@wentorai/research-plugins 1.0.0

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  1. package/LICENSE +21 -0
  2. package/README.md +204 -0
  3. package/curated/analysis/README.md +64 -0
  4. package/curated/domains/README.md +104 -0
  5. package/curated/literature/README.md +53 -0
  6. package/curated/research/README.md +62 -0
  7. package/curated/tools/README.md +87 -0
  8. package/curated/writing/README.md +61 -0
  9. package/index.ts +39 -0
  10. package/mcp-configs/academic-db/ChatSpatial.json +17 -0
  11. package/mcp-configs/academic-db/academia-mcp.json +17 -0
  12. package/mcp-configs/academic-db/academic-paper-explorer.json +17 -0
  13. package/mcp-configs/academic-db/academic-search-mcp-server.json +17 -0
  14. package/mcp-configs/academic-db/agentinterviews-mcp.json +17 -0
  15. package/mcp-configs/academic-db/all-in-mcp.json +17 -0
  16. package/mcp-configs/academic-db/apple-health-mcp.json +17 -0
  17. package/mcp-configs/academic-db/arxiv-latex-mcp.json +17 -0
  18. package/mcp-configs/academic-db/arxiv-mcp-server.json +17 -0
  19. package/mcp-configs/academic-db/bgpt-mcp.json +17 -0
  20. package/mcp-configs/academic-db/biomcp.json +17 -0
  21. package/mcp-configs/academic-db/biothings-mcp.json +17 -0
  22. package/mcp-configs/academic-db/catalysishub-mcp-server.json +17 -0
  23. package/mcp-configs/academic-db/clinicaltrialsgov-mcp-server.json +17 -0
  24. package/mcp-configs/academic-db/deep-research-mcp.json +17 -0
  25. package/mcp-configs/academic-db/dicom-mcp.json +17 -0
  26. package/mcp-configs/academic-db/enrichr-mcp-server.json +17 -0
  27. package/mcp-configs/academic-db/fec-mcp-server.json +17 -0
  28. package/mcp-configs/academic-db/fhir-mcp-server-themomentum.json +17 -0
  29. package/mcp-configs/academic-db/fhir-mcp.json +19 -0
  30. package/mcp-configs/academic-db/gget-mcp.json +17 -0
  31. package/mcp-configs/academic-db/google-researcher-mcp.json +17 -0
  32. package/mcp-configs/academic-db/idea-reality-mcp.json +17 -0
  33. package/mcp-configs/academic-db/legiscan-mcp.json +19 -0
  34. package/mcp-configs/academic-db/lex.json +17 -0
  35. package/mcp-configs/ai-platform/Adaptive-Graph-of-Thoughts-MCP-server.json +17 -0
  36. package/mcp-configs/ai-platform/ai-counsel.json +17 -0
  37. package/mcp-configs/ai-platform/atlas-mcp-server.json +17 -0
  38. package/mcp-configs/ai-platform/counsel-mcp.json +17 -0
  39. package/mcp-configs/ai-platform/cross-llm-mcp.json +17 -0
  40. package/mcp-configs/ai-platform/gptr-mcp.json +17 -0
  41. package/mcp-configs/browser/decipher-research-agent.json +17 -0
  42. package/mcp-configs/browser/deep-research.json +17 -0
  43. package/mcp-configs/browser/everything-claude-code.json +17 -0
  44. package/mcp-configs/browser/gpt-researcher.json +17 -0
  45. package/mcp-configs/browser/heurist-agent-framework.json +17 -0
  46. package/mcp-configs/data-platform/4everland-hosting-mcp.json +17 -0
  47. package/mcp-configs/data-platform/context-keeper.json +17 -0
  48. package/mcp-configs/data-platform/context7.json +19 -0
  49. package/mcp-configs/data-platform/contextstream-mcp.json +17 -0
  50. package/mcp-configs/data-platform/email-mcp.json +17 -0
  51. package/mcp-configs/note-knowledge/ApeRAG.json +17 -0
  52. package/mcp-configs/note-knowledge/In-Memoria.json +17 -0
  53. package/mcp-configs/note-knowledge/agent-memory.json +17 -0
  54. package/mcp-configs/note-knowledge/aimemo.json +17 -0
  55. package/mcp-configs/note-knowledge/biel-mcp.json +19 -0
  56. package/mcp-configs/note-knowledge/cognee.json +17 -0
  57. package/mcp-configs/note-knowledge/context-awesome.json +17 -0
  58. package/mcp-configs/note-knowledge/context-mcp.json +17 -0
  59. package/mcp-configs/note-knowledge/conversation-handoff-mcp.json +17 -0
  60. package/mcp-configs/note-knowledge/cortex.json +17 -0
  61. package/mcp-configs/note-knowledge/devrag.json +17 -0
  62. package/mcp-configs/note-knowledge/easy-obsidian-mcp.json +17 -0
  63. package/mcp-configs/note-knowledge/engram.json +17 -0
  64. package/mcp-configs/note-knowledge/gnosis-mcp.json +17 -0
  65. package/mcp-configs/note-knowledge/graphlit-mcp-server.json +19 -0
  66. package/mcp-configs/reference-mgr/arxiv-cli.json +17 -0
  67. package/mcp-configs/reference-mgr/arxiv-search-mcp.json +17 -0
  68. package/mcp-configs/reference-mgr/chiken.json +17 -0
  69. package/mcp-configs/reference-mgr/claude-scholar.json +17 -0
  70. package/mcp-configs/reference-mgr/devonthink-mcp.json +17 -0
  71. package/mcp-configs/registry.json +447 -0
  72. package/openclaw.plugin.json +21 -0
  73. package/package.json +61 -0
  74. package/skills/analysis/dataviz/color-accessibility-guide/SKILL.md +230 -0
  75. package/skills/analysis/dataviz/geospatial-viz-guide/SKILL.md +218 -0
  76. package/skills/analysis/dataviz/interactive-viz-guide/SKILL.md +287 -0
  77. package/skills/analysis/dataviz/network-visualization-guide/SKILL.md +195 -0
  78. package/skills/analysis/dataviz/publication-figures-guide/SKILL.md +238 -0
  79. package/skills/analysis/dataviz/python-dataviz-guide/SKILL.md +195 -0
