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scientific-skills/hypothesis-generation/references/experimental_design_patterns.md

@@ -4,6 +4,8 @@
 
 This reference provides patterns and frameworks for designing experiments across scientific domains. Use these patterns to develop rigorous tests for generated hypotheses.
 
+**Note on Report Structure:** When generating hypothesis reports, mention only the key experimental approach (e.g., "in vivo knockout study" or "prospective cohort design") in the main text hypothesis boxes. Include comprehensive experimental protocols with full methods, controls, sample sizes, statistical approaches, feasibility assessments, and resource requirements in **Appendix B: Detailed Experimental Designs**.
+
 ## Design Selection Framework
 
 Choose experimental approaches based on:

scientific-skills/hypothesis-generation/references/hypothesis_quality_criteria.md

@@ -4,6 +4,8 @@
 
 Use these criteria to assess the quality and rigor of generated hypotheses. A robust hypothesis should score well across multiple dimensions.
 
+**Note on Report Structure:** When generating hypothesis reports, provide a brief quality assessment summary in the main text (comparative table with ratings), and include detailed evaluation with strengths, weaknesses, and comprehensive analysis in **Appendix C: Quality Assessment**.
+
 ## Core Criteria
 
 ### 1. Testability

scientific-skills/hypothesis-generation/references/literature_search_strategies.md

@@ -367,6 +367,36 @@ Use WebSearch for:
 - What analogies exist in other systems?
 - What methods are commonly used?
 
+### Citation Organization for Hypothesis Reports
+
+**For report structure:** Organize citations for two audiences:
+
+**Main Text (15-20 key citations):**
+- Most influential papers (highly cited, seminal studies)
+- Recent definitive evidence (last 2-3 years)
+- Key papers directly supporting each hypothesis (3-5 per hypothesis)
+- Major reviews synthesizing the field
+
+**Appendix A: Comprehensive Literature Review (40-60+ citations):**
+- **Historical context:** Foundational papers establishing field
+- **Current understanding:** Recent reviews and meta-analyses
+- **Hypothesis-specific evidence:** 8-15 papers per hypothesis covering:
+  - Direct supporting evidence
+  - Analogous mechanisms in related systems
+  - Methodological precedents
+  - Theoretical framework papers
+- **Conflicting findings:** Papers representing different viewpoints
+- **Knowledge gaps:** Papers identifying limitations or unanswered questions
+
+**Target citation density:** Aim for 50+ total references to provide comprehensive support for all claims and demonstrate thorough literature grounding.
+
+**Grouping strategy for Appendix A:**
+1. Background and context papers
+2. Current understanding and established mechanisms
+3. Evidence supporting each hypothesis (separate subsections)
+4. Contradictory or alternative findings
+5. Methodological and technical papers
+
 ## Practical Search Workflow
 
 ### Step-by-Step Process