@wentorai/research-plugins 1.0.0 → 1.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (415) hide show
  1. package/README.md +22 -22
  2. package/curated/analysis/README.md +82 -56
  3. package/curated/domains/README.md +225 -69
  4. package/curated/literature/README.md +115 -46
  5. package/curated/research/README.md +106 -58
  6. package/curated/tools/README.md +107 -87
  7. package/curated/writing/README.md +92 -45
  8. package/mcp-configs/academic-db/alphafold-mcp.json +20 -0
  9. package/mcp-configs/academic-db/brightspace-mcp.json +21 -0
  10. package/mcp-configs/academic-db/climatiq-mcp.json +20 -0
  11. package/mcp-configs/academic-db/gibs-mcp.json +20 -0
  12. package/mcp-configs/academic-db/gis-mcp-server.json +22 -0
  13. package/mcp-configs/academic-db/google-earth-engine-mcp.json +21 -0
  14. package/mcp-configs/academic-db/m4-clinical-mcp.json +21 -0
  15. package/mcp-configs/academic-db/medical-mcp.json +21 -0
  16. package/mcp-configs/academic-db/nexonco-mcp.json +20 -0
  17. package/mcp-configs/academic-db/omop-mcp.json +20 -0
  18. package/mcp-configs/academic-db/onekgpd-mcp.json +20 -0
  19. package/mcp-configs/academic-db/openedu-mcp.json +20 -0
  20. package/mcp-configs/academic-db/opengenes-mcp.json +20 -0
  21. package/mcp-configs/academic-db/openstax-mcp.json +21 -0
  22. package/mcp-configs/academic-db/openstreetmap-mcp.json +21 -0
  23. package/mcp-configs/academic-db/opentargets-mcp.json +21 -0
  24. package/mcp-configs/academic-db/pdb-mcp.json +21 -0
  25. package/mcp-configs/academic-db/smithsonian-mcp.json +20 -0
  26. package/mcp-configs/ai-platform/magi-researchers.json +21 -0
  27. package/mcp-configs/ai-platform/mcp-academic-researcher.json +22 -0
  28. package/mcp-configs/ai-platform/open-paper-machine.json +21 -0
  29. package/mcp-configs/ai-platform/paper-intelligence.json +21 -0
  30. package/mcp-configs/ai-platform/paper-reader.json +21 -0
  31. package/mcp-configs/ai-platform/paperdebugger.json +21 -0
  32. package/mcp-configs/browser/exa-mcp.json +20 -0
  33. package/mcp-configs/browser/mcp-searxng.json +21 -0
  34. package/mcp-configs/browser/mcp-webresearch.json +20 -0
  35. package/mcp-configs/cloud-docs/confluence-mcp.json +37 -0
  36. package/mcp-configs/cloud-docs/google-drive-mcp.json +35 -0
  37. package/mcp-configs/cloud-docs/notion-mcp.json +29 -0
  38. package/mcp-configs/communication/discord-mcp.json +29 -0
  39. package/mcp-configs/communication/discourse-mcp.json +21 -0
  40. package/mcp-configs/communication/slack-mcp.json +29 -0
  41. package/mcp-configs/communication/telegram-mcp.json +28 -0
  42. package/mcp-configs/data-platform/automl-stat-mcp.json +21 -0
  43. package/mcp-configs/data-platform/jefferson-stats-mcp.json +22 -0
  44. package/mcp-configs/data-platform/mcp-excel-server.json +21 -0
  45. package/mcp-configs/data-platform/mcp-stata.json +21 -0
  46. package/mcp-configs/data-platform/mcpstack-jupyter.json +21 -0
  47. package/mcp-configs/data-platform/ml-mcp.json +21 -0
  48. package/mcp-configs/data-platform/nasdaq-data-link-mcp.json +20 -0
  49. package/mcp-configs/data-platform/numpy-mcp.json +21 -0
  50. package/mcp-configs/database/neo4j-mcp.json +37 -0
  51. package/mcp-configs/database/postgres-mcp.json +28 -0
  52. package/mcp-configs/database/sqlite-mcp.json +29 -0
  53. package/mcp-configs/dev-platform/geogebra-mcp.json +21 -0
  54. package/mcp-configs/dev-platform/github-mcp.json +31 -0
  55. package/mcp-configs/dev-platform/gitlab-mcp.json +34 -0
  56. package/mcp-configs/dev-platform/latex-mcp-server.json +21 -0
  57. package/mcp-configs/dev-platform/manim-mcp.json +20 -0
  58. package/mcp-configs/dev-platform/mcp-echarts.json +20 -0
  59. package/mcp-configs/dev-platform/panel-viz-mcp.json +20 -0
  60. package/mcp-configs/dev-platform/paperbanana.json +20 -0
  61. package/mcp-configs/dev-platform/texflow-mcp.json +20 -0
  62. package/mcp-configs/dev-platform/texmcp.json +20 -0
  63. package/mcp-configs/dev-platform/typst-mcp.json +21 -0
  64. package/mcp-configs/dev-platform/vizro-mcp.json +20 -0
  65. package/mcp-configs/email/email-mcp.json +40 -0
  66. package/mcp-configs/email/gmail-mcp.json +37 -0
  67. package/mcp-configs/note-knowledge/local-faiss-mcp.json +21 -0
  68. package/mcp-configs/note-knowledge/mcp-memory-service.json +21 -0
  69. package/mcp-configs/note-knowledge/mcp-obsidian.json +23 -0
  70. package/mcp-configs/note-knowledge/mcp-ragdocs.json +20 -0
  71. package/mcp-configs/note-knowledge/mcp-summarizer.json +21 -0
  72. package/mcp-configs/note-knowledge/mediawiki-mcp.json +21 -0
  73. package/mcp-configs/note-knowledge/openzim-mcp.json +20 -0
  74. package/mcp-configs/note-knowledge/zettelkasten-mcp.json +21 -0
  75. package/mcp-configs/reference-mgr/academic-paper-mcp-http.json +20 -0
  76. package/mcp-configs/reference-mgr/academix.json +20 -0
  77. package/mcp-configs/reference-mgr/arxiv-research-mcp.json +21 -0
  78. package/mcp-configs/reference-mgr/google-scholar-abstract-mcp.json +19 -0
  79. package/mcp-configs/reference-mgr/google-scholar-mcp.json +20 -0
  80. package/mcp-configs/reference-mgr/mcp-paperswithcode.json +21 -0
