Inbox Processor

Overview

Processes and organizes unstructured input files from the inbox/ directory. Classifies content, extracts actionable information, and suggests appropriate destinations for integration into the research workflow.

Core Capabilities

1. File Classification

Classify inbox files into categories based on content.

Categories:

1. Meeting Notes: Discussion records, decisions, action items
2. Protocols: Experimental procedures, SOPs
3. Ideas: Research ideas, hypotheses, brainstorming
4. Data: Raw data files, datasets
5. Literature: Papers, references, reading notes
6. Miscellaneous: Unclear or mixed content

Workflow:

1. Read file from inbox/
2. Analyze content to determine category
3. Extract key information
4. Suggest destination
5. Optionally move/process file

2. Information Extraction

Extract actionable information from unstructured content.

What to extract:

From Meeting Notes:

• Decisions made
• Action items (who, what, when)
• Key discussion points
• Follow-up questions

From Protocols:

• Procedure steps
• Required materials
• Expected outcomes
• Citations/sources

From Ideas:

• Core hypothesis
• Experimental approach
• Required resources
• Potential experiments

From Literature:

• Key findings
• Relevant methods
• Citations
• Relevance to current work

3. Destination Suggestions

Recommend where content should be integrated.

Classification Rules (from references/classification-rules.md):

Content Type	Suggested Destination	Rationale
Meeting notes	notebook/knowledge/meeting_YYYY-MM-DD.md	Reusable context
Protocol	notebook/knowledge/protocol_[name].md	Reusable procedure
Experiment idea	Create new lab notebook via /research-exp	Start experiment
Research hypothesis	Refine with hypothesis-driven skill	Improve quality
Raw data file	data/raw/[filename]	Data storage
Literature notes	notebook/knowledge/literature_[topic].md	Reference material

4. Integration Actions

After classification, take appropriate action.

Possible actions:

1. Move to knowledge/:

   mv inbox/meeting_notes.txt notebook/knowledge/meeting_2025-01-15.md
   

2. Create experiment:

   Content suggests new experiment → Use /research-exp
   

3. Add to STEERING.md:

   Important decisions → Update priorities in STEERING.md
   

4. Add to tasks.md:

   Action items → Add to notebook/tasks.md
   

5. Process for report:

   Relevant findings → Note in ongoing report
   

6. Archive:

   mv inbox/old_file.txt inbox/archive/
   

Usage Workflow

Typical Usage

1. User adds file to inbox/:

   User: "I put meeting notes in inbox/team_meeting.md"
   

2. Classify content:

   Assistant reads file, determines category: Meeting Notes
   

3. Extract information:

   Decisions:
   - Approved Exp04 (ATAC-seq analysis)
   - Prioritize cell cycle validation
   
   Action items:
   - [User] Design primers for qPCR by Friday
   - [Collaborator] Share ChIP-seq data next week
   
   Discussion:
   - Considered three-prime seq vs bulk RNA-seq
   - Decided bulk more appropriate for current question
   

4. Suggest destination:

   Suggested destination: notebook/knowledge/meeting_2025-01-15.md
   Suggested actions:
   - Add primer design to tasks.md
   - Update STEERING.md with Exp04 approval
   - Plan to receive ChIP-seq data
   

5. Implement (with user approval):

   Move file, update tasks.md, update STEERING.md
   

Batch Processing

Process multiple inbox files:

User: "Process all files in inbox/"