@saibolla/ada 0.1.2

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 (1432) hide show
  1. package/.ada/SYSTEM.md +81 -0
  2. package/.ada/agents/researcher.md +69 -0
  3. package/.ada/agents/reviewer.md +92 -0
  4. package/.ada/agents/verifier.md +45 -0
  5. package/.ada/agents/writer.md +54 -0
  6. package/.ada/settings.json +32 -0
  7. package/.ada/themes/ada.json +85 -0
  8. package/.env.example +31 -0
  9. package/AGENTS.md +79 -0
  10. package/LICENSE +191 -0
  11. package/README.md +188 -0
  12. package/bin/ada.js +26 -0
  13. package/dist/bootstrap/sync.js +143 -0
  14. package/dist/cli.js +404 -0
  15. package/dist/config/paths.js +32 -0
  16. package/dist/index.js +10 -0
  17. package/dist/model/catalog.js +255 -0
  18. package/dist/model/commands.js +180 -0
  19. package/dist/pi/launch.js +33 -0
  20. package/dist/pi/package-presets.js +55 -0
  21. package/dist/pi/runtime.js +81 -0
  22. package/dist/pi/settings.js +108 -0
  23. package/dist/pi/web-access.js +74 -0
  24. package/dist/search/commands.js +12 -0
  25. package/dist/setup/doctor.js +126 -0
  26. package/dist/setup/preview.js +117 -0
  27. package/dist/setup/prompts.js +34 -0
  28. package/dist/setup/setup.js +98 -0
  29. package/dist/setup/update.js +133 -0
  30. package/dist/system/executables.js +38 -0
  31. package/dist/system/node-version.js +31 -0
  32. package/dist/system/open-url.js +35 -0
  33. package/dist/system/promise-polyfill.js +12 -0
  34. package/dist/ui/terminal.js +64 -0
  35. package/dist/web/launch.js +48 -0
  36. package/dist/web-search.js +1 -0
  37. package/extensions/docparser/constants.ts +62 -0
  38. package/extensions/docparser/deps.ts +584 -0
  39. package/extensions/docparser/doctor.ts +353 -0
  40. package/extensions/docparser/index.ts +9 -0
  41. package/extensions/docparser/input.ts +230 -0
  42. package/extensions/docparser/request.ts +67 -0
  43. package/extensions/docparser/schema.ts +82 -0
  44. package/extensions/docparser/tool.ts +305 -0
  45. package/extensions/docparser/types.ts +99 -0
  46. package/extensions/research-tools/alpha.ts +107 -0
  47. package/extensions/research-tools/header.ts +284 -0
  48. package/extensions/research-tools/help.ts +93 -0
  49. package/extensions/research-tools/project-scaffold.ts +64 -0
  50. package/extensions/research-tools/project.ts +123 -0
  51. package/extensions/research-tools/shared.ts +16 -0
  52. package/extensions/research-tools.ts +42 -0
  53. package/logo.d.mts +3 -0
  54. package/logo.mjs +14 -0
  55. package/metadata/commands.d.mts +46 -0
  56. package/metadata/commands.mjs +133 -0
  57. package/package.json +80 -0
  58. package/prompts/audit.md +17 -0
  59. package/prompts/autoresearch.md +66 -0
  60. package/prompts/compare.md +18 -0
  61. package/prompts/deepresearch.md +189 -0
  62. package/prompts/draft.md +19 -0
  63. package/prompts/jobs.md +16 -0
  64. package/prompts/litreview.md +18 -0
  65. package/prompts/log.md +14 -0
  66. package/prompts/replicate.md +24 -0
  67. package/prompts/review.md +18 -0
  68. package/prompts/watch.md +16 -0
  69. package/scripts/build-native-bundle.mjs +349 -0
  70. package/scripts/check-node-version.mjs +35 -0
  71. package/scripts/patch-embedded-pi.mjs +588 -0
  72. package/scripts/prepare-runtime-workspace.mjs +162 -0
  73. package/scripts/prune-runtime-deps.mjs +131 -0
  74. package/scripts/release.sh +152 -0
  75. package/skills/adaptyv/SKILL.md +112 -0
  76. package/skills/adaptyv/reference/api_reference.md +308 -0
  77. package/skills/adaptyv/reference/examples.md +913 -0
  78. package/skills/adaptyv/reference/experiments.md +360 -0
  79. package/skills/adaptyv/reference/protein_optimization.md +637 -0
  80. package/skills/aeon/SKILL.md +372 -0
  81. package/skills/aeon/references/anomaly_detection.md +154 -0
  82. package/skills/aeon/references/classification.md +144 -0
  83. package/skills/aeon/references/clustering.md +123 -0
  84. package/skills/aeon/references/datasets_benchmarking.md +387 -0
  85. package/skills/aeon/references/distances.md +256 -0
  86. package/skills/aeon/references/forecasting.md +140 -0
  87. package/skills/aeon/references/networks.md +289 -0
  88. package/skills/aeon/references/regression.md +118 -0
  89. package/skills/aeon/references/segmentation.md +163 -0
  90. package/skills/aeon/references/similarity_search.md +187 -0
  91. package/skills/aeon/references/transformations.md +246 -0
  92. package/skills/alpha-research/SKILL.md +42 -0
  93. package/skills/alpha-vantage/SKILL.md +142 -0
  94. package/skills/alpha-vantage/references/commodities.md +153 -0
  95. package/skills/alpha-vantage/references/economic-indicators.md +158 -0
  96. package/skills/alpha-vantage/references/forex-crypto.md +154 -0
  97. package/skills/alpha-vantage/references/fundamentals.md +223 -0
  98. package/skills/alpha-vantage/references/intelligence.md +138 -0
  99. package/skills/alpha-vantage/references/options.md +93 -0
  100. package/skills/alpha-vantage/references/technical-indicators.md +374 -0
  101. package/skills/alpha-vantage/references/time-series.md +157 -0
  102. package/skills/alphafold-database/SKILL.md +511 -0
  103. package/skills/alphafold-database/references/api_reference.md +423 -0
  104. package/skills/anndata/SKILL.md +398 -0
  105. package/skills/anndata/references/best_practices.md +525 -0
  106. package/skills/anndata/references/concatenation.md +396 -0
  107. package/skills/anndata/references/data_structure.md +314 -0
  108. package/skills/anndata/references/io_operations.md +404 -0
  109. package/skills/anndata/references/manipulation.md +516 -0
  110. package/skills/arboreto/SKILL.md +241 -0
  111. package/skills/arboreto/references/algorithms.md +138 -0
  112. package/skills/arboreto/references/basic_inference.md +151 -0
  113. package/skills/arboreto/references/distributed_computing.md +242 -0
  114. package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  115. package/skills/arxiv-database/SKILL.md +362 -0
  116. package/skills/arxiv-database/references/api_reference.md +430 -0
  117. package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
  118. package/skills/astropy/SKILL.md +329 -0
  119. package/skills/astropy/references/coordinates.md +273 -0
  120. package/skills/astropy/references/cosmology.md +307 -0
  121. package/skills/astropy/references/fits.md +396 -0
  122. package/skills/astropy/references/tables.md +489 -0
  123. package/skills/astropy/references/time.md +404 -0
  124. package/skills/astropy/references/units.md +178 -0
  125. package/skills/astropy/references/wcs_and_other_modules.md +373 -0
  126. package/skills/autoresearch/SKILL.md +12 -0
  127. package/skills/benchling-integration/SKILL.md +478 -0
  128. package/skills/benchling-integration/references/api_endpoints.md +883 -0
  129. package/skills/benchling-integration/references/authentication.md +379 -0
  130. package/skills/benchling-integration/references/sdk_reference.md +774 -0
  131. package/skills/bgpt-paper-search/SKILL.md +81 -0
  132. package/skills/bindingdb-database/SKILL.md +332 -0
  133. package/skills/bindingdb-database/references/affinity_queries.md +178 -0
  134. package/skills/biopython/SKILL.md +441 -0
  135. package/skills/biopython/references/advanced.md +577 -0
  136. package/skills/biopython/references/alignment.md +362 -0
  137. package/skills/biopython/references/blast.md +455 -0
  138. package/skills/biopython/references/databases.md +484 -0
  139. package/skills/biopython/references/phylogenetics.md +566 -0
  140. package/skills/biopython/references/sequence_io.md +285 -0
  141. package/skills/biopython/references/structure.md +564 -0
  142. package/skills/biorxiv-database/SKILL.md +481 -0
  143. package/skills/biorxiv-database/references/api_reference.md +280 -0
  144. package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  145. package/skills/bioservices/SKILL.md +359 -0
  146. package/skills/bioservices/references/identifier_mapping.md +685 -0
  147. package/skills/bioservices/references/services_reference.md +636 -0
  148. package/skills/bioservices/references/workflow_patterns.md +811 -0
  149. package/skills/bioservices/scripts/batch_id_converter.py +347 -0
  150. package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  151. package/skills/bioservices/scripts/pathway_analysis.py +309 -0
  152. package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  153. package/skills/brenda-database/SKILL.md +717 -0
  154. package/skills/brenda-database/references/api_reference.md +537 -0
  155. package/skills/brenda-database/scripts/brenda_queries.py +844 -0
  156. package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  157. package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  158. package/skills/cbioportal-database/SKILL.md +367 -0
  159. package/skills/cbioportal-database/references/study_exploration.md +128 -0
  160. package/skills/cellxgene-census/SKILL.md +509 -0
  161. package/skills/cellxgene-census/references/census_schema.md +182 -0
  162. package/skills/cellxgene-census/references/common_patterns.md +351 -0
  163. package/skills/chembl-database/SKILL.md +387 -0
  164. package/skills/chembl-database/references/api_reference.md +272 -0
  165. package/skills/chembl-database/scripts/example_queries.py +278 -0
  166. package/skills/cirq/SKILL.md +344 -0
  167. package/skills/cirq/references/building.md +307 -0
  168. package/skills/cirq/references/experiments.md +572 -0
  169. package/skills/cirq/references/hardware.md +515 -0
  170. package/skills/cirq/references/noise.md +515 -0
  171. package/skills/cirq/references/simulation.md +350 -0
  172. package/skills/cirq/references/transformation.md +416 -0
  173. package/skills/citation-management/SKILL.md +1113 -0
  174. package/skills/citation-management/assets/bibtex_template.bib +264 -0
  175. package/skills/citation-management/assets/citation_checklist.md +386 -0
  176. package/skills/citation-management/references/bibtex_formatting.md +908 -0
  177. package/skills/citation-management/references/citation_validation.md +794 -0
  178. package/skills/citation-management/references/google_scholar_search.md +725 -0
  179. package/skills/citation-management/references/metadata_extraction.md +870 -0
  180. package/skills/citation-management/references/pubmed_search.md +839 -0
  181. package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  182. package/skills/citation-management/scripts/extract_metadata.py +569 -0
  183. package/skills/citation-management/scripts/format_bibtex.py +349 -0
  184. package/skills/citation-management/scripts/search_google_scholar.py +282 -0
  185. package/skills/citation-management/scripts/search_pubmed.py +398 -0
  186. package/skills/citation-management/scripts/validate_citations.py +497 -0
  187. package/skills/clinical-decision-support/SKILL.md +510 -0
  188. package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
  189. package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
  190. package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
  191. package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
  192. package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
  193. package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
  194. package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
  195. package/skills/clinical-decision-support/references/README.md +129 -0
  196. package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
  197. package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
  198. package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
  199. package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
  200. package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
  201. package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
  202. package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
  203. package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
  204. package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
  205. package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
  206. package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
  207. package/skills/clinical-reports/SKILL.md +1131 -0
  208. package/skills/clinical-reports/assets/case_report_template.md +352 -0
  209. package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  210. package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  211. package/skills/clinical-reports/assets/consult_note_template.md +305 -0
  212. package/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  213. package/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  214. package/skills/clinical-reports/assets/history_physical_template.md +305 -0
  215. package/skills/clinical-reports/assets/lab_report_template.md +309 -0
  216. package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  217. package/skills/clinical-reports/assets/quality_checklist.md +338 -0
  218. package/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  219. package/skills/clinical-reports/assets/soap_note_template.md +253 -0
  220. package/skills/clinical-reports/references/README.md +236 -0
  221. package/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  222. package/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  223. package/skills/clinical-reports/references/data_presentation.md +530 -0
  224. package/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  225. package/skills/clinical-reports/references/medical_terminology.md +588 -0
  226. package/skills/clinical-reports/references/patient_documentation.md +744 -0
  227. package/skills/clinical-reports/references/peer_review_standards.md +585 -0
  228. package/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  229. package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  230. package/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  231. package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  232. package/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  233. package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  234. package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  235. package/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  236. package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  237. package/skills/clinicaltrials-database/SKILL.md +505 -0
  238. package/skills/clinicaltrials-database/references/api_reference.md +358 -0
  239. package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  240. package/skills/clinpgx-database/SKILL.md +636 -0
  241. package/skills/clinpgx-database/references/api_reference.md +757 -0
  242. package/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  243. package/skills/clinvar-database/SKILL.md +360 -0
  244. package/skills/clinvar-database/references/api_reference.md +227 -0
  245. package/skills/clinvar-database/references/clinical_significance.md +218 -0
  246. package/skills/clinvar-database/references/data_formats.md +358 -0
  247. package/skills/cobrapy/SKILL.md +461 -0
  248. package/skills/cobrapy/references/api_quick_reference.md +655 -0
  249. package/skills/cobrapy/references/workflows.md +593 -0
  250. package/skills/consciousness-council/SKILL.md +150 -0
  251. package/skills/consciousness-council/references/advanced-configurations.md +96 -0
  252. package/skills/cosmic-database/SKILL.md +334 -0
  253. package/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  254. package/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  255. package/skills/crawl4ai/SKILL.md +172 -0
  256. package/skills/dask/SKILL.md +454 -0
  257. package/skills/dask/references/arrays.md +497 -0
  258. package/skills/dask/references/bags.md +468 -0
  259. package/skills/dask/references/best-practices.md +277 -0
  260. package/skills/dask/references/dataframes.md +368 -0
  261. package/skills/dask/references/futures.md +541 -0
  262. package/skills/dask/references/schedulers.md +504 -0
  263. package/skills/datacommons-client/SKILL.md +253 -0
  264. package/skills/datacommons-client/references/getting_started.md +417 -0
  265. package/skills/datacommons-client/references/node.md +250 -0
  266. package/skills/datacommons-client/references/observation.md +185 -0
  267. package/skills/datacommons-client/references/resolve.md +246 -0
  268. package/skills/datamol/SKILL.md +704 -0
  269. package/skills/datamol/references/conformers_module.md +131 -0
  270. package/skills/datamol/references/core_api.md +130 -0
  271. package/skills/datamol/references/descriptors_viz.md +195 -0
  272. package/skills/datamol/references/fragments_scaffolds.md +174 -0
  273. package/skills/datamol/references/io_module.md +109 -0
  274. package/skills/datamol/references/reactions_data.md +218 -0
  275. package/skills/deep-research/SKILL.md +12 -0
  276. package/skills/deepchem/SKILL.md +595 -0
  277. package/skills/deepchem/references/api_reference.md +303 -0
  278. package/skills/deepchem/references/workflows.md +491 -0
  279. package/skills/deepchem/scripts/graph_neural_network.py +338 -0
