@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/scientific-manuscript/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: scientific-manuscript
+description: "High-impact scientific manuscript preparation for journals like Nature, Blood, Cell. Use when writing abstracts, introductions, methods, results, discussions, or figure legends. Includes citation management, statistical reporting standards, ICMJE guidelines, and journal-specific formatting for hematology/oncology publications."
+license: Proprietary
+---
+
+# Scientific Manuscript Preparation
+
+## Document Structure for High-Impact Journals
+
+### Title
+- Concise (<15 words for Nature, <20 for Blood)
+- Include key finding and system/disease
+- Avoid jargon and abbreviations
+
+### Abstract (Structured for Blood/Clinical Journals)
+
+```markdown
+**Background:** One sentence on knowledge gap.
+**Methods:** Key approaches, patient cohort size, techniques.
+**Results:** Primary findings with statistics (P values, CIs).
+**Conclusions:** Clinical/translational significance.
+```
+
+### Introduction (~500-800 words)
+1. **Paragraph 1**: Broad context, disease burden, clinical relevance
+2. **Paragraph 2**: Current knowledge, key mechanisms
+3. **Paragraph 3**: Knowledge gap, unanswered questions
+4. **Paragraph 4**: Study aims, hypothesis, approach overview
+
+### Methods (Detailed, Reproducible)
+
+```markdown
+**Patient Cohort and Samples**
+- IRB approval number, consent process
+- Inclusion/exclusion criteria
+- Sample processing, storage conditions
+
+**Single-Cell RNA Sequencing**
+- Library preparation (10x Genomics Chromium 3' v3.1)
+- Sequencing platform, read depth
+- Quality metrics (cells/sample, genes/cell, % mitochondrial)
+
+**Computational Analysis**
+- Software versions (Scanpy 1.9.x, scvi-tools 0.20.x)
+- QC thresholds (min genes, max %MT)
+- Integration method (TotalVI, Harmony)
+- Clustering parameters (resolution, n_neighbors)
+- Differential expression (Wilcoxon, FDR < 0.05, |log2FC| > 1)
+
+**Statistical Analysis**
+- Software (R 4.3.x, Python 3.11)
+- Tests used with justification
+- Multiple testing correction method
+- Power analysis if applicable
+```
+
+### Results (~2000-3000 words)
+- Lead each paragraph with key finding
+- Reference figures in order (Figure 1A-C...)
+- Report exact P values (P = 0.003, not P < 0.05)
+- Include confidence intervals where relevant
+- Avoid interpretation; save for Discussion
+
+### Discussion (~1500-2000 words)
+
+```markdown
+**Paragraph 1**: Summarize key findings, relate to hypothesis
+
+**Paragraph 2-4**: Compare to existing literature
+- "Consistent with [Author et al.], we found..."
+- "In contrast to [Study], our analysis revealed..."
+- Mechanistic interpretation
+
+**Paragraph 5**: Translational/Clinical implications
+- Therapeutic targets
+- Biomarkers
+- Patient stratification
+
+**Paragraph 6**: Limitations
+- Sample size, cohort characteristics
+- Technical limitations
+- Generalizability
+
+**Paragraph 7**: Future directions and conclusion
+```
+
+## Statistical Reporting Standards
+
+### Continuous Variables
+- Mean ± SD (normal) or Median [IQR] (non-normal)
+- Report normality test used
+
+### Categorical Variables
+- N (%) with comparison test
+
+### P Values
+- Report exact values (P = 0.023)
+- For very small: P < 0.0001
+- Always report test used
+
+### Sample Sizes
+- "n = X patients" or "n = X cells"
+- Report for each comparison group
+
+## Figure Legends Template
+
+```markdown
+**Figure 1. Title describes main finding**
+(A) Brief description of panel A. Statistical test, P value.
+(B) Description including axis labels if not obvious.
+(C-D) Can combine similar panels.
+Scale bars: X μm. Error bars: mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001.
+n = X biological replicates from Y independent experiments.
+```
+
+## Reference Formatting
+
+### Blood Journal (Vancouver)
+```
+1. Smith JA, Jones BC. Title of article. Blood. 2024;143(5):567-578.