  81. package/mcp-configs/reference-mgr/mcp-scholarly.json +20 -0
  82. package/mcp-configs/reference-mgr/mcp-simple-arxiv.json +20 -0
  83. package/mcp-configs/reference-mgr/mcp-simple-pubmed.json +20 -0
  84. package/mcp-configs/reference-mgr/mcp-zotero.json +21 -0
  85. package/mcp-configs/reference-mgr/mendeley-mcp.json +20 -0
  86. package/mcp-configs/reference-mgr/ncbi-mcp-server.json +22 -0
  87. package/mcp-configs/reference-mgr/onecite.json +21 -0
  88. package/mcp-configs/reference-mgr/paper-search-mcp.json +21 -0
  89. package/mcp-configs/reference-mgr/pubmed-search-mcp.json +21 -0
  90. package/mcp-configs/reference-mgr/scholar-mcp.json +21 -0
  91. package/mcp-configs/reference-mgr/scholar-multi-mcp.json +21 -0
  92. package/mcp-configs/reference-mgr/seerai.json +21 -0
  93. package/mcp-configs/reference-mgr/semantic-scholar-fastmcp.json +21 -0
  94. package/mcp-configs/reference-mgr/sourcelibrary.json +20 -0
  95. package/mcp-configs/registry.json +178 -149
  96. package/mcp-configs/repository/dataverse-mcp.json +33 -0
  97. package/mcp-configs/repository/huggingface-mcp.json +29 -0
  98. package/openclaw.plugin.json +2 -2
  99. package/package.json +2 -2
  100. package/skills/analysis/dataviz/algorithm-visualizer-guide/SKILL.md +259 -0
  101. package/skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md +270 -0
  102. package/skills/analysis/dataviz/chart-image-generator/SKILL.md +229 -0
  103. package/skills/analysis/dataviz/citation-map-guide/SKILL.md +184 -0
  104. package/skills/analysis/dataviz/d3-visualization-guide/SKILL.md +281 -0
  105. package/skills/analysis/dataviz/data-visualization-principles/SKILL.md +171 -0
  106. package/skills/analysis/dataviz/echarts-visualization-guide/SKILL.md +250 -0
  107. package/skills/analysis/dataviz/metabase-analytics-guide/SKILL.md +242 -0
  108. package/skills/analysis/dataviz/plotly-interactive-guide/SKILL.md +266 -0
  109. package/skills/analysis/dataviz/redash-analytics-guide/SKILL.md +284 -0
  110. package/skills/analysis/econometrics/econml-causal-guide/SKILL.md +163 -0
  111. package/skills/analysis/econometrics/empirical-paper-analysis/SKILL.md +192 -0
  112. package/skills/analysis/econometrics/mostly-harmless-guide/SKILL.md +139 -0
  113. package/skills/analysis/econometrics/panel-data-analyst/SKILL.md +259 -0
  114. package/skills/analysis/econometrics/panel-data-regression-workflow/SKILL.md +267 -0
  115. package/skills/analysis/econometrics/python-causality-guide/SKILL.md +134 -0
  116. package/skills/analysis/econometrics/stata-accounting-guide/SKILL.md +269 -0
  117. package/skills/analysis/econometrics/stata-analyst-guide/SKILL.md +245 -0
  118. package/skills/analysis/econometrics/stata-reference-guide/SKILL.md +293 -0
  119. package/skills/analysis/statistics/data-anomaly-detection/SKILL.md +157 -0
  120. package/skills/analysis/statistics/general-statistics-guide/SKILL.md +226 -0
  121. package/skills/analysis/statistics/infiagent-benchmark-guide/SKILL.md +106 -0
  122. package/skills/analysis/statistics/ml-experiment-tracker/SKILL.md +212 -0
  123. package/skills/analysis/statistics/pywayne-statistics-guide/SKILL.md +192 -0
  124. package/skills/analysis/statistics/quantitative-methods-guide/SKILL.md +193 -0
  125. package/skills/analysis/statistics/senior-data-scientist-guide/SKILL.md +223 -0
  126. package/skills/analysis/wrangling/claude-data-analysis-guide/SKILL.md +100 -0
  127. package/skills/analysis/wrangling/csv-data-analyzer/SKILL.md +170 -0
  128. package/skills/analysis/wrangling/data-cleaning-pipeline/SKILL.md +266 -0
  129. package/skills/analysis/wrangling/data-cog-guide/SKILL.md +178 -0
  130. package/skills/analysis/wrangling/open-data-scientist-guide/SKILL.md +197 -0
  131. package/skills/analysis/wrangling/stata-data-cleaning/SKILL.md +276 -0
  132. package/skills/analysis/wrangling/streamline-analyst-guide/SKILL.md +119 -0
  133. package/skills/analysis/wrangling/survey-data-processing/SKILL.md +298 -0
  134. package/skills/domains/ai-ml/ai-agent-papers-guide/SKILL.md +146 -0
  135. package/skills/domains/ai-ml/ai-model-benchmarking/SKILL.md +209 -0
  136. package/skills/domains/ai-ml/annotated-dl-papers-guide/SKILL.md +159 -0
  137. package/skills/domains/ai-ml/anomaly-detection-papers-guide/SKILL.md +167 -0
  138. package/skills/domains/ai-ml/autonomous-agents-papers-guide/SKILL.md +178 -0
  139. package/skills/domains/ai-ml/dl-transformer-finetune/SKILL.md +239 -0
  140. package/skills/domains/ai-ml/domain-adaptation-papers-guide/SKILL.md +173 -0
  141. package/skills/domains/ai-ml/generative-ai-guide/SKILL.md +146 -0
  142. package/skills/domains/ai-ml/graph-learning-papers-guide/SKILL.md +125 -0
  143. package/skills/domains/ai-ml/huggingface-inference-guide/SKILL.md +196 -0
  144. package/skills/domains/ai-ml/keras-deep-learning/SKILL.md +210 -0
  145. package/skills/domains/ai-ml/kolmogorov-arnold-networks-guide/SKILL.md +185 -0
  146. package/skills/domains/ai-ml/llm-from-scratch-guide/SKILL.md +124 -0
  147. package/skills/domains/ai-ml/ml-pipeline-guide/SKILL.md +295 -0
  148. package/skills/domains/ai-ml/nlp-toolkit-guide/SKILL.md +247 -0
