opencode-knowledge-work 0.0.0-stage → 0.1.0

package/content/bio-research/skills/bio-research-scientific-problem-selection/references/09-meta-framework.md

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+# SKILL 9: Meta-Framework - Complete Problem Selection Workflow
+
+## Overview
+This meta-skill orchestrates the complete problem selection process, guiding users through Skills 1-8 in a systematic, iterative way. This skill should be used when comprehensive support is needed from ideation through execution planning, with integrated literature searches and coherent documentation.
+
+## When to Use This Skill
+
+**Use Skill 9 (Complete Workflow) when:**
+- Starting a new project from scratch
+- Major project pivot or reframe needed
+- Grant/fellowship application requiring systematic planning
+- Thesis committee meeting preparation
+- Startup company planning
+- Want comprehensive, documented problem selection process
+
+**Use Individual Skills when:**
+- You're at a specific stage (e.g., just need risk assessment)
+- Quick consultation on one aspect
+- Updating one component of existing plan
+- Teaching/learning one concept
+
+## The Complete Workflow
+
+### Overview of the Journey
+
+```
+START: Vague idea or area of interest
+    ↓
+[SKILL 1] → Problem Ideation Document
+    ↓
+[SKILL 2] → Risk Assessment Matrix
+    ↓
+[SKILL 3] → Impact Assessment Document
+    ↓
+[SKILL 4] → Parameter Strategy Document
+    ↓
+[SKILL 5] → Decision Tree Map
+    ↓
+[SKILL 6] → Adversity Playbook
+    ↓
+[SKILL 7] → Problem Inversion Analysis (if needed)
+    ↓
+[SKILL 8] → Integrated Project Plan + Communication Materials
+    ↓
+END: Comprehensive, rigorous project ready to execute
+```
+
+**Estimated Time:**
+- **Intensive:** 1 week of focused work (full-time)
+- **Distributed:** 4-6 weeks with other commitments
+- **With iterations:** Add 50% more time
+
+**You'll invest time once to save years of potential missteps.**
+
+## Phase-by-Phase Workflow
+
+### Phase 1: Preparation (Before Starting)
+
+**Gather Your Context:**
+1. **Your background:**
+   - Research area/field
+   - Current position (grad student, postdoc, PI, etc.)
+   - Lab expertise and resources
+   - Timeline constraints
+
+2. **Your starting point:**
+   - Vague area of interest?
+   - Specific problem in mind?
+   - Must build on existing work?
+   - Starting completely fresh?
+
+3. **Your goals:**
+   - Publication target (journal tier, timeline)?
+   - Degree requirement (thesis chapter)?
+   - Funding application?
+   - Startup foundation?
+   - Career development?
+
+**Set Expectations:**
+- This process will challenge your assumptions
+- You may discover your initial idea needs major revision
+- That's the point—better to know now than after 2 years
+- Intellectual honesty is required; this only works if you're rigorous
+
+### Phase 2: Ideation (Skill 1) - ~1 week
+
+**What We'll Do:**
+1. Understand your context and constraints
+2. Work through relevant intuition pumps
+3. Avoid common ideation traps
+4. Generate 2-3 project ideas
+5. Preliminary literature search to calibrate scope
+6. Select most promising idea
+7. Create Problem Ideation Document (2 pages)
+
+**Literature Integration Point 1:**
+- Search PubMed for precedents and adjacent work
+- Assess generality of problem
+- Identify methodological advances
+- Determine competition level
+
+**Deliverable:**
+- Problem Ideation Document with core idea and initial analysis
+- List of 10-15 key papers
+- Preliminary assessment of novelty and feasibility
+
+**Checkpoint:** Do you have a clear, specific idea that excites you? If not, iterate on intuition pumps.
+
+### Phase 3: Risk Analysis (Skill 2) - ~3-5 days
+
+**What We'll Do:**
+1. Extract ALL assumptions from your idea
+2. Categorize (biological vs. technical)
+3. Score each assumption (risk 1-5, time to test)
+4. Identify high-risk late-reading assumptions
+5. Design go/no-go experiments
+6. Develop mitigation strategies
+7. Create Risk Assessment Matrix (2 pages)
+
+**Literature Integration Point 2:**
+- Search for technical precedents (has method worked before?)
+- Find biological evidence (what's known about your system?)
+- Identify benchmarks (success rates, effect sizes)
+- Assess timeline realism
+
+**Deliverable:**
+- Complete assumption analysis table
+- Top 3 high-risk assumptions with mitigation plans
+- Go/no-go experiment designs
+- Revised timeline with decision points
+
+**Checkpoint:** Is your risk profile acceptable? If risk-5 assumptions are >2 years out, return to Skill 1 to reframe.