  280. package/skills/deepchem/scripts/predict_solubility.py +224 -0
  281. package/skills/deepchem/scripts/transfer_learning.py +375 -0
  282. package/skills/deeptools/SKILL.md +529 -0
  283. package/skills/deeptools/assets/quick_reference.md +58 -0
  284. package/skills/deeptools/references/effective_genome_sizes.md +116 -0
  285. package/skills/deeptools/references/normalization_methods.md +410 -0
  286. package/skills/deeptools/references/tools_reference.md +533 -0
  287. package/skills/deeptools/references/workflows.md +474 -0
  288. package/skills/deeptools/scripts/validate_files.py +195 -0
  289. package/skills/deeptools/scripts/workflow_generator.py +454 -0
  290. package/skills/denario/SKILL.md +213 -0
  291. package/skills/denario/references/examples.md +494 -0
  292. package/skills/denario/references/installation.md +213 -0
  293. package/skills/denario/references/llm_configuration.md +265 -0
  294. package/skills/denario/references/research_pipeline.md +471 -0
  295. package/skills/depmap/SKILL.md +300 -0
  296. package/skills/depmap/references/dependency_analysis.md +178 -0
  297. package/skills/dhdna-profiler/SKILL.md +162 -0
  298. package/skills/dhdna-profiler/references/advanced-profiling.md +72 -0
  299. package/skills/diffdock/SKILL.md +481 -0
  300. package/skills/diffdock/assets/batch_template.csv +4 -0
  301. package/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  302. package/skills/diffdock/references/confidence_and_limitations.md +182 -0
  303. package/skills/diffdock/references/parameters_reference.md +163 -0
  304. package/skills/diffdock/references/workflows_examples.md +392 -0
  305. package/skills/diffdock/scripts/analyze_results.py +334 -0
  306. package/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  307. package/skills/diffdock/scripts/setup_check.py +278 -0
  308. package/skills/dnanexus-integration/SKILL.md +381 -0
  309. package/skills/dnanexus-integration/references/app-development.md +247 -0
  310. package/skills/dnanexus-integration/references/configuration.md +646 -0
  311. package/skills/dnanexus-integration/references/data-operations.md +400 -0
  312. package/skills/dnanexus-integration/references/job-execution.md +412 -0
  313. package/skills/dnanexus-integration/references/python-sdk.md +523 -0
  314. package/skills/docker/SKILL.md +84 -0
  315. package/skills/docx/LICENSE.txt +30 -0
  316. package/skills/docx/SKILL.md +590 -0
  317. package/skills/docx/scripts/__init__.py +1 -0
  318. package/skills/docx/scripts/accept_changes.py +135 -0
  319. package/skills/docx/scripts/comment.py +318 -0
  320. package/skills/docx/scripts/office/helpers/__init__.py +0 -0
  321. package/skills/docx/scripts/office/helpers/merge_runs.py +199 -0
  322. package/skills/docx/scripts/office/helpers/simplify_redlines.py +197 -0
  323. package/skills/docx/scripts/office/pack.py +159 -0
  324. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  325. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  326. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  327. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  328. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  329. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  330. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  331. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  332. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  333. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  334. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  335. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  336. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  337. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  338. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  339. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  340. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  341. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  342. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  343. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  344. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  345. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  346. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  347. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  348. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  349. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  350. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  351. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  352. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  353. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  354. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  355. package/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
  356. package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  357. package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  358. package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  359. package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  360. package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  361. package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  362. package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  363. package/skills/docx/scripts/office/soffice.py +183 -0
  364. package/skills/docx/scripts/office/unpack.py +132 -0
  365. package/skills/docx/scripts/office/validate.py +111 -0
  366. package/skills/docx/scripts/office/validators/__init__.py +15 -0
  367. package/skills/docx/scripts/office/validators/base.py +847 -0
  368. package/skills/docx/scripts/office/validators/docx.py +446 -0
  369. package/skills/docx/scripts/office/validators/pptx.py +275 -0
  370. package/skills/docx/scripts/office/validators/redlining.py +247 -0
  371. package/skills/docx/scripts/templates/comments.xml +3 -0
  372. package/skills/docx/scripts/templates/commentsExtended.xml +3 -0
  373. package/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  374. package/skills/docx/scripts/templates/commentsIds.xml +3 -0
  375. package/skills/docx/scripts/templates/people.xml +3 -0
  376. package/skills/drugbank-database/SKILL.md +188 -0
  377. package/skills/drugbank-database/references/chemical-analysis.md +590 -0
  378. package/skills/drugbank-database/references/data-access.md +242 -0
  379. package/skills/drugbank-database/references/drug-queries.md +386 -0
  380. package/skills/drugbank-database/references/interactions.md +425 -0
  381. package/skills/drugbank-database/references/targets-pathways.md +518 -0
  382. package/skills/drugbank-database/scripts/drugbank_helper.py +350 -0
  383. package/skills/edgartools/SKILL.md +136 -0
  384. package/skills/edgartools/references/ai-integration.md +274 -0
  385. package/skills/edgartools/references/companies.md +268 -0
  386. package/skills/edgartools/references/data-objects.md +237 -0
  387. package/skills/edgartools/references/entity-facts.md +372 -0
  388. package/skills/edgartools/references/filings.md +387 -0
  389. package/skills/edgartools/references/financial-data.md +274 -0
  390. package/skills/edgartools/references/xbrl.md +373 -0
  391. package/skills/eli5/SKILL.md +25 -0
  392. package/skills/ena-database/SKILL.md +202 -0
  393. package/skills/ena-database/references/api_reference.md +490 -0
  394. package/skills/ensembl-database/SKILL.md +309 -0
  395. package/skills/ensembl-database/references/api_endpoints.md +346 -0
  396. package/skills/ensembl-database/scripts/ensembl_query.py +427 -0
  397. package/skills/esm/SKILL.md +304 -0
  398. package/skills/esm/references/esm-c-api.md +583 -0
  399. package/skills/esm/references/esm3-api.md +452 -0
  400. package/skills/esm/references/forge-api.md +657 -0
  401. package/skills/esm/references/workflows.md +685 -0
  402. package/skills/etetoolkit/SKILL.md +621 -0
  403. package/skills/etetoolkit/references/api_reference.md +583 -0
  404. package/skills/etetoolkit/references/visualization.md +783 -0
  405. package/skills/etetoolkit/references/workflows.md +774 -0
  406. package/skills/etetoolkit/scripts/quick_visualize.py +214 -0
  407. package/skills/etetoolkit/scripts/tree_operations.py +229 -0
  408. package/skills/exploratory-data-analysis/SKILL.md +444 -0
  409. package/skills/exploratory-data-analysis/assets/report_template.md +196 -0
  410. package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
  411. package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
  412. package/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
  413. package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
  414. package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
  415. package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
  416. package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
  417. package/skills/fda-database/SKILL.md +516 -0
  418. package/skills/fda-database/references/animal_veterinary.md +377 -0
  419. package/skills/fda-database/references/api_basics.md +687 -0
  420. package/skills/fda-database/references/devices.md +632 -0
  421. package/skills/fda-database/references/drugs.md +468 -0
  422. package/skills/fda-database/references/foods.md +374 -0
  423. package/skills/fda-database/references/other.md +472 -0
  424. package/skills/fda-database/scripts/fda_examples.py +335 -0
  425. package/skills/fda-database/scripts/fda_query.py +440 -0
  426. package/skills/flowio/SKILL.md +606 -0
  427. package/skills/flowio/references/api_reference.md +372 -0
  428. package/skills/fluidsim/SKILL.md +347 -0
  429. package/skills/fluidsim/references/advanced_features.md +398 -0
  430. package/skills/fluidsim/references/installation.md +68 -0
  431. package/skills/fluidsim/references/output_analysis.md +283 -0
  432. package/skills/fluidsim/references/parameters.md +198 -0
  433. package/skills/fluidsim/references/simulation_workflow.md +172 -0
  434. package/skills/fluidsim/references/solvers.md +94 -0
  435. package/skills/fred-economic-data/SKILL.md +433 -0
  436. package/skills/fred-economic-data/references/api_basics.md +212 -0
  437. package/skills/fred-economic-data/references/categories.md +442 -0
  438. package/skills/fred-economic-data/references/geofred.md +588 -0
  439. package/skills/fred-economic-data/references/releases.md +642 -0
  440. package/skills/fred-economic-data/references/series.md +584 -0
  441. package/skills/fred-economic-data/references/sources.md +423 -0
  442. package/skills/fred-economic-data/references/tags.md +485 -0
  443. package/skills/fred-economic-data/scripts/fred_examples.py +354 -0
  444. package/skills/fred-economic-data/scripts/fred_query.py +590 -0
  445. package/skills/gene-database/SKILL.md +177 -0
  446. package/skills/gene-database/references/api_reference.md +404 -0
  447. package/skills/gene-database/references/common_workflows.md +428 -0
  448. package/skills/gene-database/scripts/batch_gene_lookup.py +298 -0
  449. package/skills/gene-database/scripts/fetch_gene_data.py +277 -0
  450. package/skills/gene-database/scripts/query_gene.py +251 -0
  451. package/skills/generate-image/SKILL.md +183 -0
  452. package/skills/generate-image/scripts/generate_image.py +281 -0
  453. package/skills/geniml/SKILL.md +316 -0
  454. package/skills/geniml/references/bedspace.md +127 -0
  455. package/skills/geniml/references/consensus_peaks.md +238 -0
  456. package/skills/geniml/references/region2vec.md +90 -0
  457. package/skills/geniml/references/scembed.md +197 -0
  458. package/skills/geniml/references/utilities.md +385 -0
  459. package/skills/geo-database/SKILL.md +813 -0
  460. package/skills/geo-database/references/geo_reference.md +829 -0
  461. package/skills/geomaster/README.md +105 -0
  462. package/skills/geomaster/SKILL.md +365 -0
  463. package/skills/geomaster/references/advanced-gis.md +376 -0
  464. package/skills/geomaster/references/big-data.md +363 -0
  465. package/skills/geomaster/references/code-examples.md +531 -0
  466. package/skills/geomaster/references/coordinate-systems.md +364 -0
  467. package/skills/geomaster/references/core-libraries.md +273 -0
  468. package/skills/geomaster/references/data-sources.md +330 -0
  469. package/skills/geomaster/references/gis-software.md +369 -0
  470. package/skills/geomaster/references/industry-applications.md +420 -0
  471. package/skills/geomaster/references/machine-learning.md +462 -0
  472. package/skills/geomaster/references/programming-languages.md +456 -0
  473. package/skills/geomaster/references/remote-sensing.md +370 -0
  474. package/skills/geomaster/references/scientific-domains.md +416 -0
  475. package/skills/geomaster/references/specialized-topics.md +428 -0
  476. package/skills/geomaster/references/troubleshooting.md +439 -0
  477. package/skills/geopandas/SKILL.md +249 -0
  478. package/skills/geopandas/references/crs-management.md +243 -0
  479. package/skills/geopandas/references/data-io.md +165 -0
  480. package/skills/geopandas/references/data-structures.md +70 -0
  481. package/skills/geopandas/references/geometric-operations.md +221 -0
  482. package/skills/geopandas/references/spatial-analysis.md +184 -0
  483. package/skills/geopandas/references/visualization.md +243 -0
  484. package/skills/get-available-resources/SKILL.md +275 -0
  485. package/skills/get-available-resources/scripts/detect_resources.py +401 -0
  486. package/skills/gget/SKILL.md +869 -0
  487. package/skills/gget/references/database_info.md +300 -0
  488. package/skills/gget/references/module_reference.md +467 -0
  489. package/skills/gget/references/workflows.md +814 -0
  490. package/skills/gget/scripts/batch_sequence_analysis.py +191 -0
  491. package/skills/gget/scripts/enrichment_pipeline.py +235 -0
  492. package/skills/gget/scripts/gene_analysis.py +161 -0
  493. package/skills/ginkgo-cloud-lab/SKILL.md +56 -0
  494. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +85 -0
  495. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +71 -0
  496. package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +87 -0
  497. package/skills/glycoengineering/SKILL.md +338 -0
  498. package/skills/glycoengineering/references/glycan_databases.md +165 -0
  499. package/skills/gnomad-database/SKILL.md +395 -0
  500. package/skills/gnomad-database/references/graphql_queries.md +219 -0
  501. package/skills/gnomad-database/references/variant_interpretation.md +85 -0
  502. package/skills/gtars/SKILL.md +283 -0
  503. package/skills/gtars/references/cli.md +222 -0
  504. package/skills/gtars/references/coverage.md +172 -0
  505. package/skills/gtars/references/overlap.md +156 -0
  506. package/skills/gtars/references/python-api.md +211 -0
  507. package/skills/gtars/references/refget.md +147 -0
  508. package/skills/gtars/references/tokenizers.md +103 -0
  509. package/skills/gtex-database/SKILL.md +315 -0
  510. package/skills/gtex-database/references/api_reference.md +191 -0
  511. package/skills/gwas-database/SKILL.md +606 -0
  512. package/skills/gwas-database/references/api_reference.md +793 -0
  513. package/skills/hedgefundmonitor/SKILL.md +128 -0
  514. package/skills/hedgefundmonitor/references/api-overview.md +93 -0
  515. package/skills/hedgefundmonitor/references/datasets.md +150 -0
  516. package/skills/hedgefundmonitor/references/endpoints-combined.md +196 -0
  517. package/skills/hedgefundmonitor/references/endpoints-metadata.md +136 -0
  518. package/skills/hedgefundmonitor/references/endpoints-series-data.md +126 -0
  519. package/skills/hedgefundmonitor/references/examples.md +287 -0
  520. package/skills/hedgefundmonitor/references/parameters.md +104 -0
  521. package/skills/histolab/SKILL.md +676 -0
  522. package/skills/histolab/references/filters_preprocessing.md +514 -0
  523. package/skills/histolab/references/slide_management.md +172 -0
  524. package/skills/histolab/references/tile_extraction.md +421 -0
  525. package/skills/histolab/references/tissue_masks.md +251 -0
  526. package/skills/histolab/references/visualization.md +547 -0
  527. package/skills/hmdb-database/SKILL.md +194 -0
  528. package/skills/hmdb-database/references/hmdb_data_fields.md +267 -0
  529. package/skills/hypogenic/SKILL.md +653 -0
  530. package/skills/hypogenic/references/config_template.yaml +150 -0
  531. package/skills/hypothesis-generation/SKILL.md +297 -0
  532. package/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
  533. package/skills/hypothesis-generation/assets/hypothesis_generation.sty +307 -0
  534. package/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
  535. package/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  536. package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  537. package/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  538. package/skills/imaging-data-commons/SKILL.md +843 -0
  539. package/skills/imaging-data-commons/references/bigquery_guide.md +556 -0
  540. package/skills/imaging-data-commons/references/cli_guide.md +272 -0
  541. package/skills/imaging-data-commons/references/clinical_data_guide.md +324 -0