  149. package/skills/domains/ai-ml/npcpy-research-guide/SKILL.md +137 -0
  150. package/skills/domains/ai-ml/pytorch-guide/SKILL.md +281 -0
  151. package/skills/domains/ai-ml/pytorch-lightning-guide/SKILL.md +244 -0
  152. package/skills/domains/ai-ml/responsible-ai-guide/SKILL.md +126 -0
  153. package/skills/domains/ai-ml/tensorflow-guide/SKILL.md +241 -0
  154. package/skills/domains/ai-ml/vmas-simulator-guide/SKILL.md +129 -0
  155. package/skills/domains/biomedical/bioagents-guide/SKILL.md +308 -0
  156. package/skills/domains/biomedical/clawbio-guide/SKILL.md +167 -0
  157. package/skills/domains/biomedical/clinical-dialogue-agents-guide/SKILL.md +145 -0
  158. package/skills/domains/biomedical/ena-sequence-api/SKILL.md +175 -0
  159. package/skills/domains/biomedical/genomas-guide/SKILL.md +126 -0
  160. package/skills/domains/biomedical/genotex-benchmark-guide/SKILL.md +125 -0
  161. package/skills/domains/biomedical/med-researcher-guide/SKILL.md +161 -0
  162. package/skills/domains/biomedical/med-researcher-r1-guide/SKILL.md +146 -0
  163. package/skills/domains/biomedical/medgeclaw-guide/SKILL.md +345 -0
  164. package/skills/domains/biomedical/medical-imaging-guide/SKILL.md +305 -0
  165. package/skills/domains/biomedical/ncbi-blast-api/SKILL.md +195 -0
  166. package/skills/domains/biomedical/ncbi-datasets-api/SKILL.md +220 -0
  167. package/skills/domains/biomedical/quickgo-api/SKILL.md +181 -0
  168. package/skills/domains/business/architecture-design-guide/SKILL.md +279 -0
  169. package/skills/domains/business/innovation-management-guide/SKILL.md +257 -0
  170. package/skills/domains/business/operations-research-guide/SKILL.md +258 -0
  171. package/skills/domains/business/xpert-bi-guide/SKILL.md +84 -0
  172. package/skills/domains/chemistry/cactus-cheminformatics-guide/SKILL.md +89 -0
  173. package/skills/domains/chemistry/chemeagle-guide/SKILL.md +147 -0
  174. package/skills/domains/chemistry/chemgraph-agent-guide/SKILL.md +120 -0
  175. package/skills/domains/chemistry/molecular-dynamics-guide/SKILL.md +237 -0
  176. package/skills/domains/chemistry/pubchem-api-guide/SKILL.md +180 -0
  177. package/skills/domains/chemistry/spectroscopy-analysis-guide/SKILL.md +290 -0
  178. package/skills/domains/cs/ai-security-papers-guide/SKILL.md +103 -0
  179. package/skills/domains/cs/code-llm-papers-guide/SKILL.md +131 -0
  180. package/skills/domains/cs/distributed-systems-guide/SKILL.md +268 -0
  181. package/skills/domains/cs/formal-verification-guide/SKILL.md +298 -0
  182. package/skills/domains/cs/gaussian-splatting-papers-guide/SKILL.md +158 -0
  183. package/skills/domains/cs/llm-aiops-guide/SKILL.md +70 -0
  184. package/skills/domains/cs/software-heritage-api/SKILL.md +200 -0
  185. package/skills/domains/ecology/species-distribution-guide/SKILL.md +343 -0
  186. package/skills/domains/economics/imf-data-api-guide/SKILL.md +174 -0
  187. package/skills/domains/economics/nber-working-papers-api/SKILL.md +177 -0
  188. package/skills/domains/economics/post-labor-economics/SKILL.md +254 -0
  189. package/skills/domains/economics/pricing-psychology-guide/SKILL.md +273 -0
  190. package/skills/domains/economics/repec-economics-api/SKILL.md +188 -0
  191. package/skills/domains/economics/world-bank-data-guide/SKILL.md +179 -0
  192. package/skills/domains/education/academic-study-methods/SKILL.md +228 -0
  193. package/skills/domains/education/assessment-design-guide/SKILL.md +213 -0
  194. package/skills/domains/education/educational-research-methods/SKILL.md +179 -0
  195. package/skills/domains/education/edumcp-guide/SKILL.md +74 -0
  196. package/skills/domains/education/mooc-analytics-guide/SKILL.md +206 -0
  197. package/skills/domains/education/open-syllabus-api/SKILL.md +171 -0
  198. package/skills/domains/finance/akshare-finance-data/SKILL.md +207 -0
  199. package/skills/domains/finance/finsight-research-guide/SKILL.md +113 -0
  200. package/skills/domains/finance/options-analytics-agent-guide/SKILL.md +117 -0
  201. package/skills/domains/finance/portfolio-optimization-guide/SKILL.md +279 -0
  202. package/skills/domains/finance/risk-modeling-guide/SKILL.md +260 -0
  203. package/skills/domains/finance/stata-accounting-research/SKILL.md +372 -0
  204. package/skills/domains/geoscience/climate-modeling-guide/SKILL.md +215 -0
  205. package/skills/domains/geoscience/pangaea-data-api/SKILL.md +197 -0
  206. package/skills/domains/geoscience/satellite-remote-sensing/SKILL.md +193 -0
  207. package/skills/domains/geoscience/seismology-data-guide/SKILL.md +208 -0
  208. package/skills/domains/humanities/digital-humanities-methods/SKILL.md +232 -0
  209. package/skills/domains/humanities/ethical-philosophy-guide/SKILL.md +244 -0
  210. package/skills/domains/humanities/history-research-guide/SKILL.md +260 -0
  211. package/skills/domains/humanities/political-history-guide/SKILL.md +241 -0
  212. package/skills/domains/law/caselaw-access-api/SKILL.md +149 -0
  213. package/skills/domains/law/legal-agent-skills-guide/SKILL.md +132 -0
  214. package/skills/domains/law/legal-nlp-guide/SKILL.md +236 -0
  215. package/skills/domains/law/legal-research-methods/SKILL.md +190 -0