  80. package/skills/analysis/econometrics/causal-inference-guide/SKILL.md +197 -0
  81. package/skills/analysis/econometrics/iv-regression-guide/SKILL.md +198 -0
  82. package/skills/analysis/econometrics/panel-data-guide/SKILL.md +274 -0
  83. package/skills/analysis/econometrics/robustness-checks/SKILL.md +250 -0
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  85. package/skills/analysis/econometrics/time-series-guide/SKILL.md +235 -0
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  87. package/skills/analysis/statistics/hypothesis-testing-guide/SKILL.md +210 -0
  88. package/skills/analysis/statistics/meta-analysis-guide/SKILL.md +206 -0
  89. package/skills/analysis/statistics/nonparametric-tests-guide/SKILL.md +221 -0
  90. package/skills/analysis/statistics/power-analysis-guide/SKILL.md +240 -0
  91. package/skills/analysis/statistics/sem-guide/SKILL.md +231 -0
  92. package/skills/analysis/statistics/survival-analysis-guide/SKILL.md +195 -0
  93. package/skills/analysis/wrangling/missing-data-handling/SKILL.md +224 -0
  94. package/skills/analysis/wrangling/pandas-data-wrangling/SKILL.md +242 -0
  95. package/skills/analysis/wrangling/questionnaire-design-guide/SKILL.md +234 -0
  96. package/skills/analysis/wrangling/text-mining-guide/SKILL.md +225 -0
  97. package/skills/domains/ai-ml/computer-vision-guide/SKILL.md +213 -0
  98. package/skills/domains/ai-ml/deep-learning-papers-guide/SKILL.md +200 -0
  99. package/skills/domains/ai-ml/llm-evaluation-guide/SKILL.md +194 -0
  100. package/skills/domains/ai-ml/prompt-engineering-research/SKILL.md +233 -0
  101. package/skills/domains/ai-ml/reinforcement-learning-guide/SKILL.md +254 -0
  102. package/skills/domains/ai-ml/transformer-architecture-guide/SKILL.md +233 -0
  103. package/skills/domains/biomedical/clinical-research-guide/SKILL.md +232 -0
  104. package/skills/domains/biomedical/clinicaltrials-api/SKILL.md +177 -0
  105. package/skills/domains/biomedical/epidemiology-guide/SKILL.md +200 -0
  106. package/skills/domains/biomedical/genomics-analysis-guide/SKILL.md +270 -0
  107. package/skills/domains/business/market-analysis-guide/SKILL.md +112 -0
  108. package/skills/domains/business/strategic-management-guide/SKILL.md +154 -0
  109. package/skills/domains/chemistry/computational-chemistry-guide/SKILL.md +266 -0
  110. package/skills/domains/chemistry/retrosynthesis-guide/SKILL.md +215 -0
  111. package/skills/domains/cs/algorithms-complexity-guide/SKILL.md +194 -0
  112. package/skills/domains/cs/dblp-api/SKILL.md +129 -0
  113. package/skills/domains/cs/software-engineering-research/SKILL.md +218 -0
  114. package/skills/domains/ecology/biodiversity-data-guide/SKILL.md +296 -0
  115. package/skills/domains/ecology/conservation-biology-guide/SKILL.md +198 -0
  116. package/skills/domains/ecology/gbif-api/SKILL.md +158 -0
  117. package/skills/domains/ecology/inaturalist-api/SKILL.md +173 -0
  118. package/skills/domains/economics/behavioral-economics-guide/SKILL.md +239 -0
  119. package/skills/domains/economics/development-economics-guide/SKILL.md +181 -0
  120. package/skills/domains/economics/fred-api/SKILL.md +189 -0
  121. package/skills/domains/education/curriculum-design-guide/SKILL.md +144 -0
  122. package/skills/domains/education/learning-science-guide/SKILL.md +150 -0
  123. package/skills/domains/finance/financial-data-analysis/SKILL.md +152 -0
  124. package/skills/domains/finance/quantitative-finance-guide/SKILL.md +151 -0
  125. package/skills/domains/geoscience/climate-science-guide/SKILL.md +158 -0
  126. package/skills/domains/geoscience/gis-remote-sensing-guide/SKILL.md +129 -0
  127. package/skills/domains/humanities/digital-humanities-guide/SKILL.md +181 -0
  128. package/skills/domains/humanities/philosophy-research-guide/SKILL.md +148 -0
  129. package/skills/domains/law/courtlistener-api/SKILL.md +213 -0
  130. package/skills/domains/law/legal-research-guide/SKILL.md +250 -0
  131. package/skills/domains/math/linear-algebra-applications/SKILL.md +227 -0
  132. package/skills/domains/math/numerical-methods-guide/SKILL.md +236 -0
  133. package/skills/domains/math/oeis-api/SKILL.md +158 -0
  134. package/skills/domains/pharma/clinical-pharmacology-guide/SKILL.md +165 -0
  135. package/skills/domains/pharma/drug-development-guide/SKILL.md +177 -0
  136. package/skills/domains/physics/computational-physics-guide/SKILL.md +300 -0
  137. package/skills/domains/physics/nasa-ads-api/SKILL.md +150 -0
  138. package/skills/domains/physics/quantum-computing-guide/SKILL.md +234 -0
  139. package/skills/domains/social-science/social-research-methods/SKILL.md +194 -0
  140. package/skills/domains/social-science/survey-research-guide/SKILL.md +182 -0
  141. package/skills/literature/discovery/citation-alert-guide/SKILL.md +154 -0
  142. package/skills/literature/discovery/conference-proceedings-guide/SKILL.md +142 -0
  143. package/skills/literature/discovery/literature-mapping-guide/SKILL.md +175 -0
  144. package/skills/literature/discovery/paper-tracking-guide/SKILL.md +211 -0
