@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 +1,849 @@
1
+ # Slide Design Principles for Scientific Presentations
2
+
3
+ ## Overview
4
+
5
+ Effective slide design enhances comprehension, maintains audience attention, and ensures your scientific message is communicated clearly. This guide covers visual hierarchy, typography, color theory, layout principles, and accessibility considerations for creating professional scientific presentations.
6
+
7
+ ## Core Design Principles
8
+
9
+ ### 1. Simplicity and Clarity
10
+
11
+ **The Fundamental Rule**: Each slide should communicate ONE main idea.
12
+
13
+ **Why It Matters**:
14
+ - Audiences can only process limited information at once
15
+ - Complexity causes cognitive overload
16
+ - Simple slides are remembered; busy slides are forgotten
17
+
18
+ **Application**:
19
+ - ✅ One message per slide
20
+ - ✅ Minimal text (audiences read OR listen, not both simultaneously)
21
+ - ✅ Clear visual focus
22
+ - ✅ Generous white space
23
+ - ❌ Avoid cramming multiple concepts onto one slide
24
+
25
+ **Example Comparison**:
26
+ ```
27
+ BAD: Single slide with:
28
+ - 3 different graphs
29
+ - 8 bullet points
30
+ - 2 tables
31
+ - Dense caption text
32
+
33
+ GOOD: Three separate slides:
34
+ - Slide 1: First graph with 2-3 key points
35
+ - Slide 2: Second graph with interpretation
36
+ - Slide 3: Summary table with highlighted finding
37
+ ```
38
+
39
+ ### 2. Visual Hierarchy
40
+
41
+ Guide attention to the most important elements through size, color, and position.
42
+
43
+ **Hierarchy Levels**:
44
+ 1. **Primary**: Main message or key data (largest, highest contrast)
45
+ 2. **Secondary**: Supporting information (medium size)
46
+ 3. **Tertiary**: Details and labels (smaller, lower contrast)
47
+
48
+ **Techniques**:
49
+
50
+ **Size**:
51
+ - Title: Largest (36-54pt)
52
+ - Key findings: Large (24-32pt)
53
+ - Supporting text: Medium (18-24pt)
54
+ - Labels and notes: Smallest but legible (14-18pt)
55
+
56
+ **Color**:
57
+ - High contrast for key elements
58
+ - Accent colors for emphasis
59
+ - Muted colors for background or secondary info
60
+
61
+ **Position**:
62
+ - Top-left or top-center: Primary content (Western reading pattern)
63
+ - Center: Focal point for key visuals
64
+ - Bottom or sides: Supporting details
65
+
66
+ **Weight**:
67
+ - Bold for emphasis on key terms
68
+ - Regular weight for body text
69
+ - Light weight for de-emphasized content
70
+
71
+ ### 3. Consistency
72
+
73
+ Maintain visual consistency throughout the presentation.
74
+
75
+ **Elements to Keep Consistent**:
76
+ - **Fonts**: Same font family for all slides
77
+ - **Colors**: Defined color palette (3-5 colors)
78
+ - **Layouts**: Similar slides use same structure
79
+ - **Spacing**: Margins and padding uniform
80
+ - **Style**: Figure formats, bullet styles, numbering
81
+
82
+ **Benefits**:
83
+ - Professional appearance
84
+ - Reduced cognitive load (audiences learn your visual language)
85
+ - Focus on content, not adjusting to new formats
86
+ - Easy to identify information types
87
+
88
+ **Template Approach**:
89
+ - Create master slide with standard elements
90
+ - Design 3-5 layout variants (title, content, figure, section divider)
91
+ - Apply consistently throughout
92
+
93
+ ## Typography
94
+
95
+ ### Font Selection
96
+
97
+ **Recommended Font Types**:
98
+
99
+ **Sans-Serif Fonts** (Highly Recommended):
100
+ - **Arial**: Universal, highly legible
101
+ - **Helvetica**: Clean, professional
102
+ - **Calibri**: Modern default, works well
103
+ - **Gill Sans**: Elegant sans-serif
104
+ - **Futura**: Geometric, modern
105
+ - **Avenir**: Friendly, professional
106
+
107
+ **Serif Fonts** (Use Sparingly):
108
+ - Generally harder to read on screens
109
+ - Acceptable for titles in some contexts
110
+ - Avoid for body text in presentations
111
+
112
+ **Avoid**:
113
+ - ❌ Script or handwriting fonts (illegible from distance)
114
+ - ❌ Decorative fonts (distracting)
115
+ - ❌ Condensed fonts (hard to read)
116
+ - ❌ Multiple font families (>2 looks unprofessional)
117
+
118
+ ### Font Sizes
119
+
120
+ **Minimum Readable Sizes**:
121
+ - **Title slide title**: 44-54pt
122
+ - **Section headers**: 36-44pt
123
+ - **Slide titles**: 32-40pt
124
+ - **Body text**: 24-28pt (absolute minimum 18pt)
125
+ - **Figure labels**: 18-24pt
126
+ - **Captions and citations**: 14-16pt (use sparingly)
127
+
128
+ **The Room Test**:
129
+ - Can text be read from the back of the room?