  216. package/skills/domains/law/opencontracts-guide/SKILL.md +168 -0
  217. package/skills/domains/law/patent-analysis-guide/SKILL.md +257 -0
  218. package/skills/domains/law/regulatory-compliance-guide/SKILL.md +267 -0
  219. package/skills/domains/math/lean-theorem-proving-guide/SKILL.md +140 -0
  220. package/skills/domains/math/symbolic-computation-guide/SKILL.md +263 -0
  221. package/skills/domains/math/topology-data-analysis/SKILL.md +305 -0
  222. package/skills/domains/pharma/clinical-trial-design-guide/SKILL.md +271 -0
  223. package/skills/domains/pharma/drug-target-interaction/SKILL.md +242 -0
  224. package/skills/domains/pharma/madd-drug-discovery-guide/SKILL.md +153 -0
  225. package/skills/domains/pharma/pharmacovigilance-guide/SKILL.md +216 -0
  226. package/skills/domains/physics/astrophysics-data-guide/SKILL.md +305 -0
  227. package/skills/domains/physics/particle-physics-guide/SKILL.md +287 -0
  228. package/skills/domains/social-science/ipums-microdata-api/SKILL.md +211 -0
  229. package/skills/domains/social-science/network-analysis-guide/SKILL.md +310 -0
  230. package/skills/domains/social-science/psychology-research-guide/SKILL.md +270 -0
  231. package/skills/domains/social-science/sociology-research-guide/SKILL.md +238 -0
  232. package/skills/domains/social-science/sociology-research-methods/SKILL.md +181 -0
  233. package/skills/literature/discovery/arxiv-paper-monitoring/SKILL.md +233 -0
  234. package/skills/literature/discovery/paper-recommendation-guide/SKILL.md +120 -0
  235. package/skills/literature/discovery/papers-we-love-guide/SKILL.md +169 -0
  236. package/skills/literature/discovery/semantic-paper-radar/SKILL.md +144 -0
  237. package/skills/literature/discovery/zotero-arxiv-daily-guide/SKILL.md +94 -0
  238. package/skills/literature/fulltext/bioc-pmc-api/SKILL.md +146 -0
  239. package/skills/literature/fulltext/core-api-guide/SKILL.md +144 -0
  240. package/skills/literature/fulltext/dataverse-api/SKILL.md +215 -0
  241. package/skills/literature/fulltext/hal-archive-api/SKILL.md +218 -0
  242. package/skills/literature/fulltext/institutional-repository-guide/SKILL.md +212 -0
  243. package/skills/literature/fulltext/open-access-mining-guide/SKILL.md +341 -0
  244. package/skills/literature/fulltext/osf-api/SKILL.md +212 -0
  245. package/skills/literature/fulltext/pmc-ftp-bulk-download/SKILL.md +182 -0
  246. package/skills/literature/fulltext/zotero-ai-butler-guide/SKILL.md +166 -0
  247. package/skills/literature/fulltext/zotero-scihub-guide/SKILL.md +168 -0
  248. package/skills/literature/metadata/academic-paper-summarizer/SKILL.md +101 -0
  249. package/skills/literature/metadata/bibliometrix-guide/SKILL.md +164 -0
  250. package/skills/literature/metadata/crossref-event-data-api/SKILL.md +183 -0
  251. package/skills/literature/metadata/doi-content-negotiation/SKILL.md +202 -0
  252. package/skills/literature/metadata/orkg-api/SKILL.md +153 -0
  253. package/skills/literature/metadata/plumx-metrics-api/SKILL.md +188 -0
  254. package/skills/literature/metadata/ror-organization-api/SKILL.md +208 -0
  255. package/skills/literature/metadata/sophosia-reference-guide/SKILL.md +110 -0
  256. package/skills/literature/metadata/viaf-authority-api/SKILL.md +209 -0
  257. package/skills/literature/metadata/wikidata-api-guide/SKILL.md +156 -0
  258. package/skills/literature/metadata/zoplicate-dedup-guide/SKILL.md +147 -0
  259. package/skills/literature/metadata/zotero-actions-tags-guide/SKILL.md +212 -0
  260. package/skills/literature/metadata/zotmoov-guide/SKILL.md +120 -0
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  262. package/skills/literature/search/arxiv-batch-reporting/SKILL.md +133 -0
  263. package/skills/literature/search/arxiv-cli-tools/SKILL.md +172 -0
  264. package/skills/literature/search/arxiv-osiris/SKILL.md +199 -0
  265. package/skills/literature/search/arxiv-paper-processor/SKILL.md +141 -0
  266. package/skills/literature/search/baidu-scholar-guide/SKILL.md +110 -0
  267. package/skills/literature/search/base-academic-search/SKILL.md +196 -0
  268. package/skills/literature/search/chatpaper-guide/SKILL.md +122 -0
  269. package/skills/literature/search/citeseerx-api/SKILL.md +183 -0
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@@ -0,0 +1,220 @@
1
+ ---
2
+ name: ncbi-datasets-api
3
+ description: "Access genomes, genes, and taxonomy data via NCBI Datasets v2 API"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🧬"
7
+ category: "domains"
8
+ subcategory: "biomedical"
9
+ keywords: ["NCBI", "genome data", "gene data", "taxonomy", "RefSeq", "GenBank"]
10
+ source: "https://www.ncbi.nlm.nih.gov/datasets/"
11
+ ---
12
+
13
+ # NCBI Datasets v2 API
14
+
15
+ ## Overview
16
+
17
+ NCBI Datasets is the modern API for accessing NCBI's genomic, gene, and taxonomic data — replacing older E-utilities for sequence data retrieval. It provides clean REST endpoints for genome assemblies, gene records, taxonomy trees, and sequence downloads. Covers all organisms in NCBI's databases including RefSeq and GenBank. Free, no authentication required.