  542. package/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
  543. package/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
  544. package/skills/imaging-data-commons/references/digital_pathology_guide.md +403 -0
  545. package/skills/imaging-data-commons/references/index_tables_guide.md +146 -0
  546. package/skills/imaging-data-commons/references/sql_patterns.md +207 -0
  547. package/skills/imaging-data-commons/references/use_cases.md +186 -0
  548. package/skills/infographics/SKILL.md +563 -0
  549. package/skills/infographics/references/color_palettes.md +496 -0
  550. package/skills/infographics/references/design_principles.md +636 -0
  551. package/skills/infographics/references/infographic_types.md +907 -0
  552. package/skills/infographics/scripts/generate_infographic.py +234 -0
  553. package/skills/infographics/scripts/generate_infographic_ai.py +1290 -0
  554. package/skills/interpro-database/SKILL.md +305 -0
  555. package/skills/interpro-database/references/domain_analysis.md +159 -0
  556. package/skills/iso-13485-certification/SKILL.md +678 -0
  557. package/skills/iso-13485-certification/assets/templates/procedures/CAPA-procedure-template.md +453 -0
  558. package/skills/iso-13485-certification/assets/templates/procedures/document-control-procedure-template.md +567 -0
  559. package/skills/iso-13485-certification/assets/templates/quality-manual-template.md +521 -0
  560. package/skills/iso-13485-certification/references/gap-analysis-checklist.md +568 -0
  561. package/skills/iso-13485-certification/references/iso-13485-requirements.md +610 -0
  562. package/skills/iso-13485-certification/references/mandatory-documents.md +606 -0
  563. package/skills/iso-13485-certification/references/quality-manual-guide.md +688 -0
  564. package/skills/iso-13485-certification/scripts/gap_analyzer.py +440 -0
  565. package/skills/jaspar-database/SKILL.md +351 -0
  566. package/skills/jaspar-database/references/api_reference.md +182 -0
  567. package/skills/jobs/SKILL.md +10 -0
  568. package/skills/kegg-database/SKILL.md +375 -0
  569. package/skills/kegg-database/references/kegg_reference.md +326 -0
  570. package/skills/kegg-database/scripts/kegg_api.py +251 -0
  571. package/skills/labarchive-integration/SKILL.md +266 -0
  572. package/skills/labarchive-integration/references/api_reference.md +342 -0
  573. package/skills/labarchive-integration/references/authentication_guide.md +357 -0
  574. package/skills/labarchive-integration/references/integrations.md +425 -0
  575. package/skills/labarchive-integration/scripts/entry_operations.py +334 -0
  576. package/skills/labarchive-integration/scripts/notebook_operations.py +269 -0
  577. package/skills/labarchive-integration/scripts/setup_config.py +205 -0
  578. package/skills/lamindb/SKILL.md +388 -0
  579. package/skills/lamindb/references/annotation-validation.md +513 -0
  580. package/skills/lamindb/references/core-concepts.md +380 -0
  581. package/skills/lamindb/references/data-management.md +433 -0
  582. package/skills/lamindb/references/integrations.md +642 -0
  583. package/skills/lamindb/references/ontologies.md +497 -0
  584. package/skills/lamindb/references/setup-deployment.md +733 -0
  585. package/skills/latchbio-integration/SKILL.md +351 -0
  586. package/skills/latchbio-integration/references/data-management.md +427 -0
  587. package/skills/latchbio-integration/references/resource-configuration.md +429 -0
  588. package/skills/latchbio-integration/references/verified-workflows.md +487 -0
  589. package/skills/latchbio-integration/references/workflow-creation.md +254 -0
  590. package/skills/latex-posters/SKILL.md +1602 -0
  591. package/skills/latex-posters/assets/baposter_template.tex +257 -0
  592. package/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  593. package/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  594. package/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  595. package/skills/latex-posters/references/README.md +417 -0
  596. package/skills/latex-posters/references/latex_poster_packages.md +745 -0
  597. package/skills/latex-posters/references/poster_content_guide.md +748 -0
  598. package/skills/latex-posters/references/poster_design_principles.md +806 -0
  599. package/skills/latex-posters/references/poster_layout_design.md +900 -0
  600. package/skills/latex-posters/scripts/review_poster.sh +214 -0
  601. package/skills/literature-review/SKILL.md +637 -0
  602. package/skills/literature-review/assets/review_template.md +412 -0
  603. package/skills/literature-review/references/citation_styles.md +166 -0
  604. package/skills/literature-review/references/database_strategies.md +455 -0
  605. package/skills/literature-review/scripts/generate_pdf.py +176 -0
  606. package/skills/literature-review/scripts/search_databases.py +303 -0
  607. package/skills/literature-review/scripts/verify_citations.py +222 -0
  608. package/skills/markdown-mermaid-writing/SKILL.md +327 -0
  609. package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +221 -0
  610. package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +108 -0
  611. package/skills/markdown-mermaid-writing/references/diagrams/block.md +177 -0
  612. package/skills/markdown-mermaid-writing/references/diagrams/c4.md +136 -0
  613. package/skills/markdown-mermaid-writing/references/diagrams/class.md +246 -0
  614. package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +384 -0
  615. package/skills/markdown-mermaid-writing/references/diagrams/er.md +222 -0
  616. package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +177 -0
  617. package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +138 -0
  618. package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +74 -0
  619. package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +107 -0
  620. package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +74 -0
  621. package/skills/markdown-mermaid-writing/references/diagrams/packet.md +55 -0
  622. package/skills/markdown-mermaid-writing/references/diagrams/pie.md +52 -0
  623. package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +66 -0
  624. package/skills/markdown-mermaid-writing/references/diagrams/radar.md +59 -0
  625. package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +88 -0
  626. package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +71 -0
  627. package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +174 -0
  628. package/skills/markdown-mermaid-writing/references/diagrams/state.md +150 -0
  629. package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +96 -0
  630. package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +66 -0
  631. package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +108 -0
  632. package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +53 -0
  633. package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +71 -0
  634. package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +733 -0
  635. package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +458 -0
  636. package/skills/markdown-mermaid-writing/templates/decision_record.md +211 -0
  637. package/skills/markdown-mermaid-writing/templates/how_to_guide.md +275 -0
  638. package/skills/markdown-mermaid-writing/templates/issue.md +303 -0
  639. package/skills/markdown-mermaid-writing/templates/kanban.md +223 -0
  640. package/skills/markdown-mermaid-writing/templates/presentation.md +312 -0
  641. package/skills/markdown-mermaid-writing/templates/project_documentation.md +412 -0
  642. package/skills/markdown-mermaid-writing/templates/pull_request.md +319 -0
  643. package/skills/markdown-mermaid-writing/templates/research_paper.md +304 -0
  644. package/skills/markdown-mermaid-writing/templates/status_report.md +185 -0
  645. package/skills/market-research-reports/SKILL.md +905 -0
  646. package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
  647. package/skills/market-research-reports/assets/market_report_template.tex +1380 -0
  648. package/skills/market-research-reports/assets/market_research.sty +564 -0
  649. package/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
  650. package/skills/market-research-reports/references/report_structure_guide.md +999 -0
  651. package/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
  652. package/skills/market-research-reports/scripts/generate_market_visuals.py +529 -0
  653. package/skills/markitdown/SKILL.md +488 -0
  654. package/skills/markitdown/assets/example_usage.md +463 -0
  655. package/skills/markitdown/references/api_reference.md +396 -0
  656. package/skills/markitdown/references/file_formats.md +542 -0
  657. package/skills/markitdown/scripts/batch_convert.py +228 -0
  658. package/skills/markitdown/scripts/convert_literature.py +283 -0
  659. package/skills/markitdown/scripts/convert_with_ai.py +240 -0
  660. package/skills/matchms/SKILL.md +201 -0
  661. package/skills/matchms/references/filtering.md +288 -0
  662. package/skills/matchms/references/importing_exporting.md +416 -0
  663. package/skills/matchms/references/similarity.md +380 -0
  664. package/skills/matchms/references/workflows.md +647 -0
  665. package/skills/matlab/SKILL.md +376 -0
  666. package/skills/matlab/references/data-import-export.md +479 -0
  667. package/skills/matlab/references/executing-scripts.md +444 -0
  668. package/skills/matlab/references/graphics-visualization.md +579 -0
  669. package/skills/matlab/references/mathematics.md +553 -0
  670. package/skills/matlab/references/matrices-arrays.md +349 -0
  671. package/skills/matlab/references/octave-compatibility.md +544 -0
  672. package/skills/matlab/references/programming.md +672 -0
  673. package/skills/matlab/references/python-integration.md +433 -0
  674. package/skills/matplotlib/SKILL.md +359 -0
  675. package/skills/matplotlib/references/api_reference.md +412 -0
  676. package/skills/matplotlib/references/common_issues.md +563 -0
  677. package/skills/matplotlib/references/plot_types.md +476 -0
  678. package/skills/matplotlib/references/styling_guide.md +589 -0
  679. package/skills/matplotlib/scripts/plot_template.py +401 -0
  680. package/skills/matplotlib/scripts/style_configurator.py +409 -0
  681. package/skills/medchem/SKILL.md +404 -0
  682. package/skills/medchem/references/api_guide.md +600 -0
  683. package/skills/medchem/references/rules_catalog.md +604 -0
  684. package/skills/medchem/scripts/filter_molecules.py +418 -0
  685. package/skills/metabolomics-workbench-database/SKILL.md +257 -0
  686. package/skills/metabolomics-workbench-database/references/api_reference.md +494 -0
  687. package/skills/modal/SKILL.md +406 -0
  688. package/skills/modal/references/api_reference.md +187 -0
  689. package/skills/modal/references/examples.md +266 -0
  690. package/skills/modal/references/functions.md +260 -0
  691. package/skills/modal/references/getting-started.md +175 -0
  692. package/skills/modal/references/gpu.md +174 -0
  693. package/skills/modal/references/images.md +259 -0
  694. package/skills/modal/references/resources.md +117 -0
  695. package/skills/modal/references/scaling.md +173 -0
  696. package/skills/modal/references/scheduled-jobs.md +143 -0
  697. package/skills/modal/references/secrets.md +119 -0
  698. package/skills/modal/references/volumes.md +247 -0
  699. package/skills/modal/references/web-endpoints.md +254 -0
  700. package/skills/modal-compute/SKILL.md +56 -0
  701. package/skills/molecular-dynamics/SKILL.md +457 -0
  702. package/skills/molecular-dynamics/references/mdanalysis_analysis.md +208 -0
  703. package/skills/molfeat/SKILL.md +509 -0
  704. package/skills/molfeat/references/api_reference.md +428 -0
  705. package/skills/molfeat/references/available_featurizers.md +333 -0
  706. package/skills/molfeat/references/examples.md +723 -0
  707. package/skills/monarch-database/SKILL.md +372 -0
  708. package/skills/monarch-database/references/phenotype_ontology.md +160 -0
  709. package/skills/networkx/SKILL.md +435 -0
  710. package/skills/networkx/references/algorithms.md +383 -0
  711. package/skills/networkx/references/generators.md +378 -0
  712. package/skills/networkx/references/graph-basics.md +283 -0
  713. package/skills/networkx/references/io.md +441 -0
  714. package/skills/networkx/references/visualization.md +529 -0
  715. package/skills/neurokit2/SKILL.md +354 -0
  716. package/skills/neurokit2/references/bio_module.md +417 -0
  717. package/skills/neurokit2/references/complexity.md +715 -0
  718. package/skills/neurokit2/references/ecg_cardiac.md +355 -0
  719. package/skills/neurokit2/references/eda.md +497 -0
  720. package/skills/neurokit2/references/eeg.md +506 -0
  721. package/skills/neurokit2/references/emg.md +408 -0
  722. package/skills/neurokit2/references/eog.md +407 -0
  723. package/skills/neurokit2/references/epochs_events.md +471 -0
  724. package/skills/neurokit2/references/hrv.md +480 -0
  725. package/skills/neurokit2/references/ppg.md +413 -0
  726. package/skills/neurokit2/references/rsp.md +510 -0
  727. package/skills/neurokit2/references/signal_processing.md +648 -0
  728. package/skills/neuropixels-analysis/SKILL.md +348 -0
  729. package/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
  730. package/skills/neuropixels-analysis/references/AI_CURATION.md +345 -0
  731. package/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
  732. package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +358 -0
  733. package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
  734. package/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
  735. package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
  736. package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
  737. package/skills/neuropixels-analysis/references/api_reference.md +415 -0
  738. package/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
  739. package/skills/neuropixels-analysis/references/standard_workflow.md +385 -0
  740. package/skills/neuropixels-analysis/scripts/compute_metrics.py +178 -0
  741. package/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
  742. package/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
  743. package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +432 -0
  744. package/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
  745. package/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
  746. package/skills/offer-k-dense-web/SKILL.md +21 -0
  747. package/skills/omero-integration/SKILL.md +249 -0
  748. package/skills/omero-integration/references/advanced.md +631 -0
  749. package/skills/omero-integration/references/connection.md +369 -0
  750. package/skills/omero-integration/references/data_access.md +544 -0
  751. package/skills/omero-integration/references/image_processing.md +665 -0
  752. package/skills/omero-integration/references/metadata.md +688 -0
  753. package/skills/omero-integration/references/rois.md +648 -0
  754. package/skills/omero-integration/references/scripts.md +637 -0
  755. package/skills/omero-integration/references/tables.md +532 -0
  756. package/skills/open-notebook/SKILL.md +289 -0
  757. package/skills/open-notebook/references/api_reference.md +715 -0
  758. package/skills/open-notebook/references/architecture.md +163 -0
  759. package/skills/open-notebook/references/configuration.md +226 -0
  760. package/skills/open-notebook/references/examples.md +290 -0
  761. package/skills/open-notebook/scripts/chat_interaction.py +190 -0
  762. package/skills/open-notebook/scripts/notebook_management.py +142 -0
  763. package/skills/open-notebook/scripts/source_ingestion.py +160 -0
  764. package/skills/open-notebook/scripts/test_open_notebook_skill.py +423 -0
  765. package/skills/openalex-database/SKILL.md +496 -0
  766. package/skills/openalex-database/references/api_guide.md +371 -0
  767. package/skills/openalex-database/references/common_queries.md +381 -0
  768. package/skills/openalex-database/scripts/openalex_client.py +337 -0
  769. package/skills/openalex-database/scripts/query_helpers.py +306 -0
  770. package/skills/opentargets-database/SKILL.md +371 -0
  771. package/skills/opentargets-database/references/api_reference.md +249 -0
  772. package/skills/opentargets-database/references/evidence_types.md +306 -0
  773. package/skills/opentargets-database/references/target_annotations.md +401 -0
  774. package/skills/opentargets-database/scripts/query_opentargets.py +403 -0
  775. package/skills/opentrons-integration/SKILL.md +571 -0
  776. package/skills/opentrons-integration/references/api_reference.md +366 -0
  777. package/skills/opentrons-integration/scripts/basic_protocol_template.py +67 -0
  778. package/skills/opentrons-integration/scripts/pcr_setup_template.py +154 -0
  779. package/skills/opentrons-integration/scripts/serial_dilution_template.py +96 -0
  780. package/skills/paper-2-web/SKILL.md +495 -0
  781. package/skills/paper-2-web/references/installation.md +141 -0