130
+ - Rule: Body text should be readable at 6× screen height distance
131
+ - When in doubt: go larger
132
+
133
+ **Size Relationships**:
134
+ ```
135
+ Title: 40pt
136
+ ━━━━━━━━━━━━━━━━━
137
+ Subheading: 28pt
138
+ ─────────────
139
+ Body text: 24pt
140
+ Regular content for audience
141
+
142
+ Caption: 16pt
143
+ ```
144
+
145
+ ### Text Formatting
146
+
147
+ **Best Practices**:
148
+
149
+ **Line Length**:
150
+ - Maximum 50-60 characters per line
151
+ - Break long sentences into multiple lines
152
+ - Use phrases, not full sentences when possible
153
+
154
+ **Line Spacing**:
155
+ - 1.2-1.5× line height for readability
156
+ - More spacing for dense content
157
+ - Consistent spacing throughout
158
+
159
+ **Alignment**:
160
+ - **Left-aligned**: Best for body text (natural reading)
161
+ - **Center-aligned**: Titles, short phrases, key messages
162
+ - **Right-aligned**: Rarely used (occasionally for design balance)
163
+ - **Justified**: Avoid (creates awkward spacing)
164
+
165
+ **Emphasis**:
166
+ - ✅ **Bold** for key terms (use sparingly)
167
+ - ✅ Color for emphasis (consistent meaning)
168
+ - ✅ Size increase for importance
169
+ - ❌ Avoid italics (hard to read from distance)
170
+ - ❌ Avoid underline (confused with hyperlinks)
171
+ - ❌ AVOID ALL CAPS FOR BODY TEXT (READS AS SHOUTING)
172
+
173
+ ### The 6×6 Rule
174
+
175
+ **Guideline**: Maximum 6 bullets per slide, maximum 6 words per bullet.
176
+
177
+ **Rationale**:
178
+ - More text = audience reads instead of listens
179
+ - Bullet points are prompts, not sentences
180
+ - You provide the explanation verbally
181
+
182
+ **Better Approach**:
183
+ - 3-4 bullets optimal
184
+ - 4-8 words per bullet
185
+ - Use fragments, not complete sentences
186
+ - Consider replacing text with visuals
187
+
188
+ **Example Transformation**:
189
+ ```
190
+ TOO MUCH TEXT:
191
+ • Our study examined the relationship between dietary interventions
192
+ and cardiovascular outcomes in 1,500 participants over 5 years
193
+ • We found that participants in the intervention group showed
194
+ significantly reduced risk compared to controls
195
+ • The effect size was larger than previous studies and persisted
196
+ at long-term follow-up
197
+
198
+ BETTER:
199
+ • 5-year dietary intervention study
200
+ • 27% reduced cardiovascular risk
201
+ • Largest effect to date
202
+ ```
203
+
204
+ ## Color Theory
205
+
206
+ ### Color Palettes for Scientific Presentations
207
+
208
+ **Purpose-Driven Color Selection**:
209
+
210
+ **Professional/Academic** (Conservative):
211
+ - Navy blue (#1C3D5A), gray (#4A5568), white (#FFFFFF)
212
+ - Accent: Orange (#E67E22) or green (#27AE60)
213
+ - Use: Faculty seminars, grant presentations, institutional talks
214
+
215
+ **Modern/Engaging** (Energetic):
216
+ - Teal (#0A9396), coral (#EE6C4D), cream (#F4F1DE)
217
+ - Accent: Burgundy (#780000)
218
+ - Use: Conference talks, public engagement, TED-style talks
219
+
220
+ **High Contrast** (Maximum Legibility):
221
+ - Black text (#000000) on white (#FFFFFF)
222
+ - Dark blue (#003366) on white
223
+ - White on dark gray (#2D3748)
224
+ - Use: Large venues, virtual presentations, accessibility priority
225
+
226
+ **Data Visualization** (Color-blind Safe):
227
+ - Blue (#0173B2), orange (#DE8F05), green (#029E73), red (#CC78BC)
228
+ - Based on Wong/IBM palettes
229
+ - Use: Figures with categorical data, bar charts, line plots
230
+
231
+ ### Color Psychology in Science
232
+
233
+ **Blue**:
234
+ - Associations: Trust, stability, professionalism, intelligence
235
+ - Use: Backgrounds, institutional presentations, technology topics