18
+
19
+ ## API Endpoints
20
+
21
+ ### Base URL
22
+
23
+ ```
24
+ https://api.ncbi.nlm.nih.gov/datasets/v2
25
+ ```
26
+
27
+ ### Genome Data
28
+
29
+ ```bash
30
+ # Search genome assemblies by organism
31
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/9606?page_size=5"
32
+
33
+ # Get assembly by accession
34
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40"
35
+
36
+ # Download genome package
37
+ curl -o genome.zip \
38
+ "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCF_000001405.40/download?\
39
+ include_annotation_type=GENOME_FASTA,GENOME_GFF"
40
+ ```
41
+
42
+ ### Gene Data
43
+
44
+ ```bash
45
+ # Search genes by symbol
46
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/symbol/TP53/taxon/human"
47
+
48
+ # Get gene by NCBI Gene ID
49
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157"
50
+
51
+ # Search genes by keyword
52
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/search?query=BRCA&taxon=9606&page_size=20"
53
+
54
+ # Download gene data package
55
+ curl -o gene.zip \
56
+ "https://api.ncbi.nlm.nih.gov/datasets/v2/gene/id/7157/download?include_annotation_type=FASTA_GENE"
57
+ ```
58
+
59
+ ### Taxonomy
60
+
61
+ ```bash
62
+ # Get taxonomy info
63
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9606"
64
+
65
+ # Search taxonomy by name
66
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/name_report?taxon_query=Homo+sapiens"
67
+
68
+ # Get taxonomy tree (subtree)
69
+ curl "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon/9443/subtree"
70
+ ```
71
+
72
+ ### Query Parameters
73
+
74
+ | Parameter | Description | Example |
75
+ |-----------|-------------|---------|
76
+ | `page_size` | Results per page | `page_size=20` |
77
+ | `page_token` | Pagination token | From previous response |
78
+ | `include_annotation_type` | Download content | `GENOME_FASTA`, `GENOME_GFF`, `PROT_FASTA` |
79
+ | `filters.assembly_level` | Assembly quality | `complete_genome`, `chromosome` |
80
+ | `filters.refseq_only` | RefSeq assemblies | `true` |
81
+
82
+ ## Response Structure (Gene)
83
+
84
+ ```json
85
+ {
86
+ "genes": [
87
+ {
88
+ "gene": {
89
+ "gene_id": 7157,
90
+ "symbol": "TP53",
91
+ "description": "tumor protein p53",
92
+ "taxname": "Homo sapiens",
93
+ "tax_id": 9606,
94
+ "type": "PROTEIN_CODING",
95
+ "chromosomes": ["17"],
96
+ "genomic_ranges": [
97
+ {
98
+ "accession_version": "NC_000017.11",
99
+ "range": [{"begin": 7668402, "end": 7687550, "orientation": "minus"}]
100
+ }
101
+ ],
102
+ "nomenclature": {
103
+ "symbol": "TP53",
104
+ "name": "tumor protein p53"
105
+ },
106
+ "annotations": [
107
+ {"release_date": "2024-03-15", "release_name": "GRCh38.p14"}
108
+ ]
109
+ }
110
+ }
111
+ ]
112
+ }
113
+ ```
114
+
115
+ ## Python Usage
116
+
117
+ ```python
118
+ import requests
119
+ import zipfile
120
+ import io
121
+
122
+ BASE_URL = "https://api.ncbi.nlm.nih.gov/datasets/v2"
123
+
124
+
125
+ def search_genes(query: str, taxon: str = "human",
126
+ page_size: int = 20) -> list:
127
+ """Search NCBI genes by keyword."""
128
+ resp = requests.get(
129
+ f"{BASE_URL}/gene/search",
130
+ params={"query": query, "taxon": taxon,
131
+ "page_size": page_size},
132
+ )
133
+ resp.raise_for_status()
134
+ data = resp.json()
135
+
136
+ results = []
137
+ for item in data.get("genes", []):
138
+ gene = item.get("gene", {})
139
+ results.append({
140
+ "gene_id": gene.get("gene_id"),
141
+ "symbol": gene.get("symbol"),
142
+ "description": gene.get("description"),
143
+ "type": gene.get("type"),
144
+ "chromosomes": gene.get("chromosomes", []),
145
+ "taxname": gene.get("taxname"),
146
+ })
147
+ return results
148
+
149
+
150
+ def get_gene(gene_id: int) -> dict:
151
+ """Get detailed gene information."""
152
+ resp = requests.get(f"{BASE_URL}/gene/id/{gene_id}")
153
+ resp.raise_for_status()
154
+ genes = resp.json().get("genes", [])
155
+ return genes[0].get("gene", {}) if genes else {}
156
+
157
+
158
+ def search_genomes(taxon: str, refseq_only: bool = True,
159
+ page_size: int = 10) -> list:
160
+ """Search genome assemblies by organism."""
161
+ params = {"page_size": page_size}
162
+ if refseq_only:
163
+ params["filters.refseq_only"] = "true"
164
+
165
+ resp = requests.get(
166
+ f"{BASE_URL}/genome/taxon/{taxon}",
167
+ params=params,
168
+ )
169
+ resp.raise_for_status()
170
+ data = resp.json()
171
+
172
+ results = []
173
+ for report in data.get("reports", []):
174
+ assembly = report.get("assembly_info", {})
175
+ stats = report.get("assembly_stats", {})
176
+ results.append({
177
+ "accession": report.get("accession"),
178
+ "name": assembly.get("assembly_name"),
179
+ "level": assembly.get("assembly_level"),
180
+ "organism": report.get("organism", {}).get("organism_name"),
181
+ "total_length": stats.get("total_sequence_length"),
182
+ "contig_n50": stats.get("contig_n50"),
183
+ })
184
+ return results
185
+
186
+
187
+ # Example: search cancer-related genes
188
+ genes = search_genes("tumor suppressor", taxon="human")
189
+ for g in genes[:5]:
190
+ print(f"{g['symbol']} (ID: {g['gene_id']}): {g['description']}")
191
+ print(f" Type: {g['type']} | Chr: {', '.join(g['chromosomes'])}")
192
+
193
+ # Example: find reference genomes
194
+ genomes = search_genomes("Mus musculus", refseq_only=True)
195
+ for g in genomes[:3]:
196
+ print(f"{g['accession']}: {g['name']} ({g['level']})")
197
+ print(f" Length: {g['total_length']:,} bp")
198
+ ```
199
+
200
+ ## CLI Tool
201
+
202
+ NCBI also provides a command-line tool:
203
+
204
+ ```bash
205
+ # Install
206
+ curl -o datasets "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets"
207
+ chmod +x datasets
208
+
209
+ # Download human genome
210
+ ./datasets download genome taxon "Homo sapiens" --reference --include genome
211
+
212
+ # Download gene data
213
+ ./datasets download gene gene-id 7157 --include gene
214
+ ```
215
+
216
+ ## References
217
+
218
+ - [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/)
219
+ - [Datasets API Reference](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/)
220
+ - [Datasets CLI](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/)
@@ -0,0 +1,181 @@
1
+ ---
2
+ name: quickgo-api
3
+ description: "Browse and search Gene Ontology annotations via the QuickGO API"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🧬"
7
+ category: "domains"
8
+ subcategory: "biomedical"
9
+ keywords: ["Gene Ontology", "GO annotations", "protein function", "QuickGO", "EBI", "functional genomics"]
10
+ source: "https://www.ebi.ac.uk/QuickGO/"
11
+ ---
12
+
13
+ # QuickGO API
14
+
15
+ ## Overview
16
+
17
+ QuickGO is the EBI's fast browser and API for Gene Ontology (GO) annotations — the standard framework for describing gene/protein functions across all organisms. It provides access to 800M+ GO annotations covering biological processes, molecular functions, and cellular components. Essential for functional genomics, pathway analysis, and gene set enrichment. Free, no authentication.