  145. package/skills/literature/discovery/rss-paper-feeds/SKILL.md +214 -0
  146. package/skills/literature/discovery/semantic-scholar-recs-guide/SKILL.md +164 -0
  147. package/skills/literature/fulltext/doaj-api/SKILL.md +120 -0
  148. package/skills/literature/fulltext/interlibrary-loan-guide/SKILL.md +163 -0
  149. package/skills/literature/fulltext/open-access-guide/SKILL.md +183 -0
  150. package/skills/literature/fulltext/pmc-oai-api/SKILL.md +184 -0
  151. package/skills/literature/fulltext/preprint-servers-guide/SKILL.md +128 -0
  152. package/skills/literature/fulltext/repository-harvesting-guide/SKILL.md +207 -0
  153. package/skills/literature/fulltext/unpaywall-api/SKILL.md +113 -0
  154. package/skills/literature/metadata/altmetrics-guide/SKILL.md +132 -0
  155. package/skills/literature/metadata/citation-network-guide/SKILL.md +236 -0
  156. package/skills/literature/metadata/crossref-api/SKILL.md +133 -0
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  158. package/skills/literature/metadata/doi-resolution-guide/SKILL.md +168 -0
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  160. package/skills/literature/metadata/journal-metrics-guide/SKILL.md +188 -0
  161. package/skills/literature/metadata/opencitations-api/SKILL.md +128 -0
  162. package/skills/literature/metadata/orcid-api/SKILL.md +136 -0
  163. package/skills/literature/metadata/orcid-integration-guide/SKILL.md +178 -0
  164. package/skills/literature/search/arxiv-api/SKILL.md +95 -0
  165. package/skills/literature/search/biorxiv-api/SKILL.md +123 -0
  166. package/skills/literature/search/boolean-search-guide/SKILL.md +199 -0
  167. package/skills/literature/search/citation-chaining-guide/SKILL.md +148 -0
  168. package/skills/literature/search/database-comparison-guide/SKILL.md +100 -0
  169. package/skills/literature/search/europe-pmc-api/SKILL.md +120 -0
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  171. package/skills/literature/search/mesh-terms-guide/SKILL.md +164 -0
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  180. package/skills/research/deep-research/meta-synthesis-guide/SKILL.md +174 -0
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+ ---
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+ name: strategic-management-guide
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+ description: "Frameworks for strategic planning, resource allocation, and organizational an..."
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+ metadata:
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+ openclaw:
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+ emoji: "chess_pawn"
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+ category: "domains"
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+ subcategory: "business"
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+ keywords: ["strategic management", "operations management", "market analysis", "organizational strategy", "resource allocation"]
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+ source: "wentor"
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+ ---
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+
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+ # Strategic Management Guide
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+
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+ A research-oriented skill for applying strategic management theories and frameworks to academic case studies, organizational analysis, and business research. Covers classical and contemporary strategy frameworks with rigorous analytical methods.
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+
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+ ## Core Strategic Frameworks
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+
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+ ### Resource-Based View (RBV)
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+
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+ The RBV framework (Barney, 1991) evaluates competitive advantage through internal resources and capabilities. Apply the VRIO test:
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+
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+ | Criterion | Question | If "No" |
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+ |-----------|----------|---------|
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+ | Valuable | Does it exploit opportunity or neutralize threat? | Competitive disadvantage |
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+ | Rare | Is it controlled by few firms? | Competitive parity |
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+ | Inimitable | Is it costly to imitate? | Temporary advantage |
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+ | Organized | Is the firm organized to capture value? | Unrealized advantage |
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+
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+ All four "Yes" answers indicate a **sustained competitive advantage**.