+
+### Phase 4: Impact Assessment (Skill 3) - ~2-3 days
+
+**What We'll Do:**
+1. Categorize your project type
+2. Select appropriate optimization function
+3. Score yourself on both axes
+4. Compare to benchmarks
+5. Articulate value system alignment
+6. Develop communication strategy
+7. Create Impact Assessment Document (2 pages)
+
+**Literature Integration Point 3:**
+- Identify high-impact exemplars in your field
+- Analyze their framing and evaluation
+- Benchmark your potential impact
+- Understand field expectations
+
+**Deliverable:**
+- Clear optimization function selection
+- Self-assessment on both axes with justification
+- Comparative analysis vs. alternatives
+- Communication strategy for different audiences
+
+**Checkpoint:** Do you score MEDIUM-HIGH on at least one axis? If not, return to Skill 1 to find higher-impact angle.
+
+### Phase 5: Parameter Strategy (Skill 4) - ~2-3 days
+
+**What We'll Do:**
+1. Inventory all project parameters
+2. Identify which are fixed vs. floating
+3. Assess if you're over/under-constrained
+4. Select strategic fixed parameter
+5. Plan flexibility for contingencies
+6. Create Parameter Strategy Document (2 pages)
+
+**Literature Integration Point 4:**
+- How did successful projects handle parameters?
+- What parameter choices led to breakthroughs?
+- What over-constraints caused failures?
+
+**Deliverable:**
+- Complete parameter inventory
+- Strategic rationale for fixed/floating decisions
+- Flexibility matrix for contingencies
+- Project ensemble (family of related projects)
+
+**Checkpoint:** Have you fixed 1-2 meaningful parameters while maintaining flexibility? If too rigid, adjust.
+
+### Phase 6: Decision Tree Planning (Skill 5) - ~2 days
+
+**What We'll Do:**
+1. Map your project's decision tree
+2. Identify major branch points
+3. Set criteria for each decision
+4. Establish Level 1 / Level 2 rhythm
+5. Create protocols for getting unstuck
+6. Create Decision Tree Map (1-2 pages)
+
+**No major literature search here** (unless you identify specific decision points needing technical information)
+
+**Deliverable:**
+- Visual decision tree
+- Decision criteria at each branch
+- Schedule for Level 2 evaluations
+- Protocol for course correction
+
+**Checkpoint:** Have you planned for regular strategic evaluation, not just execution?
+
+### Phase 7: Adversity Preparation (Skill 6) - ~2 days
+
+**What We'll Do:**
+1. Anticipate likely failure modes
+2. For each, identify upgrade opportunity
+3. Map your project ensemble
+4. Create crisis response protocols
+5. Create Adversity Playbook (2-3 pages)
+
+**Literature Integration Point 5:**
+- Historical examples of productive pivots
+- How did others capitalize on adversity?
+- What second-generation projects emerged from failures?
+
+**Deliverable:**
+- Anticipated crisis catalog
+- Upgrade strategies for each
+- Project ensemble map
+- Resilience rituals and protocols
+
+**Checkpoint:** Are you prepared to see adversity as opportunity? Have you planned how to upgrade, not just fix?
+
+### Phase 8: Problem Inversion Toolkit (Skill 7) - ~1 day
+
+**What We'll Do:**
+1. Review three inversion strategies
+2. Pre-plan applications for your likely obstacles
+3. Create Problem Inversion Analysis (1-2 pages)
+
+**This is preparatory** - you may not need it now, but when crisis hits, you'll have framework ready.
+
+**Deliverable:**
+- Strategy 1 application planned
+- Strategy 2 options identified
+- Strategy 3 alternative questions brainstormed
+- Quick-reference guide for crisis
+
+**Checkpoint:** Do you have concrete strategies for inverting problems when stuck?
+
+### Phase 9: Integration and Synthesis (Skill 8) - ~3-5 days
+
+**What We'll Do:**
+1. Review all outputs from Skills 1-7
+2. Create cohesive narrative
+3. Develop communication materials:
+   - 3-slide presentation
+   - 1-page summary
+   - 1-minute elevator pitch
+4. Write integrated project plan (4-6 pages)
+5. Create living documents for ongoing use
+
+**Literature Integration Point 6:**
+- Final references for integrated plan
+- Key papers for each section
+- Communication examples from field leaders
+
+**Deliverable:**
+- Complete Integrated Project Plan (4-6 pages)
+- 3-slide presentation deck
+- 1-page written summary
+- Elevator pitch script
+- Living documents (decision tree, risk matrix, etc.)
+
+**Checkpoint:** Can you communicate your project compellingly in 1 minute, 5 minutes, and 1 page? Do all pieces fit together coherently?