18
+
19
+ ## API Endpoints
20
+
21
+ ### Base URL
22
+
23
+ ```
24
+ https://www.ebi.ac.uk/QuickGO/services
25
+ ```
26
+
27
+ ### Search GO Terms
28
+
29
+ ```bash
30
+ # Search terms by keyword
31
+ curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/search?query=apoptosis&limit=20"
32
+
33
+ # Get term details
34
+ curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915"
35
+
36
+ # Get term ancestors/descendants
37
+ curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/ancestors"
38
+ curl "https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0006915/descendants"
39
+ ```
40
+
41
+ ### Query Annotations
42
+
43
+ ```bash
44
+ # Get annotations for a protein (UniProt ID)
45
+ curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=P04637&limit=50"
46
+
47
+ # Annotations for a GO term
48
+ curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?goId=GO:0006915&taxonId=9606&limit=50"
49
+
50
+ # Filter by evidence code
51
+ curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
52
+ goId=GO:0006915&taxonId=9606&evidence=EXP,IDA,IMP&limit=50"
53
+
54
+ # Filter by aspect (ontology branch)
55
+ curl "https://www.ebi.ac.uk/QuickGO/services/annotation/search?\
56
+ geneProductId=P04637&aspect=biological_process"
57
+ ```
58
+
59
+ ### Download Annotations
60
+
61
+ ```bash
62
+ # Download as TSV
63
+ curl "https://www.ebi.ac.uk/QuickGO/services/annotation/downloadSearch?\
64
+ goId=GO:0006915&taxonId=9606&downloadLimit=10000" -o annotations.tsv
65
+ ```
66
+
67
+ ### GO Aspects
68
+
69
+ | Aspect | Code | Description |
70
+ |--------|------|-------------|
71
+ | Biological Process | `biological_process` | What the gene does |
72
+ | Molecular Function | `molecular_function` | Biochemical activity |
73
+ | Cellular Component | `cellular_component` | Where in the cell |
74
+
75
+ ### Evidence Codes
76
+
77
+ | Code | Meaning | Reliability |
78
+ |------|---------|-------------|
79
+ | `EXP` | Inferred from Experiment | High |
80
+ | `IDA` | Inferred from Direct Assay | High |
81
+ | `IMP` | Inferred from Mutant Phenotype | High |
82
+ | `IPI` | Inferred from Physical Interaction | Medium |
83
+ | `ISS` | Inferred from Sequence Similarity | Medium |
84
+ | `IEA` | Inferred from Electronic Annotation | Lower |
85
+
86
+ ## Python Usage
87
+
88
+ ```python
89
+ import requests
90
+
91
+ BASE_URL = "https://www.ebi.ac.uk/QuickGO/services"
92
+
93
+
94
+ def search_go_terms(query: str, limit: int = 20) -> list:
95
+ """Search Gene Ontology terms."""
96
+ resp = requests.get(
97
+ f"{BASE_URL}/ontology/go/search",
98
+ params={"query": query, "limit": limit},
99
+ )
100
+ resp.raise_for_status()
101
+ data = resp.json()
102
+
103
+ results = []
104
+ for term in data.get("results", []):
105
+ results.append({
106
+ "id": term.get("id"),
107
+ "name": term.get("name"),
108
+ "aspect": term.get("aspect"),
109
+ "definition": term.get("definition", {}).get("text", ""),
110
+ })
111
+ return results
112
+
113
+
114
+ def get_protein_annotations(uniprot_id: str,
115
+ aspect: str = None,
116
+ experimental_only: bool = False) -> list:
117
+ """Get GO annotations for a protein."""
118
+ params = {"geneProductId": uniprot_id, "limit": 100}
119
+ if aspect:
120
+ params["aspect"] = aspect
121
+ if experimental_only:
122
+ params["evidence"] = "EXP,IDA,IMP,IPI,IGI,IEP"
123
+
124
+ resp = requests.get(
125
+ f"{BASE_URL}/annotation/search",
126
+ params=params,
127
+ )
128
+ resp.raise_for_status()
129
+ data = resp.json()
130
+
131
+ annotations = []
132
+ for ann in data.get("results", []):
133
+ annotations.append({
134
+ "go_id": ann.get("goId"),
135
+ "go_name": ann.get("goName"),
136
+ "aspect": ann.get("goAspect"),
137
+ "evidence": ann.get("goEvidence"),
138
+ "reference": ann.get("reference"),
139
+ })
140
+ return annotations
141
+
142
+
143
+ def get_term_genes(go_id: str, taxon_id: int = 9606,
144
+ limit: int = 100) -> list:
145
+ """Get genes annotated with a GO term."""
146
+ params = {
147
+ "goId": go_id,
148
+ "taxonId": taxon_id,
149
+ "limit": limit,
150
+ }
151
+ resp = requests.get(
152
+ f"{BASE_URL}/annotation/search",
153
+ params=params,
154
+ )
155
+ resp.raise_for_status()
156
+ data = resp.json()
157
+
158
+ genes = set()
159
+ for ann in data.get("results", []):
160
+ genes.add(ann.get("geneProductId", ""))
161
+ return sorted(genes)
162
+
163
+
164
+ # Example: search for apoptosis-related GO terms
165
+ terms = search_go_terms("programmed cell death")
166
+ for t in terms[:5]:
167
+ print(f"{t['id']}: {t['name']} ({t['aspect']})")
168
+
169
+ # Example: get p53 protein annotations
170
+ annotations = get_protein_annotations("P04637",
171
+ experimental_only=True)
172
+ for a in annotations[:10]:
173
+ print(f" {a['go_id']} {a['go_name']} [{a['evidence']}]")
174
+ ```
175
+
176
+ ## References
177
+
178
+ - [QuickGO](https://www.ebi.ac.uk/QuickGO/)
179
+ - [QuickGO API Docs](https://www.ebi.ac.uk/QuickGO/api)
180
+ - [Gene Ontology](http://geneontology.org/)
181
+ - Binns, D. et al. (2009). "QuickGO: a web-based tool for Gene Ontology searching." *Bioinformatics* 25(22).
@@ -0,0 +1,279 @@
1
+ ---
2
+ name: architecture-design-guide
3
+ description: "Design principles of form, function, sustainability in architecture"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🏗️"
7
+ category: "domains"
8
+ subcategory: "business"
9
+ keywords: ["architecture", "design", "sustainability", "urban planning", "BIM", "parametric design"]
10
+ source: "https://github.com/architecture-research/resources"
11
+ ---
12
+
13
+ # Architecture Design Guide
14
+
15
+ ## Overview
16
+
17
+ Architectural research spans the technical, aesthetic, social, and environmental dimensions of the built environment. From structural engineering and building physics to urban theory and computational design, the discipline demands integration across multiple domains. Academic architecture research increasingly focuses on sustainability, computational methods, and evidence-based design -- areas where rigorous methodology is essential.