236
+ - Caution: Can feel cold; balance with warmer accents
237
+
238
+ **Green**:
239
+ - Associations: Growth, health, nature, sustainability
240
+ - Use: Biology, environmental science, health outcomes
241
+ - Caution: Avoid red-green combinations (color blindness)
242
+
243
+ **Red/Orange**:
244
+ - Associations: Energy, urgency, warning, importance
245
+ - Use: Highlighting critical findings, emphasis, calls to action
246
+ - Caution: Don't overuse; loses impact
247
+
248
+ **Purple**:
249
+ - Associations: Innovation, creativity, wisdom
250
+ - Use: Neuroscience, novel methods, creative research
251
+ - Caution: Can appear less serious in some contexts
252
+
253
+ **Gray**:
254
+ - Associations: Neutrality, professionalism, sophistication
255
+ - Use: Backgrounds, de-emphasized content, grounding
256
+ - Caution: Can feel dull if overused
257
+
258
+ ### Color Contrast and Accessibility
259
+
260
+ **WCAG Standards** (Web Content Accessibility Guidelines):
261
+ - **Level AA**: 4.5:1 contrast ratio for normal text
262
+ - **Level AAA**: 7:1 contrast ratio (preferred for presentations)
263
+
264
+ **High Contrast Combinations**:
265
+ - ✅ Black on white (21:1)
266
+ - ✅ Dark blue (#003366) on white (12.6:1)
267
+ - ✅ White on dark gray (#2D3748) (11.8:1)
268
+ - ✅ Dark text (#333333) on cream (#F4F1DE) (9.7:1)
269
+
270
+ **Low Contrast Combinations** (Avoid):
271
+ - ❌ Light gray on white
272
+ - ❌ Yellow on white
273
+ - ❌ Pastel colors on white backgrounds
274
+ - ❌ Red on black (difficult to read)
275
+
276
+ **Testing Contrast**:
277
+ - Use online tools (e.g., WebAIM Contrast Checker)
278
+ - Print slide in grayscale (should remain legible)
279
+ - View from distance (simulate audience perspective)
280
+
281
+ ### Color Blindness Considerations
282
+
283
+ **Prevalence**: ~8% of men, ~0.5% of women have color vision deficiency
284
+
285
+ **Most Common**: Red-green color blindness (protanopia/deuteranopia)
286
+
287
+ **Safe Practices**:
288
+ - ✅ Use blue/orange instead of red/green
289
+ - ✅ Add patterns or shapes in addition to color
290
+ - ✅ Use color AND other differentiators (shape, size, position)
291
+ - ✅ Test with color blindness simulator
292
+
293
+ **Color-Blind Safe Palettes**:
294
+ ```
295
+ Primary: Blue (#0173B2)
296
+ Contrast: Orange (#DE8F05) [NOT green]
297
+ Additional: Magenta (#CC78BC), Teal (#029E73)
298
+ ```
299
+
300
+ **Figure Design**:
301
+ - Don't rely solely on red vs. green lines
302
+ - Use different line styles (solid, dashed, dotted)
303
+ - Use symbols (circle, square, triangle) for scatter plots
304
+ - Label directly on plot rather than color legend only
305
+
306
+ ## Layout and Composition
307
+
308
+ ### The Rule of Thirds
309
+
310
+ Divide slide into 3×3 grid; place key elements at intersections or along lines.
311
+
312
+ **Application**:
313
+ ```
314
+ +-------+-------+-------+
315
+ | ┃ | ┃ | ┃ |
316
+ |---●---|---●---|---●---| ← Key focal points (●)
317
+ | ┃ | ┃ | ┃ |
318
+ |---●---|---●---|---●---|
319
+ | ┃ | ┃ | ┃ |
320
+ |---●---|---●---|---●---|
321
+ | ┃ | ┃ | ┃ |
322
+ +-------+-------+-------+
323
+ ```
324
+
325
+ **Benefits**:
326
+ - More visually interesting than centered layouts
327
+ - Natural eye flow
328
+ - Professional appearance
329
+ - Guides attention strategically
330
+
331
+ **Example Usage**:
332
+ - Place key figure at right third
333
+ - Text summary on left two-thirds
334
+ - Title at top third line
335
+ - Logo at bottom-right intersection
336
+
337
+ ### White Space
338
+
339
+ **Definition**: Empty space around and between elements.