  782. package/skills/paper-2-web/references/paper2poster.md +346 -0
  783. package/skills/paper-2-web/references/paper2video.md +305 -0
  784. package/skills/paper-2-web/references/paper2web.md +187 -0
  785. package/skills/paper-2-web/references/usage_examples.md +436 -0
  786. package/skills/paper-code-audit/SKILL.md +12 -0
  787. package/skills/paper-writing/SKILL.md +12 -0
  788. package/skills/parallel-web/SKILL.md +314 -0
  789. package/skills/parallel-web/references/api_reference.md +244 -0
  790. package/skills/parallel-web/references/deep_research_guide.md +362 -0
  791. package/skills/parallel-web/references/extraction_patterns.md +338 -0
  792. package/skills/parallel-web/references/search_best_practices.md +297 -0
  793. package/skills/parallel-web/references/workflow_recipes.md +456 -0
  794. package/skills/parallel-web/scripts/parallel_web.py +568 -0
  795. package/skills/parse-document/SKILL.md +139 -0
  796. package/skills/pathml/SKILL.md +164 -0
  797. package/skills/pathml/references/data_management.md +742 -0
  798. package/skills/pathml/references/graphs.md +653 -0
  799. package/skills/pathml/references/image_loading.md +448 -0
  800. package/skills/pathml/references/machine_learning.md +725 -0
  801. package/skills/pathml/references/multiparametric.md +686 -0
  802. package/skills/pathml/references/preprocessing.md +722 -0
  803. package/skills/pdb-database/SKILL.md +307 -0
  804. package/skills/pdb-database/references/api_reference.md +617 -0
  805. package/skills/pdf/LICENSE.txt +30 -0
  806. package/skills/pdf/SKILL.md +314 -0
  807. package/skills/pdf/forms.md +294 -0
  808. package/skills/pdf/reference.md +612 -0
  809. package/skills/pdf/scripts/check_bounding_boxes.py +65 -0
  810. package/skills/pdf/scripts/check_fillable_fields.py +11 -0
  811. package/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
  812. package/skills/pdf/scripts/create_validation_image.py +37 -0
  813. package/skills/pdf/scripts/extract_form_field_info.py +122 -0
  814. package/skills/pdf/scripts/extract_form_structure.py +115 -0
  815. package/skills/pdf/scripts/fill_fillable_fields.py +98 -0
  816. package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
  817. package/skills/peer-review/SKILL.md +569 -0
  818. package/skills/peer-review/references/common_issues.md +552 -0
  819. package/skills/peer-review/references/reporting_standards.md +290 -0
  820. package/skills/pennylane/SKILL.md +224 -0
  821. package/skills/pennylane/references/advanced_features.md +667 -0
  822. package/skills/pennylane/references/devices_backends.md +596 -0
  823. package/skills/pennylane/references/getting_started.md +227 -0
  824. package/skills/pennylane/references/optimization.md +671 -0
  825. package/skills/pennylane/references/quantum_chemistry.md +567 -0
  826. package/skills/pennylane/references/quantum_circuits.md +437 -0
  827. package/skills/pennylane/references/quantum_ml.md +571 -0
  828. package/skills/perplexity-search/SKILL.md +446 -0
  829. package/skills/perplexity-search/assets/.env.example +16 -0
  830. package/skills/perplexity-search/references/model_comparison.md +386 -0
  831. package/skills/perplexity-search/references/openrouter_setup.md +454 -0
  832. package/skills/perplexity-search/references/search_strategies.md +258 -0
  833. package/skills/perplexity-search/scripts/perplexity_search.py +277 -0
  834. package/skills/perplexity-search/scripts/setup_env.py +171 -0
  835. package/skills/phylogenetics/SKILL.md +404 -0
  836. package/skills/phylogenetics/references/iqtree_inference.md +181 -0
  837. package/skills/phylogenetics/scripts/phylogenetic_analysis.py +270 -0
  838. package/skills/plotly/SKILL.md +265 -0
  839. package/skills/plotly/references/chart-types.md +488 -0
  840. package/skills/plotly/references/export-interactivity.md +453 -0
  841. package/skills/plotly/references/graph-objects.md +302 -0
  842. package/skills/plotly/references/layouts-styling.md +457 -0
  843. package/skills/plotly/references/plotly-express.md +213 -0
  844. package/skills/polars/SKILL.md +385 -0
  845. package/skills/polars/references/best_practices.md +649 -0
  846. package/skills/polars/references/core_concepts.md +378 -0
  847. package/skills/polars/references/io_guide.md +557 -0
  848. package/skills/polars/references/operations.md +602 -0
  849. package/skills/polars/references/pandas_migration.md +417 -0
  850. package/skills/polars/references/transformations.md +549 -0
  851. package/skills/polars-bio/SKILL.md +374 -0
  852. package/skills/polars-bio/references/bioframe_migration.md +250 -0
  853. package/skills/polars-bio/references/configuration.md +175 -0
  854. package/skills/polars-bio/references/file_io.md +414 -0
  855. package/skills/polars-bio/references/interval_operations.md +362 -0
  856. package/skills/polars-bio/references/pileup_operations.md +176 -0
  857. package/skills/polars-bio/references/sql_processing.md +224 -0
  858. package/skills/pptx/LICENSE.txt +30 -0
  859. package/skills/pptx/SKILL.md +232 -0
  860. package/skills/pptx/editing.md +205 -0
  861. package/skills/pptx/pptxgenjs.md +420 -0
  862. package/skills/pptx/scripts/__init__.py +0 -0
  863. package/skills/pptx/scripts/add_slide.py +195 -0
  864. package/skills/pptx/scripts/clean.py +286 -0
  865. package/skills/pptx/scripts/office/helpers/__init__.py +0 -0
  866. package/skills/pptx/scripts/office/helpers/merge_runs.py +199 -0
  867. package/skills/pptx/scripts/office/helpers/simplify_redlines.py +197 -0
  868. package/skills/pptx/scripts/office/pack.py +159 -0
  869. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  870. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  871. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  872. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  873. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  874. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  875. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  876. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  877. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  878. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  879. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  880. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  881. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  882. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  883. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  884. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  885. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  886. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  887. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  888. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  889. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  890. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  891. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  892. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  893. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  894. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  895. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  896. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  897. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  898. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  899. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  900. package/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
  901. package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  902. package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  903. package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  904. package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  905. package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  906. package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  907. package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  908. package/skills/pptx/scripts/office/soffice.py +183 -0
  909. package/skills/pptx/scripts/office/unpack.py +132 -0
  910. package/skills/pptx/scripts/office/validate.py +111 -0
  911. package/skills/pptx/scripts/office/validators/__init__.py +15 -0
  912. package/skills/pptx/scripts/office/validators/base.py +847 -0
  913. package/skills/pptx/scripts/office/validators/docx.py +446 -0
  914. package/skills/pptx/scripts/office/validators/pptx.py +275 -0
  915. package/skills/pptx/scripts/office/validators/redlining.py +247 -0
  916. package/skills/pptx/scripts/thumbnail.py +289 -0
  917. package/skills/pptx-posters/SKILL.md +414 -0
  918. package/skills/pptx-posters/assets/poster_html_template.html +257 -0
  919. package/skills/pptx-posters/assets/poster_quality_checklist.md +358 -0
  920. package/skills/pptx-posters/references/poster_content_guide.md +748 -0
  921. package/skills/pptx-posters/references/poster_design_principles.md +806 -0
  922. package/skills/pptx-posters/references/poster_layout_design.md +900 -0
  923. package/skills/preview/SKILL.md +27 -0
  924. package/skills/primekg/SKILL.md +97 -0
  925. package/skills/primekg/scripts/query_primekg.py +123 -0
  926. package/skills/protocolsio-integration/SKILL.md +419 -0
  927. package/skills/protocolsio-integration/references/additional_features.md +387 -0
  928. package/skills/protocolsio-integration/references/authentication.md +100 -0
  929. package/skills/protocolsio-integration/references/discussions.md +225 -0
  930. package/skills/protocolsio-integration/references/file_manager.md +412 -0
  931. package/skills/protocolsio-integration/references/protocols_api.md +294 -0
  932. package/skills/protocolsio-integration/references/workspaces.md +293 -0
  933. package/skills/pubchem-database/SKILL.md +572 -0
  934. package/skills/pubchem-database/references/api_reference.md +440 -0
  935. package/skills/pubchem-database/scripts/bioactivity_query.py +367 -0
  936. package/skills/pubchem-database/scripts/compound_search.py +297 -0
  937. package/skills/pubmed-database/SKILL.md +458 -0
  938. package/skills/pubmed-database/references/api_reference.md +298 -0
  939. package/skills/pubmed-database/references/common_queries.md +453 -0
  940. package/skills/pubmed-database/references/search_syntax.md +436 -0
  941. package/skills/pufferlib/SKILL.md +434 -0
  942. package/skills/pufferlib/references/environments.md +508 -0
  943. package/skills/pufferlib/references/integration.md +621 -0
  944. package/skills/pufferlib/references/policies.md +653 -0
  945. package/skills/pufferlib/references/training.md +360 -0
  946. package/skills/pufferlib/references/vectorization.md +557 -0
  947. package/skills/pufferlib/scripts/env_template.py +340 -0
  948. package/skills/pufferlib/scripts/train_template.py +239 -0
  949. package/skills/pydeseq2/SKILL.md +557 -0
  950. package/skills/pydeseq2/references/api_reference.md +228 -0
  951. package/skills/pydeseq2/references/workflow_guide.md +582 -0
  952. package/skills/pydeseq2/scripts/run_deseq2_analysis.py +353 -0
  953. package/skills/pydicom/SKILL.md +432 -0
  954. package/skills/pydicom/references/common_tags.md +228 -0
  955. package/skills/pydicom/references/transfer_syntaxes.md +352 -0
  956. package/skills/pydicom/scripts/anonymize_dicom.py +137 -0
  957. package/skills/pydicom/scripts/dicom_to_image.py +172 -0
  958. package/skills/pydicom/scripts/extract_metadata.py +173 -0
  959. package/skills/pyhealth/SKILL.md +489 -0
  960. package/skills/pyhealth/references/datasets.md +178 -0
  961. package/skills/pyhealth/references/medical_coding.md +284 -0
  962. package/skills/pyhealth/references/models.md +594 -0
  963. package/skills/pyhealth/references/preprocessing.md +638 -0
  964. package/skills/pyhealth/references/tasks.md +379 -0
  965. package/skills/pyhealth/references/training_evaluation.md +648 -0
  966. package/skills/pylabrobot/SKILL.md +183 -0
  967. package/skills/pylabrobot/references/analytical-equipment.md +464 -0
  968. package/skills/pylabrobot/references/hardware-backends.md +480 -0
  969. package/skills/pylabrobot/references/liquid-handling.md +403 -0
  970. package/skills/pylabrobot/references/material-handling.md +620 -0
  971. package/skills/pylabrobot/references/resources.md +489 -0
  972. package/skills/pylabrobot/references/visualization.md +532 -0
  973. package/skills/pymatgen/SKILL.md +689 -0
  974. package/skills/pymatgen/references/analysis_modules.md +530 -0
  975. package/skills/pymatgen/references/core_classes.md +318 -0
  976. package/skills/pymatgen/references/io_formats.md +469 -0
  977. package/skills/pymatgen/references/materials_project_api.md +517 -0
  978. package/skills/pymatgen/references/transformations_workflows.md +591 -0
  979. package/skills/pymatgen/scripts/phase_diagram_generator.py +233 -0
  980. package/skills/pymatgen/scripts/structure_analyzer.py +266 -0
  981. package/skills/pymatgen/scripts/structure_converter.py +169 -0
  982. package/skills/pymc/SKILL.md +570 -0
  983. package/skills/pymc/assets/hierarchical_model_template.py +333 -0
  984. package/skills/pymc/assets/linear_regression_template.py +241 -0
  985. package/skills/pymc/references/distributions.md +320 -0
  986. package/skills/pymc/references/sampling_inference.md +424 -0
  987. package/skills/pymc/references/workflows.md +526 -0
  988. package/skills/pymc/scripts/model_comparison.py +387 -0
  989. package/skills/pymc/scripts/model_diagnostics.py +350 -0
  990. package/skills/pymoo/SKILL.md +569 -0
  991. package/skills/pymoo/references/algorithms.md +180 -0
  992. package/skills/pymoo/references/constraints_mcdm.md +417 -0
  993. package/skills/pymoo/references/operators.md +345 -0
  994. package/skills/pymoo/references/problems.md +265 -0
  995. package/skills/pymoo/references/visualization.md +353 -0
  996. package/skills/pymoo/scripts/custom_problem_example.py +181 -0
  997. package/skills/pymoo/scripts/decision_making_example.py +161 -0
  998. package/skills/pymoo/scripts/many_objective_example.py +72 -0
  999. package/skills/pymoo/scripts/multi_objective_example.py +63 -0
  1000. package/skills/pymoo/scripts/single_objective_example.py +59 -0
  1001. package/skills/pyopenms/SKILL.md +215 -0
  1002. package/skills/pyopenms/references/data_structures.md +497 -0
  1003. package/skills/pyopenms/references/feature_detection.md +410 -0
  1004. package/skills/pyopenms/references/file_io.md +349 -0
  1005. package/skills/pyopenms/references/identification.md +422 -0
  1006. package/skills/pyopenms/references/metabolomics.md +482 -0
  1007. package/skills/pyopenms/references/signal_processing.md +433 -0
  1008. package/skills/pysam/SKILL.md +263 -0
  1009. package/skills/pysam/references/alignment_files.md +280 -0
  1010. package/skills/pysam/references/common_workflows.md +520 -0
  1011. package/skills/pysam/references/sequence_files.md +407 -0
  1012. package/skills/pysam/references/variant_files.md +365 -0
  1013. package/skills/pytdc/SKILL.md +458 -0
  1014. package/skills/pytdc/references/datasets.md +246 -0
  1015. package/skills/pytdc/references/oracles.md +400 -0
  1016. package/skills/pytdc/references/utilities.md +684 -0
  1017. package/skills/pytdc/scripts/benchmark_evaluation.py +327 -0
  1018. package/skills/pytdc/scripts/load_and_split_data.py +214 -0
  1019. package/skills/pytdc/scripts/molecular_generation.py +404 -0
  1020. package/skills/pytorch-lightning/SKILL.md +172 -0
  1021. package/skills/pytorch-lightning/references/best_practices.md +724 -0
  1022. package/skills/pytorch-lightning/references/callbacks.md +564 -0
  1023. package/skills/pytorch-lightning/references/data_module.md +565 -0
  1024. package/skills/pytorch-lightning/references/distributed_training.md +643 -0
  1025. package/skills/pytorch-lightning/references/lightning_module.md +487 -0
  1026. package/skills/pytorch-lightning/references/logging.md +654 -0
  1027. package/skills/pytorch-lightning/references/trainer.md +641 -0
  1028. package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +454 -0
  1029. package/skills/pytorch-lightning/scripts/template_datamodule.py +328 -0
  1030. package/skills/pytorch-lightning/scripts/template_lightning_module.py +219 -0
  1031. package/skills/pyzotero/SKILL.md +111 -0
  1032. package/skills/pyzotero/references/authentication.md +90 -0
  1033. package/skills/pyzotero/references/cli.md +100 -0
  1034. package/skills/pyzotero/references/collections.md +113 -0
  1035. package/skills/pyzotero/references/error-handling.md +103 -0
  1036. package/skills/pyzotero/references/exports.md +102 -0
  1037. package/skills/pyzotero/references/files-attachments.md +97 -0
  1038. package/skills/pyzotero/references/full-text.md +68 -0
  1039. package/skills/pyzotero/references/pagination.md +79 -0
  1040. package/skills/pyzotero/references/read-api.md +137 -0
  1041. package/skills/pyzotero/references/saved-searches.md +77 -0
  1042. package/skills/pyzotero/references/search-params.md +90 -0
  1043. package/skills/pyzotero/references/tags.md +87 -0
  1044. package/skills/pyzotero/references/write-api.md +123 -0