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+
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+ ```python
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+ # VRIO analysis scoring framework
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+ def vrio_analysis(resources: list[dict]) -> dict:
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+ results = {}
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+ for r in resources:
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+ name = r['name']
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+ v, r_score, i, o = r['valuable'], r['rare'], r['inimitable'], r['organized']
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+ if not v:
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+ results[name] = 'competitive_disadvantage'
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+ elif not r_score:
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+ results[name] = 'competitive_parity'
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+ elif not i:
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+ results[name] = 'temporary_advantage'
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+ elif not o:
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+ results[name] = 'unrealized_advantage'
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+ else:
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+ results[name] = 'sustained_advantage'
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+ return results
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+
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+ # Example usage
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+ resources = [
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+ {'name': 'proprietary_algorithm', 'valuable': True, 'rare': True, 'inimitable': True, 'organized': True},
54
+ {'name': 'office_space', 'valuable': True, 'rare': False, 'inimitable': False, 'organized': True},
55
+ ]
56
+ print(vrio_analysis(resources))
57
+ # {'proprietary_algorithm': 'sustained_advantage', 'office_space': 'competitive_parity'}
58
+ ```
59
+
60
+ ## Strategic Planning Process
61
+
62
+ A structured approach to strategy formulation for research purposes:
63
+
64
+ ### Phase 1: Environmental Scanning
65
+
66
+ - **External analysis**: PESTEL (Political, Economic, Social, Technological, Environmental, Legal)
67
+ - **Industry analysis**: Porter's Five Forces with quantified metrics
68
+ - **Stakeholder mapping**: Power-interest matrix to prioritize engagement
69
+
70
+ ### Phase 2: Strategy Formulation
71
+
72
+ Apply Ansoff's Growth Matrix to map strategic options:
73
+
74
+ ```
75
+ Existing Products New Products
76
+ Existing Markets Market Penetration Product Development
77
+ New Markets Market Development Diversification
78
+ ```
79
+
80
+ For academic research, operationalize each quadrant with measurable indicators: market share growth rate, R&D investment ratio, geographic expansion metrics, and portfolio diversification index.
81
+
82
+ ### Phase 3: Strategy Evaluation
83
+
84
+ Use the SAFe criteria (Johnson, Whittington & Scholes):
85
+
86
+ 1. **Suitability** -- Does the strategy address key strategic issues?
87
+ 2. **Acceptability** -- Risk, return, and stakeholder reactions
88
+ 3. **Feasibility** -- Resources, capabilities, and timeline
89
+
90
+ ## Balanced Scorecard Implementation
91
+
92
+ Translate strategy into measurable objectives across four perspectives:
93
+
94
+ ```yaml
95
+ financial:
96
+ objectives:
97
+ - "Increase revenue by 15% YoY"
98
+ - "Reduce cost-to-serve by 10%"
99
+ kpis: ["revenue_growth_rate", "operating_margin"]
100
+
101
+ customer:
102
+ objectives:
103
+ - "Achieve NPS > 50"
104
+ - "Reduce churn below 5%"
105
+ kpis: ["net_promoter_score", "monthly_churn_rate"]
106
+
107
+ internal_process:
108
+ objectives:
109
+ - "Reduce cycle time by 20%"
110
+ - "Achieve 99.9% uptime"
111
+ kpis: ["avg_cycle_time_days", "system_uptime_pct"]
112
+
113
+ learning_growth:
114
+ objectives:
115
+ - "Increase training hours per employee"
116
+ - "Launch 3 new capabilities per quarter"
117
+ kpis: ["training_hours_per_fte", "new_capabilities_shipped"]
118
+ ```
119
+
120
+ ## Quantitative Strategy Tools
121
+
122
+ ### Game Theory Applications
123
+
124
+ Model competitive interactions using payoff matrices:
125
+
126
+ ```python
127
+ import numpy as np
128
+
129
+ # Prisoner's Dilemma payoff matrix
130
+ # (Row player payoff, Column player payoff)
131
+ # Strategies: Cooperate (0), Defect (1)
132
+ payoffs_row = np.array([[3, 0],
133
+ [5, 1]])
134
+ payoffs_col = np.array([[3, 5],
135
+ [0, 1]])
136
+
137
+ # Find Nash equilibria
138
+ for i in range(2):
139
+ for j in range(2):
140
+ row_best = payoffs_row[i, j] >= max(payoffs_row[:, j])
141
+ col_best = payoffs_col[i, j] >= max(payoffs_col[i, :])
142
+ if row_best and col_best:
143
+ print(f"Nash Equilibrium at ({i}, {j})")
144
+ ```
145
+
146
+ ### Scenario Planning
147
+
148
+ Structure scenario analysis with two critical uncertainties on perpendicular axes. Develop four internally consistent narratives, assign probability weights, and compute expected values for key decision variables. This approach enables robust strategy under deep uncertainty.
149
+
150
+ ## References
151
+
152
+ - Barney, J. (1991). Firm Resources and Sustained Competitive Advantage. *Journal of Management*, 17(1), 99-120.
153
+ - Porter, M. E. (1980). *Competitive Strategy*. Free Press.
154
+ - Kaplan, R. S., & Norton, D. P. (1996). *The Balanced Scorecard*. Harvard Business Press.
@@ -0,0 +1,266 @@
1
+ ---
2
+ name: computational-chemistry-guide
3
+ description: "DFT, molecular simulation, and reaction prediction tools for chemists"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "⚗"
7
+ category: "domains"
8
+ subcategory: "chemistry"
9
+ keywords: ["computational chemistry", "DFT", "quantum chemistry", "reaction prediction"]
10
+ source: "N/A"
11
+ ---
12
+
13
+ # Computational Chemistry Guide
14
+
15
+ ## Overview
16
+
17
+ Computational chemistry bridges quantum mechanics and practical chemistry, enabling researchers to predict molecular properties, reaction mechanisms, and material behaviors without stepping into a wet lab. From drug design to catalyst optimization, computational methods accelerate discovery by screening thousands of candidates before committing to synthesis.