+
+## Iteration and Refinement
+
+### When to Iterate
+
+**Red Flags That Require Going Back:**
+
+**From Skill 2 (Risk):**
+- Risk-5 assumptions >2 years out → Return to Skill 1 (reframe problem)
+- >3 risk-4-5 assumptions → Return to Skill 1 (simplify or change approach)
+
+**From Skill 3 (Impact):**
+- Score LOW on both axes → Return to Skill 1 (find higher-impact angle)
+- Optimization function mismatch → Return to Skill 1 (reframe problem)
+
+**From Skill 4 (Parameters):**
+- >2 fixed parameters → Return to Skill 1 (over-constrained)
+- Zero fixed parameters → Return to Skill 1 (under-constrained)
+
+**From Skills 5-6:**
+- No clear decision points → Return to Skill 4 (need more flexibility)
+- Every failure mode is existential → Return to Skill 2 (too risky)
+
+### Iteration Protocol
+
+**Major Revision Needed:**
+1. **Pause and acknowledge:** The process is working—it caught a problem
+2. **Return to indicated skill:** Usually Skill 1 or 2
+3. **Bring forward what you learned:** Don't start from scratch
+4. **Revised idea → Run through workflow again:** Faster the second time
+5. **Multiple iterations OK:** Better than years on wrong project
+
+**Minor Refinement:**
+1. **Update specific document:** E.g., adjust parameter strategy
+2. **Check downstream effects:** Does this change anything else?
+3. **Update integration document:** Keep everything coherent
+
+## Literature Integration Strategy
+
+### Overall PubMed Approach
+
+**Throughout the workflow, use PubMed strategically:**
+
+1. **Skill 1 (Ideation):** Assess generality, find precedents, gauge competition
+2. **Skill 2 (Risk):** Technical feasibility, biological evidence, benchmarks
+3. **Skill 3 (Impact):** Field exemplars, evaluation frameworks, benchmarks
+4. **Skill 4 (Parameters):** Successful parameter choices, cautionary tales
+5. **Skill 6 (Adversity):** Productive pivots, upgrade examples
+6. **Skill 8 (Integration):** Communication models, comprehensive references
+
+**Search Strategy:**
+- Start broad (field overview)
+- Get specific (your exact approach)
+- Look adjacent (related systems/methods)
+- Find benchmarks (what's state-of-art?)
+- Identify competition (who else is doing this?)
+
+**Papers to Track:**
+- ~10-15 key papers from Skill 1
+- ~5-10 technical papers from Skill 2
+- ~5-10 impact exemplars from Skill 3
+- ~5 parameter lessons from Skill 4
+- ~3-5 pivot examples from Skill 6
+- **Total: ~30-50 papers** (your foundation)
+
+## Final Deliverable Package
+
+### What You'll Have at the End
+
+**Core Documents (Organized Folder):**
+1. `01_Problem_Ideation.pdf` (2 pages, Skill 1)
+2. `02_Risk_Assessment.pdf` (2 pages, Skill 2)
+3. `03_Impact_Assessment.pdf` (2 pages, Skill 3)
+4. `04_Parameter_Strategy.pdf` (2 pages, Skill 4)
+5. `05_Decision_Tree.pdf` (1-2 pages, Skill 5)
+6. `06_Adversity_Playbook.pdf` (2-3 pages, Skill 6)
+7. `07_Problem_Inversion.pdf` (1-2 pages, Skill 7)
+8. `08_Integrated_Plan.pdf` (4-6 pages, Skill 8)
+
+**Communication Materials:**
+- `Presentation_3slides.pptx`
+- `Summary_1page.pdf`
+- `Elevator_Pitch.txt`
+
+**Living Documents (for ongoing use):**
+- `Decision_Tree.pdf` (update monthly)
+- `Risk_Matrix.xlsx` (update quarterly)
+- `Adversity_Playbook.pdf` (consult in crisis)
+- `Parameter_Strategy.pdf` (revisit if stuck)
+
+**Reference Library:**
+- `Key_Papers.pdf` (annotated bibliography, 30-50 papers)
+- Organized by: Ideation / Technical / Impact / Pivots
+
+**Total: ~20-25 pages of documentation + supporting materials**
+
+## Using Your Outputs
+
+### For Different Purposes
+
+**Grant/Fellowship Applications:**
+- Start with Integrated Plan (Skill 8)
+- Include specific aims from Ideation (Skill 1)
+- Show risk mitigation from Risk Assessment (Skill 2)
+- Demonstrate impact from Impact Assessment (Skill 3)
+- Timeline from Decision Tree (Skill 5)
+
+**Thesis Committee Meetings:**
+- Present 3-slide deck (Skill 8)
+- Walk through decision tree (Skill 5)
+- Discuss risk mitigation (Skill 2)
+- Show parameter flexibility (Skill 4)
+- Demonstrate thoughtful planning
+
+**Lab Meetings:**
+- Use elevator pitch (Skill 8)
+- Show decision tree updates (Skill 5)