  1045. package/skills/qiskit/SKILL.md +273 -0
  1046. package/skills/qiskit/references/algorithms.md +607 -0
  1047. package/skills/qiskit/references/backends.md +433 -0
  1048. package/skills/qiskit/references/circuits.md +197 -0
  1049. package/skills/qiskit/references/patterns.md +533 -0
  1050. package/skills/qiskit/references/primitives.md +277 -0
  1051. package/skills/qiskit/references/setup.md +99 -0
  1052. package/skills/qiskit/references/transpilation.md +286 -0
  1053. package/skills/qiskit/references/visualization.md +415 -0
  1054. package/skills/qutip/SKILL.md +316 -0
  1055. package/skills/qutip/references/advanced.md +555 -0
  1056. package/skills/qutip/references/analysis.md +523 -0
  1057. package/skills/qutip/references/core_concepts.md +293 -0
  1058. package/skills/qutip/references/time_evolution.md +348 -0
  1059. package/skills/qutip/references/visualization.md +431 -0
  1060. package/skills/rdkit/SKILL.md +778 -0
  1061. package/skills/rdkit/references/api_reference.md +432 -0
  1062. package/skills/rdkit/references/descriptors_reference.md +595 -0
  1063. package/skills/rdkit/references/smarts_patterns.md +668 -0
  1064. package/skills/rdkit/scripts/molecular_properties.py +243 -0
  1065. package/skills/rdkit/scripts/similarity_search.py +297 -0
  1066. package/skills/rdkit/scripts/substructure_filter.py +386 -0
  1067. package/skills/reactome-database/SKILL.md +276 -0
  1068. package/skills/reactome-database/references/api_reference.md +465 -0
  1069. package/skills/reactome-database/scripts/reactome_query.py +286 -0
  1070. package/skills/replication/SKILL.md +14 -0
  1071. package/skills/research-grants/SKILL.md +955 -0
  1072. package/skills/research-grants/assets/budget_justification_template.md +453 -0
  1073. package/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  1074. package/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  1075. package/skills/research-grants/references/README.md +285 -0
  1076. package/skills/research-grants/references/broader_impacts.md +392 -0
  1077. package/skills/research-grants/references/darpa_guidelines.md +636 -0
  1078. package/skills/research-grants/references/doe_guidelines.md +586 -0
  1079. package/skills/research-grants/references/nih_guidelines.md +851 -0
  1080. package/skills/research-grants/references/nsf_guidelines.md +570 -0
  1081. package/skills/research-grants/references/nstc_guidelines.md +733 -0
  1082. package/skills/research-grants/references/specific_aims_guide.md +458 -0
  1083. package/skills/research-lookup/README.md +156 -0
  1084. package/skills/research-lookup/SKILL.md +413 -0
  1085. package/skills/research-lookup/examples.py +174 -0
  1086. package/skills/research-lookup/lookup.py +187 -0
  1087. package/skills/research-lookup/research_lookup.py +566 -0
  1088. package/skills/research-lookup/scripts/research_lookup.py +566 -0
  1089. package/skills/rowan/SKILL.md +427 -0
  1090. package/skills/rowan/references/api_reference.md +413 -0
  1091. package/skills/rowan/references/molecule_handling.md +429 -0
  1092. package/skills/rowan/references/proteins_and_organization.md +499 -0
  1093. package/skills/rowan/references/rdkit_native.md +438 -0
  1094. package/skills/rowan/references/results_interpretation.md +481 -0
  1095. package/skills/rowan/references/workflow_types.md +591 -0
  1096. package/skills/runpod-compute/SKILL.md +48 -0
  1097. package/skills/scanpy/SKILL.md +384 -0
  1098. package/skills/scanpy/assets/analysis_template.py +295 -0
  1099. package/skills/scanpy/references/api_reference.md +251 -0
  1100. package/skills/scanpy/references/plotting_guide.md +352 -0
  1101. package/skills/scanpy/references/standard_workflow.md +206 -0
  1102. package/skills/scanpy/scripts/qc_analysis.py +200 -0
  1103. package/skills/scholar-evaluation/SKILL.md +298 -0
  1104. package/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  1105. package/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  1106. package/skills/scientific-brainstorming/SKILL.md +189 -0
  1107. package/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
  1108. package/skills/scientific-critical-thinking/SKILL.md +570 -0
  1109. package/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  1110. package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  1111. package/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  1112. package/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  1113. package/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  1114. package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  1115. package/skills/scientific-schematics/SKILL.md +619 -0
  1116. package/skills/scientific-schematics/references/QUICK_REFERENCE.md +207 -0
  1117. package/skills/scientific-schematics/references/README.md +327 -0
  1118. package/skills/scientific-schematics/references/best_practices.md +560 -0
  1119. package/skills/scientific-schematics/scripts/example_usage.sh +89 -0
  1120. package/skills/scientific-schematics/scripts/generate_schematic.py +139 -0
  1121. package/skills/scientific-schematics/scripts/generate_schematic_ai.py +844 -0
  1122. package/skills/scientific-slides/SKILL.md +1154 -0
  1123. package/skills/scientific-slides/assets/beamer_template_conference.tex +407 -0
  1124. package/skills/scientific-slides/assets/beamer_template_defense.tex +906 -0
  1125. package/skills/scientific-slides/assets/beamer_template_seminar.tex +870 -0
  1126. package/skills/scientific-slides/assets/powerpoint_design_guide.md +662 -0
  1127. package/skills/scientific-slides/assets/timing_guidelines.md +597 -0
  1128. package/skills/scientific-slides/references/beamer_guide.md +1019 -0
  1129. package/skills/scientific-slides/references/data_visualization_slides.md +708 -0
  1130. package/skills/scientific-slides/references/presentation_structure.md +642 -0
  1131. package/skills/scientific-slides/references/slide_design_principles.md +849 -0
  1132. package/skills/scientific-slides/references/talk_types_guide.md +687 -0
  1133. package/skills/scientific-slides/references/visual_review_workflow.md +775 -0
  1134. package/skills/scientific-slides/scripts/generate_slide_image.py +140 -0
  1135. package/skills/scientific-slides/scripts/generate_slide_image_ai.py +763 -0
  1136. package/skills/scientific-slides/scripts/pdf_to_images.py +221 -0
  1137. package/skills/scientific-slides/scripts/slides_to_pdf.py +235 -0
  1138. package/skills/scientific-slides/scripts/validate_presentation.py +403 -0
  1139. package/skills/scientific-visualization/SKILL.md +777 -0
  1140. package/skills/scientific-visualization/assets/color_palettes.py +197 -0
  1141. package/skills/scientific-visualization/assets/nature.mplstyle +63 -0
  1142. package/skills/scientific-visualization/assets/presentation.mplstyle +61 -0
  1143. package/skills/scientific-visualization/assets/publication.mplstyle +68 -0
  1144. package/skills/scientific-visualization/references/color_palettes.md +348 -0
  1145. package/skills/scientific-visualization/references/journal_requirements.md +320 -0
  1146. package/skills/scientific-visualization/references/matplotlib_examples.md +620 -0
  1147. package/skills/scientific-visualization/references/publication_guidelines.md +205 -0
  1148. package/skills/scientific-visualization/scripts/figure_export.py +343 -0
  1149. package/skills/scientific-visualization/scripts/style_presets.py +416 -0
  1150. package/skills/scientific-workflows/SKILL.md +1684 -0
  1151. package/skills/scientific-writing/SKILL.md +718 -0
  1152. package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +574 -0
  1153. package/skills/scientific-writing/assets/scientific_report.sty +606 -0
  1154. package/skills/scientific-writing/assets/scientific_report_template.tex +449 -0
  1155. package/skills/scientific-writing/references/citation_styles.md +720 -0
  1156. package/skills/scientific-writing/references/figures_tables.md +806 -0
  1157. package/skills/scientific-writing/references/imrad_structure.md +686 -0
  1158. package/skills/scientific-writing/references/professional_report_formatting.md +664 -0
  1159. package/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  1160. package/skills/scientific-writing/references/writing_principles.md +824 -0
  1161. package/skills/scikit-bio/SKILL.md +435 -0
  1162. package/skills/scikit-bio/references/api_reference.md +749 -0
  1163. package/skills/scikit-learn/SKILL.md +519 -0
  1164. package/skills/scikit-learn/references/model_evaluation.md +592 -0
  1165. package/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
  1166. package/skills/scikit-learn/references/preprocessing.md +606 -0
  1167. package/skills/scikit-learn/references/quick_reference.md +433 -0
  1168. package/skills/scikit-learn/references/supervised_learning.md +378 -0
  1169. package/skills/scikit-learn/references/unsupervised_learning.md +505 -0
  1170. package/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
  1171. package/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
  1172. package/skills/scikit-survival/SKILL.md +397 -0
  1173. package/skills/scikit-survival/references/competing-risks.md +397 -0
  1174. package/skills/scikit-survival/references/cox-models.md +182 -0
  1175. package/skills/scikit-survival/references/data-handling.md +494 -0
  1176. package/skills/scikit-survival/references/ensemble-models.md +327 -0
  1177. package/skills/scikit-survival/references/evaluation-metrics.md +378 -0
  1178. package/skills/scikit-survival/references/svm-models.md +411 -0
  1179. package/skills/scvelo/SKILL.md +321 -0
  1180. package/skills/scvelo/references/velocity_models.md +168 -0
  1181. package/skills/scvelo/scripts/rna_velocity_workflow.py +232 -0
  1182. package/skills/scvi-tools/SKILL.md +188 -0
  1183. package/skills/scvi-tools/references/differential-expression.md +581 -0
  1184. package/skills/scvi-tools/references/models-atac-seq.md +321 -0
  1185. package/skills/scvi-tools/references/models-multimodal.md +367 -0
  1186. package/skills/scvi-tools/references/models-scrna-seq.md +330 -0
  1187. package/skills/scvi-tools/references/models-spatial.md +438 -0
  1188. package/skills/scvi-tools/references/models-specialized.md +408 -0
  1189. package/skills/scvi-tools/references/theoretical-foundations.md +438 -0
  1190. package/skills/scvi-tools/references/workflows.md +546 -0
  1191. package/skills/seaborn/SKILL.md +671 -0
  1192. package/skills/seaborn/references/examples.md +822 -0
  1193. package/skills/seaborn/references/function_reference.md +770 -0
  1194. package/skills/seaborn/references/objects_interface.md +964 -0
  1195. package/skills/semantic-scholar/SKILL.md +123 -0
  1196. package/skills/session-log/SKILL.md +10 -0
  1197. package/skills/session-search/SKILL.md +26 -0
  1198. package/skills/setup/SKILL.md +216 -0
  1199. package/skills/shap/SKILL.md +564 -0
  1200. package/skills/shap/references/explainers.md +339 -0
  1201. package/skills/shap/references/plots.md +507 -0
  1202. package/skills/shap/references/theory.md +449 -0
  1203. package/skills/shap/references/workflows.md +605 -0
  1204. package/skills/simpy/SKILL.md +427 -0
  1205. package/skills/simpy/references/events.md +374 -0
  1206. package/skills/simpy/references/monitoring.md +475 -0
  1207. package/skills/simpy/references/process-interaction.md +424 -0
  1208. package/skills/simpy/references/real-time.md +395 -0
  1209. package/skills/simpy/references/resources.md +275 -0
  1210. package/skills/simpy/scripts/basic_simulation_template.py +193 -0
  1211. package/skills/simpy/scripts/resource_monitor.py +345 -0
  1212. package/skills/source-comparison/SKILL.md +12 -0
  1213. package/skills/stable-baselines3/SKILL.md +297 -0
  1214. package/skills/stable-baselines3/references/algorithms.md +333 -0
  1215. package/skills/stable-baselines3/references/callbacks.md +556 -0
  1216. package/skills/stable-baselines3/references/custom_environments.md +526 -0
  1217. package/skills/stable-baselines3/references/vectorized_envs.md +568 -0
  1218. package/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
  1219. package/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
  1220. package/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
  1221. package/skills/statistical-analysis/SKILL.md +630 -0
  1222. package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
  1223. package/skills/statistical-analysis/references/bayesian_statistics.md +661 -0
  1224. package/skills/statistical-analysis/references/effect_sizes_and_power.md +581 -0
  1225. package/skills/statistical-analysis/references/reporting_standards.md +469 -0
  1226. package/skills/statistical-analysis/references/test_selection_guide.md +129 -0
  1227. package/skills/statistical-analysis/scripts/assumption_checks.py +539 -0
  1228. package/skills/statsmodels/SKILL.md +612 -0
  1229. package/skills/statsmodels/references/discrete_choice.md +669 -0
  1230. package/skills/statsmodels/references/glm.md +619 -0
  1231. package/skills/statsmodels/references/linear_models.md +447 -0
  1232. package/skills/statsmodels/references/stats_diagnostics.md +859 -0
  1233. package/skills/statsmodels/references/time_series.md +716 -0
  1234. package/skills/string-database/SKILL.md +532 -0
  1235. package/skills/string-database/references/string_reference.md +455 -0
  1236. package/skills/string-database/scripts/string_api.py +369 -0
  1237. package/skills/sympy/SKILL.md +498 -0
  1238. package/skills/sympy/references/advanced-topics.md +635 -0
  1239. package/skills/sympy/references/code-generation-printing.md +599 -0
  1240. package/skills/sympy/references/core-capabilities.md +348 -0
  1241. package/skills/sympy/references/matrices-linear-algebra.md +526 -0
  1242. package/skills/sympy/references/physics-mechanics.md +592 -0
  1243. package/skills/tiledbvcf/SKILL.md +459 -0
  1244. package/skills/timesfm-forecasting/SKILL.md +785 -0
  1245. package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +524 -0
  1246. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +448 -0
  1247. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
  1248. package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +568 -0
  1249. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
  1250. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +59 -0
  1251. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +109 -0
  1252. package/skills/timesfm-forecasting/examples/global-temperature/README.md +178 -0
  1253. package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +147 -0
  1254. package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +248 -0
  1255. package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +544 -0
  1256. package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +5441 -0
  1257. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
  1258. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +13 -0
  1259. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +188 -0
  1260. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
  1261. package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +5939 -0
  1262. package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +53 -0
  1263. package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +167 -0
  1264. package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +37 -0
  1265. package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +123 -0
  1266. package/skills/timesfm-forecasting/references/api_reference.md +231 -0
  1267. package/skills/timesfm-forecasting/references/data_preparation.md +272 -0
  1268. package/skills/timesfm-forecasting/references/system_requirements.md +201 -0
  1269. package/skills/timesfm-forecasting/scripts/check_system.py +520 -0
  1270. package/skills/timesfm-forecasting/scripts/forecast_csv.py +269 -0
  1271. package/skills/torch-geometric/SKILL.md +674 -0
  1272. package/skills/torch-geometric/references/datasets_reference.md +574 -0
  1273. package/skills/torch-geometric/references/layers_reference.md +485 -0
  1274. package/skills/torch-geometric/references/transforms_reference.md +679 -0
  1275. package/skills/torch-geometric/scripts/benchmark_model.py +309 -0
  1276. package/skills/torch-geometric/scripts/create_gnn_template.py +529 -0
  1277. package/skills/torch-geometric/scripts/visualize_graph.py +313 -0
  1278. package/skills/torchdrug/SKILL.md +448 -0
  1279. package/skills/torchdrug/references/core_concepts.md +565 -0
  1280. package/skills/torchdrug/references/datasets.md +380 -0
  1281. package/skills/torchdrug/references/knowledge_graphs.md +320 -0
  1282. package/skills/torchdrug/references/models_architectures.md +541 -0
  1283. package/skills/torchdrug/references/molecular_generation.md +352 -0
  1284. package/skills/torchdrug/references/molecular_property_prediction.md +169 -0
  1285. package/skills/torchdrug/references/protein_modeling.md +272 -0
  1286. package/skills/torchdrug/references/retrosynthesis.md +436 -0
  1287. package/skills/transformers/SKILL.md +162 -0