18
+
19
+ This guide covers the major computational chemistry paradigms: Density Functional Theory (DFT) for electronic structure calculations, molecular dynamics (MD) for simulating atomic motion, machine learning potentials for scaling up simulations, and reaction prediction tools for retrosynthesis and mechanism elucidation. Each section includes tool recommendations, typical workflows, and code examples.
20
+
21
+ Whether you are a chemistry PhD student running your first Gaussian calculations, a materials scientist exploring new alloys with VASP, or a medicinal chemist using ML-based property prediction, this skill provides the conceptual framework and practical recipes to get productive quickly.
22
+
23
+ ## Density Functional Theory (DFT)
24
+
25
+ ### When to Use DFT
26
+
27
+ DFT is the workhorse of quantum chemistry. It provides a good balance of accuracy and computational cost for systems of up to a few hundred atoms.
28
+
29
+ | Property | DFT Suitability | Typical Error |
30
+ |----------|----------------|---------------|
31
+ | Molecular geometry | Excellent | < 0.02 Angstrom |
32
+ | Vibrational frequencies | Good | 3-5% |
33
+ | Reaction barriers | Good with correction | 2-5 kcal/mol |
34
+ | Band gaps | Fair (tends to underestimate) | 0.5-1.0 eV |
35
+ | Van der Waals interactions | Requires dispersion correction | Varies |
36
+ | Excited states | Fair (TD-DFT) | 0.2-0.5 eV |
37
+
38
+ ### Software Comparison
39
+
40
+ | Software | License | Strengths | Basis Sets |
41
+ |----------|---------|-----------|-----------|
42
+ | Gaussian | Commercial | Broad functionality, well-documented | Gaussian-type |
43
+ | ORCA | Free (academic) | DFT + wavefunction methods, excellent support | Gaussian-type |
44
+ | VASP | Commercial | Periodic systems, materials science | Plane-wave |
45
+ | Quantum ESPRESSO | Open source | Periodic DFT, phonons | Plane-wave |
46
+ | Psi4 | Open source | Reference implementations, Python API | Gaussian-type |
47
+ | CP2K | Open source | Mixed Gaussian/plane-wave, large systems | Mixed |
48
+
49
+ ### ORCA DFT Workflow Example
50
+
51
+ ```
52
+ # geometry_optimization.inp
53
+ ! B3LYP def2-TZVP D3BJ OPT FREQ
54
+ # B3LYP functional, triple-zeta basis, D3 dispersion, optimize + frequencies
55
+
56
+ %pal
57
+ nprocs 8
58
+ end
59
+
60
+ %maxcore 4000
61
+
62
+ * xyz 0 1
63
+ C 0.000 0.000 0.000
64
+ O 1.200 0.000 0.000
65
+ H -0.500 0.866 0.000
66
+ H -0.500 -0.866 0.000
67
+ *
68
+ ```
69
+
70
+ Run with:
71
+ ```bash
72
+ orca geometry_optimization.inp > geometry_optimization.out
73
+ ```
74
+
75
+ ### Analyzing DFT Results with Python
76
+
77
+ ```python
78
+ from ase.io import read
79
+ from ase.visualize import view
80
+
81
+ # Read optimized geometry from ORCA output
82
+ atoms = read('geometry_optimization.xyz')
83
+
84
+ # Extract energies from output file
85
+ import re
86
+
87
+ with open('geometry_optimization.out') as f:
88
+ text = f.read()
89
+
90
+ # Total energy
91
+ energy = float(re.search(r'FINAL SINGLE POINT ENERGY\s+([-\d.]+)', text).group(1))
92
+ print(f"Total energy: {energy:.6f} Hartree")
93
+ print(f"Total energy: {energy * 627.509:.2f} kcal/mol")
94
+
95
+ # Thermochemistry
96
+ gibbs_match = re.search(r'Final Gibbs free energy\s+\.\.\.\s+([-\d.]+)', text)
97
+ if gibbs_match:
98
+ gibbs = float(gibbs_match.group(1))
99
+ print(f"Gibbs free energy: {gibbs:.6f} Hartree")
100
+ ```
101
+
102
+ ## Molecular Dynamics Simulations
103
+
104
+ ### MD Pipeline
105
+
106
+ ```
107
+ Initial Structure (.pdb/.mol2)
108
+ |
109
+ v
110
+ [Parameterization] --> Force field assignment (AMBER, CHARMM, OPLS)
111
+ |
112
+ v
113
+ [Solvation] --> Add solvent box, ions
114
+ |
115
+ v
116
+ [Minimization] --> Energy minimization (steepest descent)
117
+ |
118
+ v
119
+ [Equilibration] --> NVT then NPT ensemble (100 ps - 1 ns)
120
+ |
121
+ v
122
+ [Production] --> NPT ensemble (10 ns - microseconds)
123
+ |
124
+ v
125
+ [Analysis] --> RMSD, RMSF, hydrogen bonds, free energy
126
+ ```
127
+
128
+ ### OpenMM Quick Start
129
+
130
+ ```python
131
+ from openmm.app import *
132
+ from openmm import *
133
+ from openmm.unit import *
134
+
135
+ # Load structure
136
+ pdb = PDBFile('protein.pdb')
137
+ forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
138
+
139
+ # Create system
140
+ modeller = Modeller(pdb.topology, pdb.positions)
141
+ modeller.addSolvent(forcefield, model='tip3p', padding=1.0*nanometers)
142
+