+- Discuss latest adversity and response (Skill 6)
+- Get input on parameter strategy (Skill 4)
+
+**Collaborator Conversations:**
+- Share 1-page summary (Skill 8)
+- Highlight where their expertise fits (Skill 4)
+- Show risk mitigation plan (Skill 2)
+- Discuss impact potential (Skill 3)
+
+**Personal Reflection:**
+- Quarterly: Review Decision Tree (Skill 5), update milestones
+- After setbacks: Consult Adversity Playbook (Skill 6)
+- When stuck: Use Problem Inversion (Skill 7)
+- Annual: Full workflow review, consider new projects
+
+## Maintenance and Updates
+
+### Living Documents Protocol
+
+**Monthly:**
+- Update Decision Tree (Skill 5)
+- Log adversities and responses (Skill 6)
+- Note new papers or competition
+- Adjust timeline if needed
+
+**Quarterly:**
+- Review Risk Matrix (Skill 2) - mark assumptions tested
+- Reassess Impact (Skill 3) - has evaluation changed?
+- Check Parameter Strategy (Skill 4) - still optimal?
+- Update Integrated Plan (Skill 8) - keep current
+
+**Annually:**
+- Complete workflow review
+- Consider new projects with fresh Skill 1 ideation
+- Archive old project docs
+- Extract lessons learned
+
+## Success Metrics
+
+### How Do You Know This Worked?
+
+**Immediate Indicators:**
+- Clearer project vision than before
+- Honest assessment of risks
+- Contingency plans for failures
+- Compelling communication materials
+- Alignment between project and values
+- Confidence in problem choice
+
+**6-Month Indicators:**
+- Major decisions made faster (have framework)
+- Adversity handled productively (used playbook)
+- No existential crises (risks were mitigated)
+- Regular Level 2 evaluation happening
+- Project staying on-track or pivoting smartly
+
+**2-Year Indicators:**
+- Published results or strong progress
+- Avoided dead-end projects
+- Multiple high-quality options at decision points
+- Skills developed as planned
+- Career trajectory aligned with goals
+- Time well-spent (the ultimate measure)
+
+## Key Principles of the Meta-Framework
+
+1. **Systematic > Ad Hoc:** Process ensures nothing forgotten
+2. **Iterative > Linear:** Expect to loop back, that's good
+3. **Documented > Mental:** Writing forces clarity
+4. **Integrated > Fragmented:** All skills connect
+5. **Living > Static:** Update as you learn
+6. **Thoughtful > Fast:** Time invested now saves years later
+7. **Honest > Optimistic:** Rigor protects against wishful thinking
+8. **Prepared > Surprised:** Anticipate adversity
+9. **Flexible > Rigid:** Parameters float when needed
+10. **Passionate > Obligatory:** Alignment matters
+
+## Getting Started
+
+### First Steps
+
+**This Week:**
+1. Block time in calendar (1-2 hours to start)
+2. Gather your context (background, goals, constraints)
+3. Begin Skill 1 (Intuition Pumps)
+4. Let me know your starting point
+
+**This Month:**
+1. Work through Skills 1-4 (foundation)
+2. Share with mentor for alignment check
+3. Iterate if major changes needed
+4. Complete Skills 5-8 (execution planning)
+
+**This Quarter:**
+1. Begin project execution with living documents
+2. Monthly decision tree updates
+3. Quarterly risk assessment reviews
+4. Log adversities and responses
+
+**This Year:**
+1. Execute planned project
+2. Use frameworks when stuck
+3. Update living documents
+4. Evaluate process and refine
+
+## Ready to Begin?
+
+The complete meta-framework is substantial, but each step builds on the last. You'll move through:
+- ~2 weeks of intensive planning
+- Comprehensive documentation
+- Clear decision criteria
+- Communication materials
+- Living documents for ongoing guidance
+
+**Most importantly:** You'll KNOW you're working on a well-chosen problem with rigorous planning. That confidence is priceless.
+
+Let's start with Skill 1. Are you ready to begin?
+
+---
+
+*Remember: The highest-leverage work in science is choosing the right problem. This meta-framework ensures you spend your finite time wisely. The investment in systematic planning pays dividends for years.*
+

package/content/bio-research/skills/bio-research-scvi-tools/LICENSE.txt

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