18
+
19
+ This guide covers the core principles that inform architectural research: the interplay of form and function, structural logic, environmental performance, and human experience. It also addresses the computational tools (BIM, parametric design, simulation) that have transformed how architects investigate and validate design decisions.
20
+
21
+ Whether you are conducting research on building performance, urban morphology, computational design methods, or the social impact of built environments, this guide provides the frameworks and tools to ground your work in established architectural theory and current best practices.
22
+
23
+ ## Fundamental Design Principles
24
+
25
+ ### The Vitruvian Triad (Updated)
26
+
27
+ ```
28
+ Classical framework (Vitruvius, 1st century BCE):
29
+
30
+ FIRMITAS (Structural Integrity)
31
+ - Structural systems: load paths, material behavior, safety factors
32
+ - Building physics: thermal, acoustic, moisture performance
33
+ - Durability: service life, maintenance, resilience to hazards
34
+ - Modern addition: seismic, wind, and climate resilience
35
+
36
+ UTILITAS (Function)
37
+ - Program: spatial organization, adjacency requirements
38
+ - Circulation: movement patterns, wayfinding, accessibility
39
+ - Flexibility: adaptability to changing uses over time
40
+ - Modern addition: Universal design, inclusive environments
41
+
42
+ VENUSTAS (Delight)
43
+ - Proportion, rhythm, scale, materiality
44
+ - Light: natural and artificial, atmosphere, perception
45
+ - Cultural meaning: symbolism, context, identity
46
+ - Modern addition: Biophilic design, multisensory experience
47
+
48
+ Contemporary additions:
49
+ SUSTAINABILITY (since 1990s)
50
+ - Energy performance, carbon footprint, resource efficiency
51
+ - Lifecycle assessment, circular economy principles
52
+ - Passive strategies, renewable energy integration
53
+
54
+ SOCIAL RESPONSIBILITY (since 2000s)
55
+ - Equity, community engagement, participatory design
56
+ - Affordable housing, public space, social infrastructure
57
+ - Post-occupancy evaluation, evidence-based design
58
+ ```
59
+
60
+ ### Design Thinking Process
61
+
62
+ | Phase | Activities | Outputs |
63
+ |-------|-----------|---------|
64
+ | Research | Site analysis, precedent study, user research | Brief, program, constraints |
65
+ | Concept | Parti development, diagramming, massing | Concept diagrams, parti models |
66
+ | Schematic Design | Spatial organization, form development | Floor plans, sections, elevations |
67
+ | Design Development | Material selection, systems integration | Detailed drawings, specifications |
68
+ | Documentation | Construction documents, specifications | Building permit package |
69
+ | Post-Occupancy | Performance monitoring, user satisfaction | POE report, design feedback |
70
+
71
+ ## Structural Systems
72
+
73
+ ### Structural Logic for Researchers
74
+
75
+ ```
76
+ Primary structural systems and their research applications:
77
+
78
+ FRAME STRUCTURES
79
+ - Material: Steel, reinforced concrete, timber
80
+ - Behavior: Moment-resisting frames, braced frames
81
+ - Research topics: Connection design, progressive collapse,
82
+ fire resistance, seismic performance
83
+
84
+ SHELL STRUCTURES
85
+ - Types: Vaults, domes, hyperbolic paraboloids
86
+ - Behavior: Membrane forces (compression/tension), minimal bending
87
+ - Research topics: Form-finding, buckling, computational geometry
88
+ - Key method: Thrust network analysis (Block, 2009)
89
+
90
+ TENSILE STRUCTURES
91
+ - Types: Cable-stayed, membrane, tensegrity
92
+ - Behavior: Pure tension, anticlastic curvature
93
+ - Research topics: Form-finding, wind loading, material durability
94
+ - Key method: Dynamic relaxation, force density method
95
+
96
+ MASS TIMBER
97
+ - Types: CLT (cross-laminated timber), glulam, mass plywood
98
+ - Behavior: Orthotropic, fire charring provides structural reserve
99
+ - Research topics: Tall timber buildings, connections, moisture
100
+ - Growing field: embodied carbon advantages over concrete/steel
101
+ ```
102
+
103
+ ### Structural Analysis Methods
104
+
105
+ ```python
106
+ # Simple structural analysis for research
107
+ # Finite element analysis using Python (for educational purposes)
108
+
109
+ import numpy as np
110
+
111
+ def analyze_simply_supported_beam(
112
+ length: float, # meters
113
+ load: float, # kN/m (uniform distributed load)
114
+ E: float, # Young's modulus (GPa)
115
+ I: float, # Moment of inertia (mm^4)
116
+ n_elements: int = 20,
117
+ ) -> dict:
118
+ """
119
+ Analyze a simply supported beam under uniform load.
120
+ Returns deflection, moment, and shear diagrams.