143
+ system = forcefield.createSystem(
144
+ modeller.topology,
145
+ nonbondedMethod=PME,
146
+ nonbondedCutoff=1.0*nanometers,
147
+ constraints=HBonds
148
+ )
149
+
150
+ # Set up simulation
151
+ integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
152
+ simulation = Simulation(modeller.topology, system, integrator)
153
+ simulation.context.setPositions(modeller.positions)
154
+
155
+ # Minimize
156
+ simulation.minimizeEnergy()
157
+
158
+ # Run production (10 ns)
159
+ simulation.reporters.append(DCDReporter('trajectory.dcd', 1000))
160
+ simulation.reporters.append(
161
+ StateDataReporter('log.csv', 1000, step=True,
162
+ potentialEnergy=True, temperature=True)
163
+ )
164
+ simulation.step(2500000) # 10 ns at 4 fs timestep
165
+ ```
166
+
167
+ ## Machine Learning in Computational Chemistry
168
+
169
+ ### ML Potential Energy Surfaces
170
+
171
+ Machine learning potentials achieve near-DFT accuracy at a fraction of the cost:
172
+
173
+ | Method | Speed vs DFT | Accuracy | Training Data |
174
+ |--------|-------------|----------|---------------|
175
+ | ANI | 1000x faster | ~1 kcal/mol | Pre-trained |
176
+ | SchNet | 100-1000x | ~1 kcal/mol | 1K-100K configs |
177
+ | MACE | 100-1000x | < 1 kcal/mol | 1K-100K configs |
178
+ | GemNet | 100-1000x | < 1 kcal/mol | 1K-100K configs |
179
+
180
+ ### Property Prediction with RDKit
181
+
182
+ ```python
183
+ from rdkit import Chem
184
+ from rdkit.Chem import Descriptors, AllChem
185
+ import numpy as np
186
+
187
+ def compute_molecular_features(smiles):
188
+ """Compute molecular descriptors from SMILES string."""
189
+ mol = Chem.MolFromSmiles(smiles)
190
+ if mol is None:
191
+ return None
192
+
193
+ features = {
194
+ 'molecular_weight': Descriptors.MolWt(mol),
195
+ 'logp': Descriptors.MolLogP(mol),
196
+ 'hbd': Descriptors.NumHDonors(mol),
197
+ 'hba': Descriptors.NumHAcceptors(mol),
198
+ 'tpsa': Descriptors.TPSA(mol),
199
+ 'rotatable_bonds': Descriptors.NumRotatableBonds(mol),
200
+ 'aromatic_rings': Descriptors.NumAromaticRings(mol),
201
+ 'heavy_atoms': mol.GetNumHeavyAtoms(),
202
+ }
203
+
204
+ # Morgan fingerprint (ECFP4)
205
+ fp = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=2048)
206
+ features['fingerprint'] = np.array(fp)
207
+
208
+ return features
209
+
210
+ # Lipinski's Rule of Five check
211
+ def check_druglikeness(smiles):
212
+ feats = compute_molecular_features(smiles)
213
+ if feats is None:
214
+ return False
215
+ return (feats['molecular_weight'] <= 500 and
216
+ feats['logp'] <= 5 and
217
+ feats['hbd'] <= 5 and
218
+ feats['hba'] <= 10)
219
+ ```
220
+
221
+ ## Reaction Prediction
222
+
223
+ ### Retrosynthesis Tools
224
+
225
+ | Tool | Approach | Access |
226
+ |------|----------|--------|
227
+ | ASKCOS | Template-based + ML | MIT, web interface |
228
+ | IBM RXN | Transformer-based | Free API |
229
+ | Syntheseus | Multi-model framework | Open source |
230
+ | RetroTRAE | Transformer | Open source |
231
+
232
+ ### Using RDKit for Reaction Processing
233
+
234
+ ```python
235
+ from rdkit.Chem import AllChem, Draw
236
+
237
+ # Define a reaction (Suzuki coupling)
238
+ rxn_smarts = '[c:1][B](O)O.[c:2][Cl]>>[c:1][c:2]'
239
+ rxn = AllChem.ReactionFromSmarts(rxn_smarts)
240
+
241
+ # Apply reaction
242
+ reactant1 = Chem.MolFromSmiles('c1ccc(B(O)O)cc1') # Phenylboronic acid
243
+ reactant2 = Chem.MolFromSmiles('c1ccc(Cl)cc1') # Chlorobenzene
244
+
245
+ products = rxn.RunReactants((reactant1, reactant2))
246
+ for product_set in products:
247
+ for product in product_set:
248
+ print(Chem.MolToSmiles(product)) # Biphenyl
249
+ ```
250
+
251
+ ## Best Practices
252
+
253
+ - **Benchmark your method.** Always validate your computational protocol against known experimental data before applying it to new systems.
254
+ - **Use appropriate levels of theory.** Do not use MP2 when B3LYP suffices, and do not use B3LYP when you need CCSD(T) accuracy.
255
+ - **Include dispersion corrections.** D3BJ or D4 corrections are essential for non-covalent interactions.
256
+ - **Check convergence.** Verify that geometry optimizations, SCF calculations, and MD simulations have properly converged.
257
+ - **Report computational details completely.** Functional, basis set, dispersion correction, solvent model, and software version should all be stated.
258
+ - **Archive your input/output files.** Computational chemistry is reproducible only if all parameters are preserved.