340
+
341
+ **Purpose**:
342
+ - Gives content room to "breathe"
343
+ - Increases focus on important elements
344
+ - Prevents overwhelming the audience
345
+ - Projects professionalism and confidence
346
+
347
+ **Guidelines**:
348
+ - Margins: Minimum 5-10% of slide on all sides
349
+ - Element spacing: Clear separation between unrelated items
350
+ - Text padding: Space around text blocks
351
+ - Don't fill every pixel: Empty space is valuable
352
+
353
+ **Common Mistakes**:
354
+ - Cramming too much on one slide
355
+ - Extending content to edges
356
+ - No space between elements
357
+ - Fear of "wasting" space
358
+
359
+ ### Layout Patterns
360
+
361
+ **Title + Content**:
362
+ ```
363
+ ┌─────────────────────────┐
364
+ │ Slide Title │
365
+ ├─────────────────────────┤
366
+ │ │
367
+ │ Content Area │
368
+ │ (text, figure, │
369
+ │ or combination) │
370
+ │ │
371
+ └─────────────────────────┘
372
+ ```
373
+ Use: Standard slide type, most common
374
+
375
+ **Two Column**:
376
+ ```
377
+ ┌─────────────────────────┐
378
+ │ Slide Title │
379
+ ├───────────┬─────────────┤
380
+ │ │ │
381
+ │ Text │ Figure │
382
+ │ Column │ Column │
383
+ │ │ │
384
+ └───────────┴─────────────┘
385
+ ```
386
+ Use: Comparing items, text + figure
387
+
388
+ **Full-Slide Figure**:
389
+ ```
390
+ ┌─────────────────────────┐
391
+ │ │
392
+ │ │
393
+ │ Large Figure or │
394
+ │ Image │
395
+ │ │
396
+ │ │
397
+ └─────────────────────────┘
398
+ ```
399
+ Use: Key results, impactful visuals
400
+
401
+ **Text Overlay**:
402
+ ```
403
+ ┌─────────────────────────┐
404
+ │ ┌─────────────┐ │
405
+ │ │ Text Box │ │
406
+ │ └─────────────┘ │
407
+ │ Background Image │
408
+ │ │
409
+ └─────────────────────────┘
410
+ ```
411
+ Use: Title slide, section dividers
412
+
413
+ **Grid Layout**:
414
+ ```
415
+ ┌─────────────────────────┐
416
+ │ Title │
417
+ ├─────────┬───────┬───────┤
418
+ │ Item 1 │ Item 2│ Item 3│
419
+ ├─────────┼───────┼───────┤
420
+ │ Item 4 │ Item 5│ Item 6│
421
+ └─────────┴───────┴───────┘
422
+ ```
423
+ Use: Multiple related items, comparisons
424
+
425
+ ### Alignment
426
+
427
+ **Principle**: Align elements to create visual order and relationships.