121
+ """
122
+ x = np.linspace(0, length, n_elements + 1)
123
+ dx = length / n_elements
124
+
125
+ # Analytical solutions
126
+ # Maximum moment: wL^2/8
127
+ max_moment = load * length**2 / 8 # kN-m
128
+
129
+ # Moment diagram: M(x) = (w*x/2)*(L-x)
130
+ moment = (load * x / 2) * (length - x)
131
+
132
+ # Shear diagram: V(x) = w*(L/2 - x)
133
+ shear = load * (length / 2 - x)
134
+
135
+ # Deflection: delta(x) = (w*x)/(24*E*I) * (L^3 - 2*L*x^2 + x^3)
136
+ E_pa = E * 1e9 # Convert GPa to Pa
137
+ I_m4 = I * 1e-12 # Convert mm^4 to m^4
138
+ w_nm = load * 1e3 # Convert kN/m to N/m
139
+ deflection = (w_nm * x) / (24 * E_pa * I_m4) * (
140
+ length**3 - 2 * length * x**2 + x**3
141
+ )
142
+ max_deflection = 5 * w_nm * length**4 / (384 * E_pa * I_m4)
143
+
144
+ return {
145
+ "x": x,
146
+ "moment_kNm": moment,
147
+ "shear_kN": shear,
148
+ "deflection_mm": deflection * 1000,
149
+ "max_moment_kNm": max_moment,
150
+ "max_deflection_mm": max_deflection * 1000,
151
+ "span_to_deflection_ratio": length / max_deflection if max_deflection > 0 else float("inf"),
152
+ }
153
+ ```
154
+
155
+ ## Sustainability and Performance
156
+
157
+ ### Building Performance Metrics
158
+
159
+ | Metric | Unit | Benchmark (Office) | Tool |
160
+ |--------|------|-------------------|------|
161
+ | Energy Use Intensity (EUI) | kWh/m2/yr | < 100 (LEED Gold) | EnergyPlus, IES-VE |
162
+ | Embodied carbon | kgCO2e/m2 | < 500 (RIBA 2030) | One Click LCA, Tally |
163
+ | Operational carbon | kgCO2e/m2/yr | < 20 (net zero target) | EnergyPlus |
164
+ | Daylight factor | % | > 2% in 80% of area | Radiance, DIVA |
165
+ | Thermal comfort | PMV/PPD | PMV -0.5 to +0.5 | CBE Thermal Comfort Tool |
166
+ | Indoor air quality | CO2 ppm | < 800 ppm | CONTAM, CFD |
167
+
168
+ ### Passive Design Strategies
169
+
170
+ ```
171
+ Climate-responsive design strategies:
172
+
173
+ HOT-ARID CLIMATE
174
+ - Thermal mass: Thick walls absorb daytime heat, release at night
175
+ - Courtyard typology: Microclimate creation, stack ventilation
176
+ - Shading: Deep overhangs, mashrabiya screens
177
+ - Evaporative cooling: Water features, vegetation
178
+
179
+ HOT-HUMID CLIMATE
180
+ - Cross ventilation: Openings on opposite facades
181
+ - Elevated structures: Raise above ground for air circulation
182
+ - Lightweight construction: Low thermal mass (rapid cooling)
183
+ - Solar shading: Extended roofs, louvers
184
+
185
+ COLD CLIMATE
186
+ - Compact form: Minimize surface-to-volume ratio
187
+ - Superinsulation: R-40+ walls, R-60+ roof, triple glazing
188
+ - Solar gain: South-facing glazing (N hemisphere), thermal storage
189
+ - Air tightness: < 0.6 ACH50 (Passive House standard)
190
+
191
+ TEMPERATE CLIMATE
192
+ - Mixed-mode: Natural ventilation + mechanical when needed
193
+ - Balanced glazing: Optimize daylight vs. heat gain/loss
194
+ - Thermal mass: Moderate mass with night purge ventilation
195
+ - Responsive facades: Operable shading, automated louvers
196
+ ```
197
+
198
+ ## Computational Design Methods
199
+
200
+ ### Parametric Design with Grasshopper/Python
201
+
202
+ ```python
203
+ # Example: Parametric facade panel generation
204
+ # (Illustrative -- actual implementation uses Grasshopper + RhinoCommon)
205
+
206
+ import numpy as np
207
+
208
+ def generate_parametric_facade(
209
+ width: float,
210
+ height: float,
211
+ panel_count_x: int,
212
+ panel_count_y: int,
213
+ solar_data: np.ndarray, # Solar radiation per panel position
214
+ min_opening: float = 0.1,
215
+ max_opening: float = 0.8,
216
+ ) -> list:
217
+ """
218
+ Generate facade panel openings responsive to solar radiation.
219
+ Higher radiation = smaller opening (reduce heat gain).
220
+ """
221
+ panels = []
222
+ for i in range(panel_count_x):
223
+ for j in range(panel_count_y):
224
+ radiation = solar_data[i, j]
225
+ normalized = (radiation - solar_data.min()) / (solar_data.max() - solar_data.min())
226
+ # Inverse: more sun = smaller opening
227
+ opening_ratio = max_opening - normalized * (max_opening - min_opening)
228
+
229
+ panels.append({
230
+ "position": (i * width / panel_count_x, j * height / panel_count_y),
231
+ "size": (width / panel_count_x, height / panel_count_y),
232
+ "opening_ratio": round(opening_ratio, 3),
233
+ "solar_radiation": round(radiation, 1),
234
+ })
235
+ return panels
236
+ ```
237
+
238
+ ### BIM for Research
239
+
240
+ ```
241
+ Building Information Modeling (BIM) in academic research:
242
+
243
+ APPLICATIONS:
244
+ 1. Performance simulation integration (energy, daylight, acoustics)
245
+ 2. Construction logistics and scheduling research
246
+ 3. Facility management and digital twin studies
247
+ 4. Heritage documentation and conservation
248
+ 5. Parametric and generative design exploration
249
+
250
+ INTEROPERABILITY STANDARDS:
251
+ - IFC (Industry Foundation Classes): Open BIM exchange format
252
+ - gbXML: Energy simulation data exchange
253
+ - COBie: Facility management data
254
+ - CityGML: Urban-scale modeling
255
+
256
+ RESEARCH TOOLS:
257
+ - Revit + Dynamo: Parametric BIM authoring
258
+ - ArchiCAD + Grasshopper Live Connection
259
+ - BlenderBIM: Open-source BIM (IFC native)
260
+ - OpenStudio + EnergyPlus: Energy simulation
261
+ - Ladybug/Honeybee: Environmental analysis (Grasshopper)
262
+ ```
263
+
264
+ ## Best Practices
265
+
266
+ - **Ground design claims in evidence.** Post-occupancy evaluation and simulation results strengthen design arguments.
267
+ - **Use multiple performance metrics.** Energy, daylight, thermal comfort, and embodied carbon often trade off against each other.
268
+ - **Document design rationale.** The reasoning behind decisions is as important as the decisions themselves.
269
+ - **Engage with architectural theory.** Computational methods are tools, not substitutes for critical thinking about space, meaning, and experience.
270
+ - **Validate simulations against measured data.** Calibrated models are far more credible than uncalibrated predictions.
271
+ - **Consider the full lifecycle.** Embodied carbon in materials can exceed operational carbon over 60 years.
272
+
273
+ ## References
274
+
275
+ - Ching, F. D. K. (2014). Architecture: Form, Space, and Order, 4th ed. Wiley.
276
+ - [ArchDaily](https://www.archdaily.com/) -- Architectural project database and analysis
277
+ - [Ladybug Tools](https://www.ladybug.tools/) -- Environmental analysis for Grasshopper
278
+ - Block, P. et al. (2017). Beyond Bending: Reimagining Compression Shells. DETAIL.
279
+ - [RIBA 2030 Climate Challenge](https://www.architecture.com/about/policy/climate-action/2030-climate-challenge) -- Carbon benchmarks