  1288. package/skills/transformers/references/generation.md +467 -0
  1289. package/skills/transformers/references/models.md +361 -0
  1290. package/skills/transformers/references/pipelines.md +335 -0
  1291. package/skills/transformers/references/tokenizers.md +447 -0
  1292. package/skills/transformers/references/training.md +500 -0
  1293. package/skills/treatment-plans/SKILL.md +1580 -0
  1294. package/skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md +185 -0
  1295. package/skills/treatment-plans/assets/chronic_disease_management_plan.tex +665 -0
  1296. package/skills/treatment-plans/assets/general_medical_treatment_plan.tex +547 -0
  1297. package/skills/treatment-plans/assets/medical_treatment_plan.sty +222 -0
  1298. package/skills/treatment-plans/assets/mental_health_treatment_plan.tex +774 -0
  1299. package/skills/treatment-plans/assets/one_page_treatment_plan.tex +193 -0
  1300. package/skills/treatment-plans/assets/pain_management_plan.tex +799 -0
  1301. package/skills/treatment-plans/assets/perioperative_care_plan.tex +753 -0
  1302. package/skills/treatment-plans/assets/quality_checklist.md +471 -0
  1303. package/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
  1304. package/skills/treatment-plans/references/README.md +488 -0
  1305. package/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  1306. package/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  1307. package/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  1308. package/skills/treatment-plans/references/specialty_specific_guidelines.md +655 -0
  1309. package/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
  1310. package/skills/treatment-plans/scripts/check_completeness.py +318 -0
  1311. package/skills/treatment-plans/scripts/generate_template.py +244 -0
  1312. package/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  1313. package/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  1314. package/skills/umap-learn/SKILL.md +477 -0
  1315. package/skills/umap-learn/references/api_reference.md +532 -0
  1316. package/skills/uniprot-database/SKILL.md +193 -0
  1317. package/skills/uniprot-database/references/api_examples.md +413 -0
  1318. package/skills/uniprot-database/references/api_fields.md +275 -0
  1319. package/skills/uniprot-database/references/id_mapping_databases.md +285 -0
  1320. package/skills/uniprot-database/references/query_syntax.md +256 -0
  1321. package/skills/uniprot-database/scripts/uniprot_client.py +341 -0
  1322. package/skills/usfiscaldata/SKILL.md +163 -0
  1323. package/skills/usfiscaldata/references/api-basics.md +86 -0
  1324. package/skills/usfiscaldata/references/datasets-debt.md +163 -0
  1325. package/skills/usfiscaldata/references/datasets-fiscal.md +196 -0
  1326. package/skills/usfiscaldata/references/datasets-interest-rates.md +182 -0
  1327. package/skills/usfiscaldata/references/datasets-securities.md +216 -0
  1328. package/skills/usfiscaldata/references/examples.md +258 -0
  1329. package/skills/usfiscaldata/references/parameters.md +155 -0
  1330. package/skills/usfiscaldata/references/response-format.md +176 -0
  1331. package/skills/uspto-database/SKILL.md +605 -0
  1332. package/skills/uspto-database/references/additional_apis.md +394 -0
  1333. package/skills/uspto-database/references/patentsearch_api.md +266 -0
  1334. package/skills/uspto-database/references/peds_api.md +212 -0
  1335. package/skills/uspto-database/references/trademark_api.md +358 -0
  1336. package/skills/uspto-database/scripts/patent_search.py +290 -0
  1337. package/skills/uspto-database/scripts/peds_client.py +285 -0
  1338. package/skills/uspto-database/scripts/trademark_client.py +311 -0
  1339. package/skills/vaex/SKILL.md +180 -0
  1340. package/skills/vaex/references/core_dataframes.md +367 -0
  1341. package/skills/vaex/references/data_processing.md +555 -0
  1342. package/skills/vaex/references/io_operations.md +703 -0
  1343. package/skills/vaex/references/machine_learning.md +728 -0
  1344. package/skills/vaex/references/performance.md +571 -0
  1345. package/skills/vaex/references/visualization.md +613 -0
  1346. package/skills/venue-templates/SKILL.md +688 -0
  1347. package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
  1348. package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
  1349. package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
  1350. package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
  1351. package/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  1352. package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  1353. package/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  1354. package/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  1355. package/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  1356. package/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  1357. package/skills/venue-templates/references/cell_press_style.md +483 -0
  1358. package/skills/venue-templates/references/conferences_formatting.md +564 -0
  1359. package/skills/venue-templates/references/cs_conference_style.md +463 -0
  1360. package/skills/venue-templates/references/grants_requirements.md +787 -0
  1361. package/skills/venue-templates/references/journals_formatting.md +486 -0
  1362. package/skills/venue-templates/references/medical_journal_styles.md +535 -0
  1363. package/skills/venue-templates/references/ml_conference_style.md +556 -0
  1364. package/skills/venue-templates/references/nature_science_style.md +405 -0
  1365. package/skills/venue-templates/references/posters_guidelines.md +628 -0
  1366. package/skills/venue-templates/references/reviewer_expectations.md +417 -0
  1367. package/skills/venue-templates/references/venue_writing_styles.md +321 -0
  1368. package/skills/venue-templates/scripts/customize_template.py +206 -0
  1369. package/skills/venue-templates/scripts/query_template.py +260 -0
  1370. package/skills/venue-templates/scripts/validate_format.py +255 -0
  1371. package/skills/watch/SKILL.md +12 -0
  1372. package/skills/what-if-oracle/SKILL.md +168 -0
  1373. package/skills/what-if-oracle/references/scenario-templates.md +137 -0
  1374. package/skills/writing/SKILL.md +414 -0
  1375. package/skills/xlsx/LICENSE.txt +30 -0
  1376. package/skills/xlsx/SKILL.md +292 -0
  1377. package/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
  1378. package/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
  1379. package/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
  1380. package/skills/xlsx/scripts/office/pack.py +159 -0
  1381. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  1382. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  1383. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  1384. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  1385. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  1386. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  1387. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  1388. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  1389. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  1390. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  1391. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  1392. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  1393. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  1394. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  1395. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  1396. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  1397. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  1398. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  1399. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  1400. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  1401. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  1402. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  1403. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  1404. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  1405. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  1406. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  1407. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  1408. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  1409. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  1410. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  1411. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  1412. package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
  1413. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  1414. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  1415. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  1416. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  1417. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  1418. package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  1419. package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  1420. package/skills/xlsx/scripts/office/soffice.py +183 -0
  1421. package/skills/xlsx/scripts/office/unpack.py +132 -0
  1422. package/skills/xlsx/scripts/office/validate.py +111 -0
  1423. package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
  1424. package/skills/xlsx/scripts/office/validators/base.py +847 -0
  1425. package/skills/xlsx/scripts/office/validators/docx.py +446 -0
  1426. package/skills/xlsx/scripts/office/validators/pptx.py +275 -0
  1427. package/skills/xlsx/scripts/office/validators/redlining.py +247 -0
  1428. package/skills/xlsx/scripts/recalc.py +184 -0
  1429. package/skills/zarr-python/SKILL.md +777 -0
  1430. package/skills/zarr-python/references/api_reference.md +515 -0
  1431. package/skills/zinc-database/SKILL.md +402 -0
  1432. package/skills/zinc-database/references/api_reference.md +692 -0
@@ -0,0 +1,907 @@
1
+ # Infographic Types Reference Guide
2
+
3
+ This reference provides extended templates, examples, and prompt patterns for each infographic type.
4
+
5
+ ---
6
+
7
+ ## 1. Statistical/Data-Driven Infographics
8
+
9
+ ### Purpose
10
+ Present quantitative data, statistics, survey results, and numerical comparisons in an engaging visual format.
11
+
12
+ ### Visual Elements
13
+ - **Bar charts**: Horizontal or vertical for comparisons
14
+ - **Pie/donut charts**: For proportions and percentages
15
+ - **Line charts**: For trends over time
16
+ - **Large number callouts**: Highlight key statistics
17
+ - **Icons**: Represent categories visually
18
+ - **Progress bars**: Show percentages or completion
19
+
20
+ ### Layout Patterns
21
+ - **Single-stat hero**: One large number with supporting context
22
+ - **Multi-stat grid**: 3-6 statistics in a grid layout
23
+ - **Chart-centric**: Large visualization with supporting text
24
+ - **Comparison bars**: Side-by-side bar comparisons
25
+
26
+ ### Prompt Templates
27
+
28
+ **Single Statistic Hero:**
29
+ ```
30
+ Statistical infographic featuring one key statistic about [TOPIC]:
31
+ Main stat: [LARGE NUMBER] [UNIT/CONTEXT]
32
+ Supporting context: [2-3 sentences explaining the significance]
33
+ Large bold number in center, supporting text below,
34
+ relevant icon or illustration, [COLOR] accent color,
35
+ clean minimal design, white background.
36
+ ```
37
+
38
+ **Multi-Statistic Grid:**
39
+ ```
40
+ Statistical infographic presenting [TOPIC] data:
41
+ Stat 1: [NUMBER] [LABEL] (icon: [ICON])
42
+ Stat 2: [NUMBER] [LABEL] (icon: [ICON])
43
+ Stat 3: [NUMBER] [LABEL] (icon: [ICON])
44
+ Stat 4: [NUMBER] [LABEL] (icon: [ICON])
45
+ 2x2 grid layout, large bold numbers, small icons above each,
46
+ [COLOR SCHEME], modern clean typography, white background.
47
+ ```
48
+
49
+ **Chart-Focused:**
50
+ ```
51
+ Statistical infographic with [CHART TYPE] showing [TOPIC]:
52
+ Data points: [VALUE 1], [VALUE 2], [VALUE 3], [VALUE 4]
53
+ Labels: [LABEL 1], [LABEL 2], [LABEL 3], [LABEL 4]
54
+ Large [bar/pie/donut] chart as main element,
55
+ title at top, legend below chart, [COLOR SCHEME],
56
+ data labels on chart, clean professional design.
57
+ ```
58
+
59
+ ### Example Prompts
60
+
61
+ **Healthcare Statistics:**
62
+ ```bash
63
+ python skills/generate-image/scripts/generate_image.py \
64
+ "Statistical infographic about heart disease: \
65
+ Main stat: 17.9 million deaths per year globally. \
66
+ Supporting stats in grid: 1 in 4 deaths caused by heart disease, \
67
+ 80% of heart disease is preventable, \
68
+ 150 minutes of exercise weekly reduces risk by 30%. \
69
+ Heart icon, red and pink color scheme with gray accents, \
70
+ large bold numbers, clean medical professional design, white background" \
71
+ --output figures/heart_disease_stats.png
72
+ ```
73
+
74
+ **Business Metrics:**
75
+ ```bash
76
+ python skills/generate-image/scripts/generate_image.py \
77
+ "Statistical infographic for Q4 business results: \
78
+ Revenue: $2.4M (+15% YoY), Customers: 12,500 (+22%), \
79
+ NPS Score: 78 (+8 points), Retention: 94%. \
80
+ 4-stat grid with upward arrow indicators for growth, \
81
+ bar chart showing quarterly trend, \
82
+ navy blue and gold corporate color scheme, \
83
+ professional business design, white background" \
84
+ --output figures/q4_metrics.png
85
+ ```
86
+
87
+ ---
88
+
89
+ ## 2. Timeline Infographics
90
+
91
+ ### Purpose
92
+ Display events, milestones, or developments in chronological order.
93
+
94
+ ### Visual Elements
95
+ - **Timeline axis**: Horizontal or vertical line
96
+ - **Date markers**: Years, months, or specific dates
97
+ - **Event nodes**: Circles, icons, or images at each point
98
+ - **Description boxes**: Brief text for each event
99
+ - **Connecting elements**: Lines, arrows, or paths
100
+
101
+ ### Layout Patterns
102
+ - **Horizontal timeline**: Left-to-right progression
103
+ - **Vertical timeline**: Top-to-bottom progression
104
+ - **Winding/snake timeline**: S-curve for many events
105
+ - **Circular timeline**: For cyclical or repeating events
106
+
107
+ ### Prompt Templates
108
+
109
+ **Horizontal Timeline:**
110
+ ```
111
+ Horizontal timeline infographic showing [TOPIC] from [START YEAR] to [END YEAR]:
112
+ [YEAR 1]: [EVENT 1] - [brief description]
113
+ [YEAR 2]: [EVENT 2] - [brief description]
114
+ [YEAR 3]: [EVENT 3] - [brief description]
115
+ [YEAR 4]: [EVENT 4] - [brief description]
116
+ Left-to-right timeline with circular nodes for each event,
117
+ connecting line between nodes, icons above each node,
118
+ [COLOR] gradient from past to present, date labels below,
119
+ clean modern design, white background.
120
+ ```
121
+
122
+ **Vertical Timeline:**
123
+ ```
124
+ Vertical timeline infographic showing [TOPIC]:
125
+ Top (earliest): [YEAR] - [EVENT]
126
+ Middle events: [YEAR] - [EVENT], [YEAR] - [EVENT]
127
+ Bottom (latest): [YEAR] - [EVENT]
128
+ Top-to-bottom flow, alternating left-right event boxes,
129
+ central vertical line connecting all events,
130
+ circular nodes with dates, [COLOR SCHEME],
131
+ professional clean design, white background.
132
+ ```
133
+
134
+ **Project Milestone Timeline:**
135
+ ```
136
+ Project timeline infographic for [PROJECT NAME]:
137
+ Phase 1: [DATES] - [MILESTONE] (status: complete)
138
+ Phase 2: [DATES] - [MILESTONE] (status: in progress)
139
+ Phase 3: [DATES] - [MILESTONE] (status: upcoming)
140
+ Phase 4: [DATES] - [MILESTONE] (status: planned)
141
+ Gantt-style horizontal bars, color-coded by status,
142
+ green for complete, yellow for in progress, gray for upcoming,
143
+ project name header, clean professional design.
144
+ ```
145
+
146
+ ### Example Prompts
147
+
148
+ **Technology Evolution:**
149
+ ```bash
150
+ python skills/generate-image/scripts/generate_image.py \
151
+ "Horizontal timeline infographic: Evolution of Mobile Phones \
152
+ 1983: First mobile phone (Motorola DynaTAC), \
153
+ 1992: First smartphone (IBM Simon), \
154
+ 2007: iPhone launches touchscreen era, \
155
+ 2010: First 4G networks, \
156
+ 2019: First 5G phones, \
157
+ 2023: Foldable phones mainstream. \
158
+ Phone icons evolving at each node, gradient from gray (old) to blue (new), \
159
+ connecting timeline arrow, year labels, clean tech design" \
160
+ --output figures/mobile_evolution.png
161
+ ```
162
+
163
+ **Company History:**
164
+ ```bash
165
+ python skills/generate-image/scripts/generate_image.py \
166
+ "Vertical timeline infographic: Our Company Journey \
167
+ 2010: Founded in garage with 2 employees, \
168
+ 2012: First major client signed, \
169
+ 2015: Reached 100 employees, \
170
+ 2018: IPO on NASDAQ, \
171
+ 2022: Expanded to 30 countries, \
172
+ 2025: 10,000 employees worldwide. \
173
+ Milestone icons for each event, alternating left-right layout, \
174
+ blue and gold corporate colors, growth trajectory feel, \
175
+ professional business design" \
176
+ --output figures/company_history.png
177
+ ```
178
+
179
+ ---
180
+
181
+ ## 3. Process/How-To Infographics
182
+
183
+ ### Purpose
184
+ Explain step-by-step procedures, workflows, instructions, or methodologies.
