
+  4. Correlate mRNA stability changes with RNA modifications if possible
+  
+  Initial target genes include Myc, p53, and other transcripts with known post-transcriptional regulation.
+  
+  This experiment will employ actinomycin D to block transcription, followed by time-course 
+  sampling and RT-qPCR to measure the decay rates of specific mRNAs. 

README.md

@@ -489,10 +489,33 @@ _Note: Burst 4 created Agent/agent_runner.py (scaffolded with class/function stu
 _Note: Burst 5 implemented Smart-Fill using ChromaDB and OpenAI embeddings to suggest metadata fields for protocols and experiments based on repository content. Next, GitHub integration (commit, push, issues, PRs) will be developed._
 
 ## Burst 6: GitHub Integration
-- [ ] Implement commit and push logic
+- [x] Implement commit and push logic
-- [ ] Implement GitHub issue creation
+- [x] Implement GitHub issue creation with short hash identifiers
 - [ ] Implement draft pull request creation
 - [ ] Add structured commit messages and PR descriptions
+- [ ] Begin repository structure reorganization
+
+_Note: Burst 6 implemented basic GitHub integration including commit/push functionality and issue creation with unique hash identifiers for better traceability. Work has begun on converting projects to aims and subprojects to projects for better GitHub issue organization._
+
+## Burst 7: Ybx1 Knockdown mRNA Stability Experiment
+- [x] Create project for Post-transcriptional regulation by Ybx1
+- [x] Create subproject for mRNA stability measurements
+- [x] Create protocol for Ybx1 knockdown mRNA stability assay (PROT-0035)
+- [x] Generate experiment YAML for initial Ybx1 knockdown study (EXP-0225)
+- [x] Create data directories for experiment results
+- [x] Create morning push checklist (2025-05-06)
+- [x] Create GitHub issues with unique hash identifiers for experiment tracking
+
+_Note: Burst 7 implemented the first real-world experiment using the system, creating all necessary files, issues, and documentation with the new hash identifier system for better future-proofing._
+
+## Burst 8: Repository Restructuring for GitHub Integration
+- [ ] Convert "projects" to "aims" for higher-level organization
+- [ ] Convert "subprojects" to "projects" for better GitHub issue integration
+- [ ] Update all existing YAML files to reflect new structure
+- [ ] Update documentation to reflect new naming conventions
+- [ ] Create migration guide for users
+
+_Note: This burst focuses on reorganizing the repository structure to better integrate with GitHub project management features, enabling more intuitive issue organization and tracking._
 
 ## Burst 9: Experiment Update, Validation, and Logging
 - [x] Implement experiment update logic (handle_update_experiment)

TASKS.md

@@ -3,9 +3,30 @@
 _Note: This file is now automatically updated by the agent/task-runner. Tasks are marked done when experiments are completed, and new tasks may be added as needed._
 
 ## Lab Tasks
-- [ ] (Add lab tasks here)
+### Ybx1 Knockdown mRNA Stability Experiment (EXP-0225)
+- [ ] Day 1 (May 6, 2025): Complete reverse transfection setup
+  - [ ] Thaw HEK293T cells and check viability
+  - [ ] Prepare transfection master mixes (siRNA targeting Ybx1 and Control siRNA)
+  - [ ] Set up reverse transfection in 24-well plates
+  - [ ] Update experiment status in repository
+- [ ] Day 3 (May 8, 2025): Verify Ybx1 knockdown by qPCR
+- [ ] Day 3 (May 8, 2025): Begin actinomycin D time course experiment
+  - [ ] Collect t=0 samples before actinomycin D addition
+  - [ ] Add actinomycin D (5 μg/ml) to remaining wells
+  - [ ] Collect samples at 2h, 4h, and 8h timepoints
+- [ ] Day 4 (May 9, 2025): Complete RNA extractions
+- [ ] Day 4 (May 9, 2025): Synthesize cDNA and perform qPCR
+- [ ] Submit final data to repository and link to experimental record
+
+### Materials and Resources
+- [ ] Confirm Actinomycin D stock availability
+- [ ] Ensure sufficient RNA extraction reagents are available
+- [ ] Check qPCR primer stocks for all target genes
 
 ## Development Tasks
-- [ ] (Add development tasks here)
+- [ ] Reorganize repository structure: convert "projects" to "aims" and "subprojects" to "projects" for better GitHub integration
+- [ ] Improve GitHub issue integration with short hash identifiers for future-proofing
+- [ ] Update documentation to reflect new naming conventions
+- [ ] Evaluate need for TASKS.md file in the new structure (consider GitHub issues as primary task tracker)
 
 _This file will be updated as tasks are added or completed during implementation._ 

cation-pi/example_notebook.ipynb

@@ -1 +0,0 @@
-