259
+
260
+ ## References
261
+
262
+ - [ORCA Documentation](https://www.faccts.de/docs/orca/6.0/manual/) -- Free quantum chemistry software
263
+ - [OpenMM Documentation](http://docs.openmm.org/) -- GPU-accelerated molecular dynamics
264
+ - [RDKit Documentation](https://www.rdkit.org/docs/) -- Cheminformatics toolkit
265
+ - [Psi4 Documentation](https://psicode.org/) -- Open-source quantum chemistry
266
+ - [A Hitchhiker's Guide to DFT](https://onlinelibrary.wiley.com/doi/book/10.1002/3527600043) -- Koch and Holthausen
@@ -0,0 +1,215 @@
1
+ ---
2
+ name: retrosynthesis-guide
3
+ description: "Retrosynthetic analysis and computational reaction prediction"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "flask"
7
+ category: "domains"
8
+ subcategory: "chemistry"
9
+ keywords: ["retrosynthesis", "reaction prediction", "organic chemistry", "computational chemistry"]
10
+ source: "wentor-research-plugins"
11
+ ---
12
+
13
+ # Retrosynthesis Guide
14
+
15
+ Plan synthetic routes for target molecules using retrosynthetic analysis principles and computational tools, from Corey's logic to modern AI-driven approaches.
16
+
17
+ ## What Is Retrosynthesis?
18
+
19
+ Retrosynthesis works backward from a target molecule to identify simpler, commercially available precursors:
20
+
21
+ ```
22
+ Target Molecule (TM)
23
+ |
24
+ [Disconnection 1] ← Apply transform (reverse of a known reaction)
25
+ |
26
+ Synthon A + Synthon B
27
+ | |
28
+ [Available] [Disconnection 2]
29
+ |
30
+ Synthon C + Synthon D
31
+ | |
32
+ [Available] [Available]
33
+ ```
34
+
35
+ Key terminology:
36
+ - **Target Molecule (TM)**: The molecule you want to synthesize
37
+ - **Synthon**: Idealized reactive fragment from a disconnection
38
+ - **Synthetic Equivalent**: Real reagent corresponding to a synthon
39
+ - **Transform**: Reverse of a chemical reaction (retro-reaction)
40
+ - **FGI (Functional Group Interconversion)**: Convert one functional group to another to enable a disconnection
41
+
42
+ ## Corey's Retrosynthetic Strategies
43
+
44
+ ### Strategic Bond Disconnections
45
+
46
+ | Strategy | Description | When to Use |
47
+ |----------|-------------|------------|
48
+ | **FGI** | Convert functional groups to enable disconnections | When direct disconnection is not possible |
49
+ | **C-C Bond disconnection** | Break carbon-carbon bonds | Building the carbon skeleton |
50
+ | **C-X Bond disconnection** | Break carbon-heteroatom bonds | Functional group installation |
51
+ | **Ring disconnection** | Open rings to identify acyclic precursors | Cyclic target molecules |
52
+ | **Symmetry exploitation** | Use molecular symmetry to simplify analysis | Symmetric molecules |
53
+ | **Convergent synthesis** | Combine two complex fragments late | Minimize linear step count |
54
+
55
+ ### Common Disconnection Patterns
56
+
57
+ ```
58
+ # Alcohol (C-OH) → Carbonyl reduction
59
+ R-CH(OH)-R' ⟹ R-CO-R' + NaBH4/LiAlH4
60
+
61
+ # Amine (C-N) → Reductive amination
62
+ R-CH2-NH-R' ⟹ R-CHO + R'-NH2
63
+
64
+ # C-C Bond (aldol) → Aldol retro
65
+ R-CH(OH)-CH2-CO-R' ⟹ R-CHO + CH3-CO-R'
66
+
67
+ # C-C Bond (Grignard) → Grignard retro
68
+ R-CH(OH)-R' ⟹ R-CHO + R'-MgBr
69
+
70
+ # Ester (C-O) → Fischer esterification retro
71
+ R-COO-R' ⟹ R-COOH + R'-OH
72
+
73
+ # Amide (C-N) → Amide coupling retro
74
+ R-CO-NH-R' ⟹ R-COOH + R'-NH2
75
+
76
+ # Diels-Alder → Retro Diels-Alder
77
+ Cyclohexene derivative ⟹ Diene + Dienophile
78
+
79
+ # Wittig → Retro Wittig
80
+ R-CH=CH-R' ⟹ R-CHO + R'-CH2-PPh3
81
+ ```
82
+
83
+ ## Computational Retrosynthesis Tools
84
+
85
+ ### Tool Comparison
86
+
87
+ | Tool | Developer | Method | Access |
88
+ |------|-----------|--------|--------|
89
+ | ASKCOS | MIT | Template-based + neural | Free (askcos.mit.edu) |
90
+ | IBM RXN | IBM Research | Transformer seq2seq | Free (rxn.res.ibm.com) |
91
+ | Reaxys | Elsevier | Database-backed | Subscription |
92
+ | SciFinder-n | CAS | Database + AI | Subscription |
93
+ | Spaya | Iktos | Graph neural network | Commercial |
94
+ | AiZynthFinder | AstraZeneca | Monte Carlo tree search | Open source |
95
+
96
+ ### Using ASKCOS
97
+
98
+ ```python
99
+ import requests
100
+
101
+ # ASKCOS API for retrosynthetic planning
102
+ # (requires running ASKCOS locally or using the hosted version)
103
+
104
+ target_smiles = "CC(=O)Oc1ccccc1C(=O)O" # Aspirin
105
+
106
+ # One-step retrosynthesis
107
+ response = requests.post(
108
+ "https://askcos.mit.edu/api/retro/",