185
+
186
+ ### Visual Elements
187
+ - **Numbered steps**: Clear sequence indicators
188
+ - **Arrows/connectors**: Show flow and direction
189
+ - **Action icons**: Illustrate each step
190
+ - **Brief descriptions**: Concise action text
191
+ - **Start/end indicators**: Clear beginning and conclusion
192
+
193
+ ### Layout Patterns
194
+ - **Vertical cascade**: Steps flow top-to-bottom
195
+ - **Horizontal flow**: Left-to-right progression
196
+ - **Circular process**: Steps form a cycle
197
+ - **Branching flow**: Decision points with alternatives
198
+
199
+ ### Prompt Templates
200
+
201
+ **Linear Process:**
202
+ ```
203
+ Process infographic: How to [ACCOMPLISH GOAL]
204
+ Step 1: [ACTION] - [brief explanation] (icon: [ICON])
205
+ Step 2: [ACTION] - [brief explanation] (icon: [ICON])
206
+ Step 3: [ACTION] - [brief explanation] (icon: [ICON])
207
+ Step 4: [ACTION] - [brief explanation] (icon: [ICON])
208
+ Step 5: [ACTION] - [brief explanation] (icon: [ICON])
209
+ Numbered circles connected by arrows, icons for each step,
210
+ [VERTICAL/HORIZONTAL] flow, [COLOR SCHEME],
211
+ clear step labels, clean instructional design, white background.
212
+ ```
213
+
214
+ **Circular Process:**
215
+ ```
216
+ Circular process infographic showing [CYCLE NAME]:
217
+ Step 1: [ACTION] leads to
218
+ Step 2: [ACTION] leads to
219
+ Step 3: [ACTION] leads to
220
+ Step 4: [ACTION] returns to Step 1
221
+ Circular arrangement with arrows forming a cycle,
222
+ icons at each point, step numbers, [COLOR SCHEME],
223
+ continuous flow design, white background.
224
+ ```
225
+
226
+ **Decision Flowchart:**
227
+ ```
228
+ Decision flowchart infographic for [SCENARIO]:
229
+ Start: [INITIAL QUESTION]
230
+ If Yes: [PATH A] → [OUTCOME A]
231
+ If No: [PATH B] → [OUTCOME B]
232
+ Diamond shapes for decisions, rectangles for actions,
233
+ arrows connecting all elements, [COLOR SCHEME],
234
+ clear yes/no labels, flowchart style, white background.
235
+ ```
236
+
237
+ ### Example Prompts
238
+
239
+ **Recipe Process:**
240
+ ```bash
241
+ python skills/generate-image/scripts/generate_image.py \
242
+ "Process infographic: How to Make Perfect Coffee \
243
+ Step 1: Grind fresh beans (coffee grinder icon), \
244
+ Step 2: Heat water to 200°F (thermometer icon), \
245
+ Step 3: Add 2 tablespoons per 6 oz water (measuring spoon icon), \
246
+ Step 4: Brew for 4 minutes (timer icon), \
247
+ Step 5: Serve and enjoy (coffee cup icon). \
248
+ Vertical flow with large numbered circles, \
249
+ brown and cream coffee color scheme, \
250
+ arrows between steps, cozy design feel" \
251
+ --output figures/coffee_process.png
252
+ ```
253
+
254
+ **Onboarding Workflow:**
255
+ ```bash
256
+ python skills/generate-image/scripts/generate_image.py \
257
+ "Process infographic: New Employee Onboarding \
258
+ Day 1: Welcome orientation and paperwork (clipboard icon), \
259
+ Week 1: Meet your team and set up workspace (people icon), \
260
+ Week 2: Training and system access (laptop icon), \
261
+ Week 3: Shadow senior colleagues (handshake icon), \
262
+ Week 4: First independent project (checkmark icon). \
263
+ Horizontal timeline flow with milestones, \
264
+ teal and coral corporate colors, \
265
+ professional HR design style" \
266
+ --output figures/onboarding_process.png
267
+ ```
268
+
269
+ ---
270
+
271
+ ## 4. Comparison Infographics
272
+
273
+ ### Purpose
274
+ Compare two or more options, products, concepts, or choices side by side.
275
+
276
+ ### Visual Elements
277
+ - **Split layout**: Clear division between options
278
+ - **Matching rows**: Same categories for fair comparison
279
+ - **Check/cross marks**: Quick visual indicators
280
+ - **Rating systems**: Stars, bars, or numbers
281
+ - **Headers**: Clear identification of each option
282
+
283
+ ### Layout Patterns
284
+ - **Two-column split**: Left vs Right
285
+ - **Table format**: Rows and columns
286
+ - **Venn diagram**: Overlapping comparisons
287
+ - **Feature matrix**: Multi-option comparison grid
288
+
289
+ ### Prompt Templates
290
+
291
+ **Two-Option Comparison:**
292
+ ```
293
+ Comparison infographic: [OPTION A] vs [OPTION B]
294
+ Header: [OPTION A] on left | [OPTION B] on right
295
+ Row 1 - [CATEGORY 1]: [A VALUE] | [B VALUE]
296
+ Row 2 - [CATEGORY 2]: [A VALUE] | [B VALUE]
297
+ Row 3 - [CATEGORY 3]: [A VALUE] | [B VALUE]
298
+ Row 4 - [CATEGORY 4]: [A VALUE] | [B VALUE]
299
+ Row 5 - [CATEGORY 5]: [A VALUE] | [B VALUE]
300
+ Split layout with [COLOR A] for left, [COLOR B] for right,
301
+ icons for each option header, checkmarks for advantages,
302
+ clean symmetrical design, white background.
303
+ ```
304
+
305
+ **Multi-Option Matrix:**
306
+ ```
307
+ Comparison matrix infographic: [TOPIC]
308
+ Options: [OPTION 1], [OPTION 2], [OPTION 3]
309
+ Feature 1: [✓/✗ for each]
310
+ Feature 2: [✓/✗ for each]
311
+ Feature 3: [✓/✗ for each]
312
+ Feature 4: [✓/✗ for each]
313
+ Table layout with colored headers for each option,
314
+ checkmarks and X marks in cells, [COLOR SCHEME],
315
+ clean grid design, white background.
316
+ ```
317
+
318
+ **Pros and Cons:**
319
+ ```
320
+ Pros and Cons infographic for [TOPIC]:
321
+ Pros (left side, green):
322
+ - [PRO 1]
323
+ - [PRO 2]
324
+ - [PRO 3]
325
+ Cons (right side, red):
326
+ - [CON 1]
327
+ - [CON 2]
328
+ - [CON 3]
329
+ Split layout with green left side, red right side,
330
+ thumbs up icon for pros, thumbs down for cons,
331
+ balanced visual weight, white background.
332
+ ```
333
+
334
+ ### Example Prompts
335
+
336
+ **Software Comparison:**
337
+ ```bash
338
+ python skills/generate-image/scripts/generate_image.py \
339
+ "Comparison infographic: Slack vs Microsoft Teams \
340
+ Pricing: Both offer free tiers with paid upgrades, \
341
+ Integration: Slack 2000+ apps, Teams Microsoft ecosystem, \
342
+ Video calls: Teams native, Slack via Huddles, \
343
+ File storage: Teams 1TB, Slack 5GB free, \
344
+ Best for: Slack small teams, Teams enterprise. \
345
+ Purple left side (Slack), blue right side (Teams), \
346
+ logos at top, feature comparison rows, \
347
+ checkmarks for strengths, modern tech design" \
348
+ --output figures/slack_vs_teams.png
349
+ ```
350
+
351
+ **Diet Comparison:**
352
+ ```bash
353
+ python skills/generate-image/scripts/generate_image.py \
354
+ "Comparison infographic: Keto Diet vs Mediterranean Diet \
355
+ Weight loss: Both effective, Keto faster initial, \
356
+ Heart health: Mediterranean better long-term, \
357
+ Sustainability: Mediterranean easier to maintain, \
358
+ Foods allowed: Keto high fat low carb, Med balanced, \
359
+ Research support: Mediterranean more studied. \
360
+ Green left (Keto), blue right (Mediterranean), \
361
+ food icons for each, health/heart icons, \
362
+ clean wellness design style" \
363
+ --output figures/diet_comparison.png
364
+ ```
365
+
366
+ ---
367
+
368
+ ## 5. List/Informational Infographics
369
+
370
+ ### Purpose
371
+ Present tips, facts, key points, or information in an organized, scannable format.
372
+
373
+ ### Visual Elements
374
+ - **Numbers or bullets**: Clear list indicators
375
+ - **Icons**: Visual representation of each point
376
+ - **Brief text**: Concise descriptions
377
+ - **Header**: Topic introduction
378
+ - **Consistent styling**: Uniform treatment of all items
379
+
380
+ ### Layout Patterns
381
+ - **Vertical list**: Standard top-to-bottom
382
+ - **Two-column list**: For longer lists
383
+ - **Icon grid**: Icons with labels below
384
+ - **Cards**: Each point in a card/box
385
+
386
+ ### Prompt Templates
387
+
388
+ **Numbered List:**
389
+ ```
390
+ List infographic: [NUMBER] [TOPIC]
391
+ 1. [POINT 1] - [brief explanation] (icon: [ICON])
392
+ 2. [POINT 2] - [brief explanation] (icon: [ICON])
393
+ 3. [POINT 3] - [brief explanation] (icon: [ICON])
394
+ 4. [POINT 4] - [brief explanation] (icon: [ICON])
395
+ 5. [POINT 5] - [brief explanation] (icon: [ICON])
396
+ Large numbers in circles, icons next to each point,
397
+ brief text descriptions, [COLOR SCHEME],
398
+ vertical layout with spacing, white background.
399
+ ```
400
+
401
+ **Tips Format:**
402
+ ```
403
+ Tips infographic: [NUMBER] Tips for [TOPIC]
404
+ Tip 1: [TIP] (lightbulb icon)
405
+ Tip 2: [TIP] (star icon)
406
+ Tip 3: [TIP] (checkmark icon)
407
+ Tip 4: [TIP] (target icon)
408
+ Tip 5: [TIP] (rocket icon)
409
+ Colorful tip boxes or cards, icons for each tip,
410
+ [COLOR SCHEME], engaging friendly design,
411
+ header at top, white background.
412
+ ```
413
+
414
+ **Facts Format:**
415
+ ```
416
+ Facts infographic: [NUMBER] Facts About [TOPIC]
417
+ Fact 1: [INTERESTING FACT]
418
+ Fact 2: [INTERESTING FACT]
419
+ Fact 3: [INTERESTING FACT]
420
+ Fact 4: [INTERESTING FACT]
421
+ Fact 5: [INTERESTING FACT]
422
+ Speech bubble or card style for each fact,
423
+ relevant icons, [COLOR SCHEME],
424
+ educational engaging design, white background.
425
+ ```
426
+
427
+ ### Example Prompts
428
+
429
+ **Productivity Tips:**
430
+ ```bash
431
+ python skills/generate-image/scripts/generate_image.py \
432
+ "List infographic: 7 Productivity Tips for Remote Workers \
433
+ 1. Create a dedicated workspace (desk icon), \
434
+ 2. Set regular working hours (clock icon), \
435
+ 3. Take scheduled breaks (coffee icon), \
436
+ 4. Use noise-canceling headphones (headphones icon), \
437
+ 5. Batch similar tasks together (stack icon), \
438
+ 6. Limit social media during work (phone icon), \
439
+ 7. End each day with tomorrow's plan (checklist icon). \
440
+ Large colorful numbers, icons beside each tip, \
441
+ teal and orange color scheme, friendly modern design" \
442
+ --output figures/remote_work_tips.png
443
+ ```
444
+
445
+ **Fun Facts:**
446
+ ```bash
447
+ python skills/generate-image/scripts/generate_image.py \
448
+ "Facts infographic: 5 Amazing Facts About Honey \
449
+ Fact 1: Honey never spoils - 3000 year old honey is still edible, \
450
+ Fact 2: Bees visit 2 million flowers to make 1 lb of honey, \
451
+ Fact 3: Honey can be used to treat wounds and burns, \
452
+ Fact 4: A bee produces only 1/12 teaspoon in its lifetime, \
453
+ Fact 5: Honey contains natural antibiotics. \
454
+ Hexagon honeycomb shapes for each fact, \
455
+ golden yellow and black color scheme, bee illustrations, \
456
+ fun educational design" \
457
+ --output figures/honey_facts.png
458
+ ```
459
+
460
+ ---
461
+
462
+ ## 6. Geographic/Map-Based Infographics
463
+
464
+ ### Purpose
465
+ Display location-based data, regional statistics, or geographic trends.
466
+
467
+ ### Visual Elements
468
+ - **Map visualization**: World, country, or region
469
+ - **Color coding**: Data intensity by region
470
+ - **Data callouts**: Key statistics for regions
471
+ - **Legend**: Color scale explanation
472
+ - **Labels**: Region or country names
473
+
474
+ ### Layout Patterns
475
+ - **Full map**: Map as primary element
476
+ - **Map with sidebar**: Data summary alongside
477
+ - **Regional focus**: Zoomed map section
478
+ - **Multi-map**: Several maps showing different data
479
+
480
+ ### Prompt Templates
481
+
482
+ **World Map Data:**
483
+ ```
484
+ Geographic infographic showing [TOPIC] globally:
485
+ Highest: [REGION/COUNTRY] - [VALUE]
486
+ Medium: [REGIONS] - [VALUE RANGE]
487
+ Lowest: [REGION/COUNTRY] - [VALUE]
488
+ World map with color-coded countries,
489
+ [DARK COLOR] for highest values, [LIGHT COLOR] for lowest,
490
+ legend showing color scale, key statistics callout,
491
+ clean cartographic design, light gray background.
492
+ ```
493
+
494
+ **Country/Region Focus:**
495
+ ```
496
+ Geographic infographic showing [TOPIC] in [COUNTRY/REGION]:
497
+ Region 1: [VALUE]
498
+ Region 2: [VALUE]
499
+ Region 3: [VALUE]
500
+ Map of [COUNTRY/REGION] with color-coded areas,
501
+ data labels for key regions, [COLOR] gradient,
502
+ legend with value scale, clean map design.
503
+ ```
504
+
505
+ ### Example Prompts
506
+
507
+ **Global Data:**
508
+ ```bash
509
+ python skills/generate-image/scripts/generate_image.py \
510
+ "Geographic infographic: Global Renewable Energy Adoption 2025 \
511
+ Leaders: Iceland 100%, Norway 98%, Costa Rica 95%, \
512
+ Growing: Germany 50%, UK 45%, China 30%, \
513
+ Emerging: USA 22%, India 20%, Brazil 18%. \
514
+ World map with green gradient coloring, \
515
+ darker green for higher adoption, \
516
+ legend showing percentage scale, \
517
+ key country callouts with percentages, \
518
+ clean modern cartographic style" \
519
+ --output figures/renewable_map.png
520
+ ```
521
+
522
+ **US Regional:**
523
+ ```bash
524
+ python skills/generate-image/scripts/generate_image.py \
525
+ "Geographic infographic: Tech Jobs by US Region 2025 \
526
+ West Coast: 35% of tech jobs (California, Washington), \
527
+ Northeast: 25% (New York, Massachusetts), \
528
+ South: 22% (Texas, Florida, Georgia), \
529
+ Midwest: 18% (Illinois, Colorado, Michigan). \
530
+ US map with color-coded regions, \
531
+ percentage labels on each region, \
532
+ blue and purple tech color scheme, \
533
+ legend showing job concentration, \
534
+ professional business design" \
535
+ --output figures/tech_jobs_map.png
536
+ ```
537
+
538
+ ---
539
+
540
+ ## 7. Hierarchical/Pyramid Infographics
541
+
542
+ ### Purpose
543
+ Show levels of importance, organizational structures, or ranked information.