428
+
429
+ **Types**:
430
+
431
+ **Edge Alignment**:
432
+ - Align left edges of text blocks
433
+ - Align right edges of figures
434
+ - Align top edges of items in row
435
+
436
+ **Center Alignment**:
437
+ - Center title on slide
438
+ - Center key messages
439
+ - Center lone figures
440
+
441
+ **Grid Alignment**:
442
+ - Use invisible grid
443
+ - Snap elements to grid lines
444
+ - Maintains consistency across slides
445
+
446
+ **Visual Impact**:
447
+ - Aligned elements look intentional and professional
448
+ - Misaligned elements appear careless
449
+ - Small misalignments are very noticeable
450
+
451
+ ## Background Design
452
+
453
+ ### Background Colors
454
+
455
+ **Best Practices**:
456
+
457
+ **Light Backgrounds** (Most Common):
458
+ - White or off-white (#FFFFFF, #F8F9FA)
459
+ - Very light gray (#F5F5F5)
460
+ - Cream/beige (#FAF8F3)
461
+
462
+ **Advantages**:
463
+ - Maximum contrast for dark text
464
+ - Works in any lighting
465
+ - Professional and clean
466
+ - Easier on projectors
467
+
468
+ **Dark Backgrounds**:
469
+ - Dark gray (#2D3748)
470
+ - Navy blue (#1A202C)
471
+ - Black (#000000)
472
+
473
+ **Advantages**:
474
+ - Modern, sophisticated
475
+ - Good for dark venues
476
+ - Reduces eye strain in dark rooms
477
+ - Makes colors pop
478
+
479
+ **Disadvantages**:
480
+ - Requires light-colored text
481
+ - Can be difficult in bright rooms
482
+ - Some projectors handle poorly
483
+
484
+ **Gradient Backgrounds**:
485
+ - ✅ Subtle gradients acceptable (light to lighter)
486
+ - ❌ Avoid busy or high-contrast gradients
487
+ - ❌ Don't distract from content
488
+
489
+ **Image Backgrounds**:
490
+ - Use only for title/section slides
491
+ - Ensure sufficient contrast with text
492
+ - Add semi-transparent overlay if needed
493
+ - Avoid busy or cluttered images
494
+
495
+ ### Borders and Frames
496
+
497
+ **Minimal Approach** (Recommended):
498
+ - No borders on most slides
499
+ - Let white space define boundaries
500
+ - Clean, modern appearance
501
+
502
+ **Selective Borders**:
503
+ - Around key figures for emphasis
504
+ - Separating distinct sections
505
+ - Highlighting callout boxes
506
+ - Simple, thin lines only
507
+
508
+ **Avoid**:
509
+ - Decorative borders
510
+ - Thick, colorful frames
511
+ - Clipart-style elements
512
+ - 3D effects and shadows
513
+
514
+ ## Visual Elements
515
+
516
+ ### Icons and Graphics
517
+
518
+ **Purpose**:
519
+ - Visual anchors for concepts
520
+ - Break up text-heavy slides
521
+ - Quick recognition of section types
522
+ - Add visual interest
523
+
524
+ **Best Practices**:
525
+ - ✅ Consistent style (all outline or all filled)
526
+ - ✅ Simple, recognizable designs
527
+ - ✅ Appropriate size (not too large or small)
528
+ - ✅ Limited color palette matching theme
529
+ - ❌ Avoid clipart or cartoonish graphics (unless appropriate)
530
+ - ❌ Don't use for decoration only (should convey meaning)
531
+
532
+ **Sources**:
533
+ - Font Awesome
534
+ - Noun Project
535
+ - Material Design Icons
536
+ - Custom scientific illustrations
537
+
538
+ ### Bullets and Lists
539
+
540
+ **Bullet Styles**:
541
+ - **Simple shapes**: Circle (•), square (■), dash (−)
542
+ - **Avoid**: Complex symbols, changing bullet styles within list
543
+ - **Hierarchy**: Different bullets for different levels
544
+
545
+ **List Best Practices**:
546
+ - Maximum 4-6 items per list
547
+ - Parallel structure (all start with verb, or all nouns, etc.)
548
+ - Use fragments, not complete sentences
549
+ - Adequate spacing between items (1.5-2× line height)
550
+
551
+ **Alternative to Bullets**:
552
+ - **Numbered lists**: When order matters
553
+ - **Icons**: Visual representation of each point
554
+ - **Progressive builds**: Reveal one point at a time
555
+ - **Separate slides**: One concept per slide
556
+
557
+ ### Shapes and Dividers
558
+
559
+ **Uses**:
560
+ - Background rectangles to highlight content
561
+ - Arrows showing relationships or flow
562
+ - Circles for emphasis or grouping
563
+ - Lines separating sections
564
+
565
+ **Guidelines**:
566
+ - Keep shapes simple (rectangles, circles, lines)
567
+ - Use brand colors
568
+ - Maintain consistency
569
+ - Avoid 3D effects
570
+ - Don't overuse
571
+
572
+ ## Animation and Builds
573
+
574
+ ### When to Use Animation
575
+
576
+ **Appropriate Uses**:
577
+ - **Progressive disclosure**: Reveal bullet points one at a time
578
+ - **Build complex figures**: Add layers incrementally
579
+ - **Show process**: Illustrate sequential steps
580
+ - **Emphasize transitions**: Highlight connections
581
+ - **Control pacing**: Prevent audience from reading ahead
582
+
583
+ **Inappropriate Uses**:
584
+ - ❌ Decoration or entertainment
585
+ - ❌ Every slide transition
586
+ - ❌ Multiple animations per slide
587
+ - ❌ Distracting effects (spin, bounce, etc.)