+```
+
+### Nature (Author-Year)
+```
+Smith, J.A. & Jones, B.C. Title of article. Nature 620, 567–578 (2024).
+```
+
+## Journal-Specific Requirements
+
+### Blood (ASH)
+- Word limit: 4000 (full article)
+- Figures: 7 max
+- References: 60 max
+- Structured abstract: 250 words
+
+### Nature
+- Word limit: ~3000 (Article)
+- Main text figures: 6-8
+- Methods: no limit, separate section
+- Extended Data for supplementary figures
+
+### Cell
+- Word limit: 7000 (Article)
+- STAR Methods format
+- Graphical abstract required
+
+## HIPAA Compliance Reminders
+
+- No patient identifiers in any form
+- Use Specimen IDs, not patient names/MRNs
+- Aggregate data for small groups (n < 5)
+- IRB approval statement required
+- Data availability statement (GEO accession for sequencing)
+
+## Writing Style
+
+- Active voice preferred
+- Past tense for results ("We found...")
+- Present tense for established facts
+- Avoid "interesting," "significant" (unless statistical)
+- Be specific: "83.9-fold increase" not "marked increase"
+
+See `references/journal_templates.md` for specific formats.
+See `references/statistical_tests.md` for test selection guide.
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/scientific-problem-selection/SKILL.md

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+---
+name: scientific-problem-selection
+description: This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
+---
+
+# Scientific Problem Selection Skills
+
+A conversational framework for systematic scientific problem selection based on Fischbach & Walsh's "Problem choice and decision trees in science and engineering" (Cell, 2024).
+
+## Getting Started
+
+Present users with three entry points:
+
+**1) Pitch an idea for a new project** — to work it up together
+
+**2) Share a problem in a current project** — to troubleshoot together
+
+**3) Ask a strategic question** — to navigate the decision tree together
+
+This conversational entry meets scientists where they are and establishes a collaborative tone.
+
+---
+
+## Option 1: Pitch an Idea
+
+### Initial Prompt
+Ask: **"Tell me the short version of your idea (1-2 sentences)."**
+
+### Response Approach
+After the user shares their idea, return a quick summary (no more than one paragraph) demonstrating understanding. Note the general area of research and rephrase the idea in a way that highlights its kernel—showing alignment and readiness to dive into details.
+
+### Follow-up Prompt
+Then ask for more detail: "Now give me a bit more detail. You might include, however briefly or even say where you are unsure:
+1. What exactly you want to do
+2. How you currently plan to do it
+3. If it works, why will it be a big deal
+4. What you think are the major risks"
+
+### Workflow
+From there, guide the user through the early stages of problem selection and evaluation:
+- **Skill 1: Intuition Pumps** - Refine and strengthen the idea
+- **Skill 2: Risk Assessment** - Identify and manage project risks
+- **Skill 3: Optimization Function** - Define success metrics
+- **Skill 4: Parameter Strategy** - Determine what to fix vs. keep flexible
+
+See `references/01-intuition-pumps.md`, `references/02-risk-assessment.md`, `references/03-optimization-function.md`, and `references/04-parameter-strategy.md` for detailed guidance.
+
+---
+
+## Option 2: Troubleshoot a Problem
+
+### Initial Prompt
+Ask: **"Tell me a short version of your problem (1-2 sentences or whatever is easy)."**
+
+### Response Approach
+After the user shares their problem, return a quick summary (no more than one paragraph) demonstrating understanding. Note the context of the project where the problem occurred and rephrase the problem—highlighting its core essence—so the user knows the situation is understood. Also raise additional questions that seem important to discuss.
+
+### Follow-up Prompt
+Then ask: "Now give me a bit more detail. You might include, however briefly:
+1. The overall goal of your project (if we have not talked about it before)
+2. What exactly went wrong
+3. Your current ideas for fixing it"
+
+### Workflow
+From there, guide the user through troubleshooting and decision tree navigation:
+- **Skill 5: Decision Tree Navigation** - Plan decision points and navigate between execution and strategic thinking
+- **Skill 4: Parameter Strategy** - Fix one parameter at a time, let others float
+- **Skill 6: Adversity Response** - Frame problems as opportunities for growth
+- **Skill 7: Problem Inversion** - Strategies for navigating around obstacles
+
+Always include workarounds that might be useful whether or not the problem can be fixed easily.