109
+ json={
110
+ "smiles": target_smiles,
111
+ "num_results": 10,
112
+ "max_depth": 5
113
+ }
114
+ )
115
+
116
+ results = response.json()
117
+ for i, result in enumerate(results.get("precursors", [])[:5]):
118
+ print(f"Route {i+1}:")
119
+ print(f" Precursors: {result['smiles']}")
120
+ print(f" Template: {result.get('template', 'N/A')}")
121
+ print(f" Score: {result.get('score', 'N/A')}")
122
+ ```
123
+
124
+ ### Using IBM RXN for Chemistry
125
+
126
+ ```python
127
+ # IBM RXN API
128
+ from rxn4chemistry import RXN4ChemistryWrapper
129
+
130
+ api_key = os.environ["RXN4CHEM_API_KEY"]
131
+ rxn = RXN4ChemistryWrapper(api_key=api_key)
132
+ rxn.create_project("retrosynthesis_example")
133
+
134
+ # Predict retrosynthesis
135
+ response = rxn.predict_automatic_retrosynthesis(
136
+ product="CC(=O)Oc1ccccc1C(=O)O", # Aspirin
137
+ max_steps=3
138
+ )
139
+
140
+ # Get results
141
+ results = rxn.get_predict_automatic_retrosynthesis_results(response["prediction_id"])
142
+ for route in results.get("retrosynthetic_paths", []):
143
+ print(f"Route confidence: {route.get('confidence', 'N/A')}")
144
+ for step in route.get("steps", []):
145
+ print(f" Reaction: {step.get('reaction_smiles', 'N/A')}")
146
+ ```
147
+
148
+ ### Using AiZynthFinder (Open Source)
149
+
150
+ ```python
151
+ from aizynthfinder.aizynthfinder import AiZynthFinder
152
+
153
+ # Configure the finder
154
+ finder = AiZynthFinder()
155
+ finder.stock.load("zinc_stock.hdf5") # Commercial building blocks
156
+ finder.expansion_policy.load("expansion_policy_model.onnx") # Retro model
157
+
158
+ # Set target
159
+ finder.target_smiles = "CC(=O)Oc1ccccc1C(=O)O" # Aspirin
160
+
161
+ # Run tree search
162
+ finder.config.search.time_limit = 120 # seconds
163
+ finder.config.search.iteration_limit = 500
164
+ finder.tree_search()
165
+
166
+ # Extract and analyze routes
167
+ finder.build_routes()
168
+ for i, route in enumerate(finder.routes):
169
+ print(f"Route {i+1} (score: {route.score:.3f}):")
170
+ print(f" Steps: {len(route.reactions)}")
171
+ for rxn in route.reactions:
172
+ print(f" {rxn}")
173
+ ```
174
+
175
+ ## SMILES Notation for Chemistry
176
+
177
+ SMILES (Simplified Molecular Input Line Entry System) is the standard text representation:
178
+
179
+ ```
180
+ # Common SMILES patterns
181
+ Water: O
182
+ Ethanol: CCO
183
+ Benzene: c1ccccc1
184
+ Aspirin: CC(=O)Oc1ccccc1C(=O)O
185
+ Caffeine: Cn1c(=O)c2c(ncn2C)n(C)c1=O
186
+ Ibuprofen: CC(C)Cc1ccc(cc1)C(C)C(=O)O
187
+
188
+ # SMILES rules
189
+ # Atoms: C, N, O, S, P, F, Cl, Br, I
190
+ # Bonds: - (single, implicit), = (double), # (triple)
191
+ # Branches: () for branching
192
+ # Rings: numbers for ring closure (c1ccccc1 = benzene)
193
+ # Aromatic: lowercase letters
194
+ # Stereochemistry: / \ for E/Z, @ @@ for R/S
195
+ ```
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+
197
+ ## Reaction Databases
198
+
199
+ | Database | Coverage | Features | Access |
200
+ |----------|----------|----------|--------|
201
+ | Reaxys | 130M+ reactions | Experimental conditions, yields | Subscription |
202
+ | SciFinder / CAS | 160M+ reactions | Commercial availability, safety data | Subscription |
203
+ | USPTO | 3.7M reactions | US patent reactions | Free (open data) |
204
+ | Open Reaction Database (ORD) | Growing | Structured reaction data, conditions | Free |
205
+ | RMG (Reaction Mechanism Generator) | Kinetics | Automated mechanism generation | Free (MIT) |
206
+
207
+ ## Best Practices for Route Planning
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+
209
+ 1. **Start simple**: Begin with the most obvious disconnections before trying exotic transforms.
210
+ 2. **Consider availability**: Check if precursors are commercially available (Sigma-Aldrich, TCI, Alfa Aesar).
211
+ 3. **Minimize steps**: Convergent synthesis (combining two complex halves) is generally preferred over linear synthesis.
212
+ 4. **Protect and deprotect wisely**: Minimize protecting group manipulations; each adds 2 steps (protection + deprotection).
213
+ 5. **Check literature**: Search Reaxys or SciFinder for precedent before attempting novel transformations.
214
+ 6. **Validate computationally**: Use forward reaction prediction to verify that proposed retrosynthetic steps are feasible.
215
+ 7. **Consider scale**: Reactions that work at milligram scale may fail at gram scale. Check for scalability issues (exothermic reactions, heterogeneous mixing).