544
+
545
+ ### Visual Elements
546
+ - **Pyramid shape**: Triangle with levels
547
+ - **Level labels**: Clear tier identification
548
+ - **Size progression**: Larger at base, smaller at top
549
+ - **Color progression**: Gradient or distinct colors per level
550
+ - **Icons**: Optional for each level
551
+
552
+ ### Layout Patterns
553
+ - **Traditional pyramid**: Wide base, narrow top
554
+ - **Inverted pyramid**: Narrow base, wide top
555
+ - **Org chart**: Tree structure
556
+ - **Stacked blocks**: Square levels
557
+
558
+ ### Prompt Templates
559
+
560
+ **Classic Pyramid:**
561
+ ```
562
+ Hierarchical pyramid infographic: [TOPIC]
563
+ Top (Level 1 - most important/rare): [ITEM]
564
+ Level 2: [ITEM]
565
+ Level 3: [ITEM]
566
+ Level 4: [ITEM]
567
+ Base (Level 5 - foundation/most common): [ITEM]
568
+ Triangle pyramid with 5 horizontal sections,
569
+ [COLOR] gradient from [TOP COLOR] to [BASE COLOR],
570
+ labels on each tier, icons optional,
571
+ clean geometric design, white background.
572
+ ```
573
+
574
+ **Organizational Hierarchy:**
575
+ ```
576
+ Organizational chart infographic for [ORGANIZATION]:
577
+ Top: [CEO/LEADER]
578
+ Level 2: [VPs/DIRECTORS] (3-4 boxes)
579
+ Level 3: [MANAGERS] (6-8 boxes)
580
+ Level 4: [TEAM LEADS] (multiple boxes)
581
+ Tree structure flowing down, connecting lines between levels,
582
+ [COLOR SCHEME], professional corporate design,
583
+ role titles in boxes, white background.
584
+ ```
585
+
586
+ ### Example Prompts
587
+
588
+ **Learning Pyramid:**
589
+ ```bash
590
+ python skills/generate-image/scripts/generate_image.py \
591
+ "Hierarchical pyramid infographic: Learning Retention Rates \
592
+ Top: Teaching others - 90% retention, \
593
+ Level 2: Practice by doing - 75% retention, \
594
+ Level 3: Discussion groups - 50% retention, \
595
+ Level 4: Demonstration - 30% retention, \
596
+ Level 5: Audio/Visual - 20% retention, \
597
+ Base: Lecture/Reading - 5-10% retention. \
598
+ Colorful pyramid with 6 levels, \
599
+ gradient from green (top) to red (base), \
600
+ percentage labels, educational design" \
601
+ --output figures/learning_pyramid.png
602
+ ```
603
+
604
+ **Energy Pyramid:**
605
+ ```bash
606
+ python skills/generate-image/scripts/generate_image.py \
607
+ "Hierarchical pyramid infographic: Ecological Energy Pyramid \
608
+ Top: Apex predators (eagles, wolves) - smallest, \
609
+ Level 2: Secondary consumers (snakes, foxes), \
610
+ Level 3: Primary consumers (rabbits, deer), \
611
+ Base: Producers (plants, algae) - largest. \
612
+ Triangle pyramid with animal silhouettes, \
613
+ green gradient from base to top, \
614
+ energy flow arrows on side, \
615
+ scientific educational design" \
616
+ --output figures/energy_pyramid.png
617
+ ```
618
+
619
+ ---
620
+
621
+ ## 8. Anatomical/Visual Metaphor Infographics
622
+
623
+ ### Purpose
624
+ Explain complex systems using familiar visual metaphors (bodies, machines, trees, etc.).
625
+
626
+ ### Visual Elements
627
+ - **Central metaphor image**: The main visual (body, tree, machine)
628
+ - **Labeled parts**: Components identified
629
+ - **Callout lines**: Connecting labels to parts
630
+ - **Descriptions**: Explanations for each part
631
+ - **Color coding**: Different parts in different colors
632
+
633
+ ### Layout Patterns
634
+ - **Central image with callouts**: Labels pointing to parts
635
+ - **Exploded view**: Parts separated but arranged
636
+ - **Cross-section**: Inside view of metaphor
637
+ - **Before/after**: Metaphor in different states
638
+
639
+ ### Prompt Templates
640
+
641
+ **Body Metaphor:**
642
+ ```
643
+ Anatomical infographic using human body to explain [TOPIC]:
644
+ Brain represents [CONCEPT] - [explanation]
645
+ Heart represents [CONCEPT] - [explanation]
646
+ Hands represent [CONCEPT] - [explanation]
647
+ Feet represent [CONCEPT] - [explanation]
648
+ Human body silhouette with labeled callouts,
649
+ [COLOR SCHEME], clean medical illustration style,
650
+ connecting lines to descriptions, white background.
651
+ ```
652
+
653
+ **Machine Metaphor:**
654
+ ```
655
+ Anatomical infographic using machine/engine to explain [TOPIC]:
656
+ Fuel tank represents [CONCEPT]
657
+ Engine represents [CONCEPT]
658
+ Wheels represent [CONCEPT]
659
+ Steering represents [CONCEPT]
660
+ Machine illustration with labeled components,
661
+ callout lines and descriptions, [COLOR SCHEME],
662
+ technical illustration style, white background.
663
+ ```
664
+
665
+ ### Example Prompts
666
+
667
+ **Business as Body:**
668
+ ```bash
669
+ python skills/generate-image/scripts/generate_image.py \
670
+ "Anatomical infographic: A Business is Like a Human Body \
671
+ Brain = Leadership and strategy (makes decisions), \
672
+ Heart = Company culture (pumps energy), \
673
+ Arms = Sales and marketing (reaches out), \
674
+ Legs = Operations (keeps moving forward), \
675
+ Skeleton = Systems and processes (provides structure). \
676
+ Human body silhouette in blue, \
677
+ labeled callout boxes for each part, \
678
+ professional corporate design, white background" \
679
+ --output figures/business_body.png
680
+ ```
681
+
682
+ **Computer as House:**
683
+ ```bash
684
+ python skills/generate-image/scripts/generate_image.py \
685
+ "Anatomical infographic: Computer as a House \
686
+ CPU = The brain/office (processes information), \
687
+ RAM = The desk (temporary workspace), \
688
+ Hard Drive = The filing cabinet (long-term storage), \
689
+ GPU = The entertainment room (handles visuals), \
690
+ Motherboard = The foundation (connects everything). \
691
+ House illustration with cutaway view, \
692
+ labeled rooms matching computer parts, \
693
+ blue and gray tech colors, educational style" \
694
+ --output figures/computer_house.png
695
+ ```
696
+
697
+ ---
698
+
699
+ ## 9. Resume/Professional Infographics
700
+
701
+ ### Purpose
702
+ Present professional information, skills, experience, and achievements visually.
703
+
704
+ ### Visual Elements
705
+ - **Photo/avatar section**: Personal branding
706
+ - **Skills visualization**: Bars, charts, ratings
707
+ - **Timeline**: Career progression
708
+ - **Contact icons**: Email, phone, social
709
+ - **Achievement badges**: Certifications, awards
710
+
711
+ ### Layout Patterns
712
+ - **Single column**: Vertical flow
713
+ - **Two column**: Info left, skills right
714
+ - **Header focus**: Large header with photo
715
+ - **Modular**: Distinct sections/cards
716
+
717
+ ### Prompt Templates
718
+
719
+ **Professional Resume:**
720
+ ```
721
+ Resume infographic for [NAME], [PROFESSION]:
722
+ Photo area: Circular avatar placeholder
723
+ Skills: [SKILL 1] 90%, [SKILL 2] 85%, [SKILL 3] 75%
724
+ Experience: [YEAR-YEAR] [ROLE] at [COMPANY], [YEAR-YEAR] [ROLE] at [COMPANY]
725
+ Education: [DEGREE] from [INSTITUTION]
726
+ Contact: Email, LinkedIn, Portfolio icons
727
+ Professional photo area at top, horizontal skill bars,
728
+ timeline for experience, [COLOR SCHEME],
729
+ modern professional design, white background.
730
+ ```
731
+
732
+ ### Example Prompts
733
+
734
+ **Designer Resume:**
735
+ ```bash
736
+ python skills/generate-image/scripts/generate_image.py \
737
+ "Resume infographic for a Graphic Designer: \
738
+ Circular avatar placeholder at top, \
739
+ Skills with colored bars: Adobe Suite 95%, UI/UX 90%, Branding 85%, Motion 75%. \
740
+ Experience timeline: 2018-2020 Junior Designer at Agency X, \
741
+ 2020-2023 Senior Designer at Studio Y, 2023-Present Creative Director at Company Z. \
742
+ Education: BFA Graphic Design. \
743
+ Contact icons row at bottom. \
744
+ Coral and teal color scheme, creative modern design" \
745
+ --output figures/designer_resume.png
746
+ ```
747
+
748
+ ---
749
+
750
+ ## 10. Social Media/Interactive Infographics
751
+
752
+ ### Purpose
753
+ Create shareable, engaging content optimized for social media platforms.
754
+
755
+ ### Visual Elements
756
+ - **Bold headlines**: Attention-grabbing text
757
+ - **Minimal text**: Quick to read
758
+ - **Vibrant colors**: Stand out in feeds
759
+ - **Central visual**: Eye-catching image or icon
760
+ - **Call to action**: Engagement prompt
761
+
762
+ ### Layout Patterns
763
+ - **Square format**: Instagram, Facebook
764
+ - **Vertical format**: Pinterest, Stories
765
+ - **Carousel**: Multi-slide series
766
+ - **Quote card**: Impactful statement focus
767
+
768
+ ### Platform Dimensions
769
+ - **Instagram Square**: 1080x1080px
770
+ - **Instagram Portrait**: 1080x1350px
771
+ - **Twitter/X**: 1200x675px
772
+ - **LinkedIn**: 1200x627px
773
+ - **Pinterest**: 1000x1500px
774
+
775
+ ### Prompt Templates
776
+
777
+ **Social Quote Card:**
778
+ ```
779
+ Social media infographic: Inspirational quote
780
+ Quote: "[QUOTE TEXT]"
781
+ Attribution: - [AUTHOR]
782
+ Large quotation marks, centered quote text,
783
+ author name below, [COLOR SCHEME],
784
+ Instagram square format, bold typography,
785
+ solid gradient background.
786
+ ```
787
+
788
+ **Quick Stats Social:**
789
+ ```
790
+ Social media infographic: [TOPIC] in Numbers
791
+ Headline: [ATTENTION-GRABBING HEADLINE]
792
+ Stat 1: [BIG NUMBER] [CONTEXT]
793
+ Stat 2: [BIG NUMBER] [CONTEXT]
794
+ Call to action: [CTA]
795
+ Bold numbers, minimal text, [COLOR SCHEME],
796
+ vibrant engaging design, social media optimized,
797
+ Instagram square format.
798
+ ```
799
+
800
+ ### Example Prompts
801
+
802
+ **Inspirational Quote:**
803
+ ```bash
804
+ python skills/generate-image/scripts/generate_image.py \
805
+ "Social media infographic quote card: \
806
+ Quote: 'The best time to plant a tree was 20 years ago. \
807
+ The second best time is now.' \
808
+ Attribution: Chinese Proverb. \
809
+ Large decorative quotation marks, centered text, \
810
+ gradient background from deep green to teal, \
811
+ tree silhouette illustration, Instagram square format, \
812
+ modern inspirational design" \
813
+ --output figures/tree_quote.png
814
+ ```
815
+
816
+ **Engagement Stats:**
817
+ ```bash
818
+ python skills/generate-image/scripts/generate_image.py \
819
+ "Social media infographic: Email Marketing Stats \
820
+ Headline: Is Your Email Strategy Working? \
821
+ Stat 1: 4400% ROI on email marketing, \
822
+ Stat 2: 59% of consumers say email influences purchases, \
823
+ Call to action: Double tap if you're an email marketer! \
824
+ Bold colorful numbers, envelope icons, \
825
+ purple and yellow vibrant colors, \
826
+ Instagram square format, engaging design" \
827
+ --output figures/email_stats_social.png
828
+ ```
829
+
830
+ ---
831
+
832
+ ## Style Variations by Industry
833
+
834
+ ### Corporate/Business Style
835
+ - Colors: Navy, gray, gold accents
836
+ - Typography: Clean sans-serif (Arial, Helvetica)
837
+ - Design: Minimal, professional, structured
838
+ - Elements: Charts, icons, clean lines
839
+
840
+ ### Healthcare/Medical Style
841
+ - Colors: Blue, teal, green, white
842
+ - Typography: Clear, readable
843
+ - Design: Trust-inducing, clean, clinical
844
+ - Elements: Medical icons, anatomy, research imagery
845
+
846
+ ### Technology/Data Style
847
+ - Colors: Dark backgrounds, neon accents, blue/purple
848
+ - Typography: Modern sans-serif, monospace for data
849
+ - Design: Futuristic, clean, dark mode friendly
850
+ - Elements: Circuit patterns, data visualizations, glows
851
+
852
+ ### Education/Academic Style
853
+ - Colors: Neutral tones, soft blues, warm accents
854
+ - Typography: Readable, slightly traditional
855
+ - Design: Organized, clear hierarchy, accessible
856
+ - Elements: Books, lightbulbs, graduation icons
857
+
858
+ ### Marketing/Creative Style
859
+ - Colors: Bold, vibrant, trendy combinations
860
+ - Typography: Mix of display and body fonts
861
+ - Design: Eye-catching, dynamic, playful
862
+ - Elements: Abstract shapes, gradients, illustrations
863
+
864
+ ---
865
+
866
+ ## Prompt Modifiers Reference
867
+
868
+ Add these modifiers to any prompt to adjust style:
869
+
870
+ ### Design Style
871
+ - "clean minimal design"
872
+ - "modern professional design"
873
+ - "flat design with bold colors"
874
+ - "hand-drawn illustration style"
875
+ - "3D isometric style"
876
+ - "vintage retro style"
877
+ - "corporate business style"
878
+ - "playful friendly design"
879
+
880
+ ### Color Instructions
881
+ - "[color] and [color] color scheme"
882
+ - "monochromatic [color] palette"
883
+ - "colorblind-safe palette"
884
+ - "warm/cool color tones"
885
+ - "high contrast design"
886
+ - "muted pastel colors"
887
+ - "bold vibrant colors"
888
+
889
+ ### Layout Instructions
890
+ - "vertical layout"
891
+ - "horizontal layout"
892
+ - "centered composition"
893
+ - "asymmetrical balance"
894
+ - "grid-based layout"
895
+ - "flowing organic layout"
896
+
897
+ ### Background Options
898
+ - "white background"
899
+ - "light gray background"
900
+ - "dark background"
901
+ - "gradient background from [color] to [color]"
902
+ - "subtle pattern background"
903
+ - "solid [color] background"
904
+
905
+ ---
906
+
907
+ Use these templates and examples as starting points, then customize for your specific needs.