+
+See `references/05-decision-tree.md`, `references/06-adversity-planning.md`, `references/07-problem-inversion.md`, and `references/04-parameter-strategy.md` for detailed guidance.
+
+---
+
+## Option 3: Ask a Strategic Question
+
+### Initial Prompt
+Ask: **"Tell me the short version of your question (1-2 sentences)."**
+
+### Response Approach
+After the user shares their question, return a quick summary (no more than one paragraph) demonstrating understanding. Note the broader context and rephrase the question—highlighting its crux—to confirm alignment with their thinking.
+
+### Follow-up Prompt
+Then ask: "Now give me a bit more detail. You might include, however briefly:
+1. The setting (i.e., is this about a current or future project)
+2. A bit more detail about what you're thinking"
+
+### Workflow
+From there, draw on the specific modules from the problem choice framework most appropriate to the question:
+- **Skills 1-4** for future project planning (ideation, risk, optimization, parameters)
+- **Skills 5-7** for current project navigation (decision trees, adversity, inversion)
+- **Skill 8** for communication and synthesis
+- **Skill 9** for comprehensive workflow orchestration
+
+See the complete reference materials in the `references/` folder.
+
+---
+
+## Core Framework Concepts
+
+### The Central Insight
+**Problem Choice >> Execution Quality**
+
+Even brilliant execution of a mediocre problem yields incremental impact. Good execution of an important problem yields substantial impact.
+
+### The Time Paradox
+Scientists typically spend:
+- **Days** choosing a problem
+- **Years** solving it
+
+This imbalance limits impact. These skills help invest more time choosing wisely.
+
+### Evaluation Axes
+**For Evaluating Ideas:**
+- **X-axis:** Likelihood of success
+- **Y-axis:** Impact if successful
+
+Skills help move ideas rightward (more feasible) and upward (more impactful).
+
+### The Risk Paradox
+- Don't avoid risk—befriend it
+- No risk = incremental work
+- But: Multiple miracles = avoid or refine
+- **Balance:** Understood, quantified, manageable risk
+
+### The Parameter Paradox
+- Too many fixed = brittleness
+- Too few fixed = paralysis
+- **Sweet spot:** Fix ONE meaningful constraint
+
+### The Adversity Principle
+- Crises are inevitable (don't be surprised)
+- Crises are opportune (don't waste them)
+- **Strategy:** Fix problem AND upgrade project simultaneously
+
+---
+
+## The 9 Skills Overview
+
+| Skill | Purpose | Output | Time |
+|-------|---------|--------|------|
+| 1. Intuition Pumps | Generate high-quality research ideas | Problem Ideation Document | ~1 week |
+| 2. Risk Assessment | Identify and manage project risks | Risk Assessment Matrix | 3-5 days |
+| 3. Optimization Function | Define success metrics | Impact Assessment Document | 2-3 days |
+| 4. Parameter Strategy | Decide what to fix vs. keep flexible | Parameter Strategy Document | 2-3 days |
+| 5. Decision Tree Navigation | Plan decision points and altitude dance | Decision Tree Map | 2 days |
+| 6. Adversity Response | Prepare for crises as opportunities | Adversity Playbook | 2 days |
+| 7. Problem Inversion | Navigate around obstacles | Problem Inversion Analysis | 1 day |
+| 8. Integration & Synthesis | Synthesize into coherent plan | Project Communication Package | 3-5 days |
+| 9. Meta-Framework | Orchestrate complete workflow | Complete Project Package | 1-6 weeks |
+
+---
+
+## Skill Workflow
+
+```
+SKILL 1: Intuition Pumps
+         | (generates idea)
+         v
+SKILL 2: Risk Assessment
+         | (evaluates feasibility)
+         v
+SKILL 3: Optimization Function
+         | (defines success metrics)
+         v
+SKILL 4: Parameter Strategy
+         | (determines flexibility)
+         v
+SKILL 5: Decision Tree
+         | (plans execution and evaluation)
+         v
+SKILL 6: Adversity Planning
+         | (prepares for failure modes)
+         v
+SKILL 7: Problem Inversion
+         | (provides pivot strategies)
+         v
+SKILL 8: Integration & Communication
+         | (synthesizes into coherent plan)
+         v
+SKILL 9: Meta-Skill
+         (orchestrates complete workflow)
+```
+
+---
+
+## Key Design Principles
+
+1. **Conversational Entry** - Meet users where they are with three clear starting points
+2. **Thoughtful Interaction** - Ask clarifying questions; low confidence prompts additional input
+3. **Literature Integration** - Use PubMed searches at strategic points for validation
+4. **Concrete Outputs** - Every skill produces tangible 1-2 page documents
+5. **Building Specificity** - Progressive detail emerges through targeted questions
+6. **Flexibility** - Skills work independently, sequentially, or iteratively
+7. **Scientific Rigor** - Claims about generality and feasibility should be evidence-based
+
+---
+
+## Who Should Use These Skills
+
+### Graduate Students (Primary Audience)
+- **When:** Choosing thesis projects, qualifying exams, committee meetings
+- **Focus:** Skills 1-3 (ideation, risk, impact) + Skill 9 (complete workflow)
+- **Timeline:** 2-4 weeks for comprehensive planning
+
+### Postdocs
+- **When:** Starting new position, planning independent projects, fellowship applications
+- **Focus:** All skills, emphasizing independence and risk management
+- **Timeline:** 1-2 weeks intensive planning
+
+### Principal Investigators
+- **When:** New lab, new direction, mentoring trainees, grant cycles
+- **Focus:** Skills 1, 3, 4, 6 (ideation, impact, parameters, adversity)
+- **Timeline:** Ongoing, integrate into lab culture
+
+### Startup Founders
+- **When:** Company inception, pivot decisions, investor pitches
+- **Focus:** Skills 1-4 (ideation through parameters) + Skill 8 (communication)
+- **Timeline:** 1-2 weeks for initial planning, revisit quarterly
+
+---
+
+## Reference Materials
+
+Detailed skill documentation is available in the `references/` folder:
+
+| File | Content | Search Patterns |
+|------|---------|-----------------|
+| `01-intuition-pumps.md` | Generate research ideas | `Intuition Pump #`, `Trap #`, `Phase [0-9]` |
+| `02-risk-assessment.md` | Risk identification | `Risk.*1-5`, `go/no-go`, `assumption` |
+| `03-optimization-function.md` | Success metrics | `Generality.*Learning`, `optimization`, `impact` |
+| `04-parameter-strategy.md` | Parameter fixation | `fixed.*float`, `constraint`, `parameter` |
+| `05-decision-tree.md` | Decision tree navigation | `altitude`, `Level [0-9]`, `decision` |
+| `06-adversity-planning.md` | Adversity response | `adversity`, `crisis`, `ensemble` |
+| `07-problem-inversion.md` | Problem inversion strategies | `Strategy [0-9]`, `inversion`, `goal` |
+| `08-integration-synthesis.md` | Integration and synthesis | `narrative`, `communication`, `story` |
+| `09-meta-framework.md` | Complete workflow | `Phase`, `workflow`, `orchestrat` |
+
+---
+
+## Expected Outcomes
+
+### Immediate (After Completing Workflow)
+- Clear project vision
+- Honest risk assessment
+- Contingency plans
+- Communication materials ready
+- Confidence in problem choice
+
+### 6-Month
+- Faster decisions (have framework)
+- Productive adversity handling
+- No existential crises (risks mitigated)
+
+### 2-Year
+- Published results or strong progress
+- Avoided dead-end projects
+- Career aligned with goals
+- **Time well-spent** (ultimate measure)
+
+---
+
+## Foundational Reference
+
+**Fischbach, M.A., & Walsh, C.T. (2024).** "Problem choice and decision trees in science and engineering." *Cell*, 187, 1828-1833.
+
+Based on course BIOE 395 taught at Stanford University.