588
+
589
+ ### Types of Animations
590
+
591
+ **Entrance**:
592
+ - **Appear**: Instant (good for fast-paced talks)
593
+ - **Fade**: Subtle, professional
594
+ - **Wipe**: Directional reveal
595
+ - Avoid: Fly in, bounce, spiral, etc.
596
+
597
+ **Exit**:
598
+ - Rarely needed
599
+ - Use to remove intermediary steps
600
+ - Keep simple (fade or disappear)
601
+
602
+ **Emphasis**:
603
+ - Color change for highlighting
604
+ - Bold/underline to draw attention
605
+ - Grow slightly for importance
606
+ - Use very sparingly
607
+
608
+ **Builds**:
609
+ - Reveal bullet points progressively
610
+ - Add elements to complex figure
611
+ - Show before/after states
612
+ - Demonstrate process steps
613
+
614
+ **Best Practices**:
615
+ - Fast transitions (0.2-0.3 seconds)
616
+ - Consistent animation type throughout
617
+ - Click to advance (not automatic timing)
618
+ - Builds should add clarity, not complexity
619
+
620
+ ## Common Design Mistakes
621
+
622
+ ### Content Mistakes
623
+
624
+ **Too Much Text**:
625
+ - Problem: Audience reads instead of listening
626
+ - Fix: Use key phrases, not paragraphs; move details to notes
627
+
628
+ **Too Many Concepts per Slide**:
629
+ - Problem: Cognitive overload, unclear focus
630
+ - Fix: One idea per slide; split complex slides into multiple
631
+
632
+ **Inconsistent Formatting**:
633
+ - Problem: Looks unprofessional, distracting
634
+ - Fix: Use templates, maintain style guide
635
+
636
+ **Poor Contrast**:
637
+ - Problem: Illegible from distance
638
+ - Fix: Test at actual presentation size, use high-contrast combinations
639
+
640
+ **Tiny Fonts**:
641
+ - Problem: Unreadable for audience
642
+ - Fix: Minimum 18pt, preferably 24pt+ for body text
643
+
644
+ ### Visual Mistakes
645
+
646
+ **Cluttered Slides**:
647
+ - Problem: No clear focal point, overwhelming
648
+ - Fix: Embrace white space, remove non-essential elements
649
+
650
+ **Low-Quality Images**:
651
+ - Problem: Pixelated or blurry figures
652
+ - Fix: Use high-resolution images (300 DPI minimum)
653
+
654
+ **Distracting Backgrounds**:
655
+ - Problem: Competes with content
656
+ - Fix: Simple, solid colors or subtle gradients
657
+
658
+ **Overuse of Effects**:
659
+ - Problem: Looks amateurish, distracting
660
+ - Fix: Minimal or no shadows, gradients, 3D effects
661
+
662
+ **Misaligned Elements**:
663
+ - Problem: Appears careless
664
+ - Fix: Use alignment tools, grids, and guides
665
+
666
+ ### Color Mistakes
667
+
668
+ **Insufficient Contrast**:
669
+ - Problem: Hard to read
670
+ - Fix: Test with contrast checker, use dark on light or light on dark
671
+
672
+ **Too Many Colors**:
673
+ - Problem: Chaotic, unprofessional
674
+ - Fix: Limit to 3-5 colors total
675
+
676
+ **Red-Green Combinations**:
677
+ - Problem: Invisible to color-blind audience members
678
+ - Fix: Use blue-orange or add patterns/shapes
679
+
680
+ **Clashing Colors**:
681
+ - Problem: Visually jarring
682
+ - Fix: Use color palette tools, test combinations
683
+
684
+ ## Accessibility
685
+
686
+ ### Designing for All Audiences
687
+
688
+ **Visual Impairments**:
689
+ - High contrast text (minimum 4.5:1, preferably 7:1)
690
+ - Large fonts (minimum 18pt, prefer 24pt+)
691
+ - Simple, clear fonts
692
+ - No reliance on color alone to convey meaning
693
+
694
+ **Color Blindness**:
695
+ - Avoid red-green combinations
696
+ - Use patterns, shapes, or labels in addition to color
697
+ - Test with color blindness simulator
698
+ - Provide alternative visual cues
699
+
700
+ **Cognitive Considerations**:
701
+ - Simple, uncluttered layouts
702
+ - One concept per slide
703
+ - Clear visual hierarchy
704
+ - Consistent navigation and structure
705
+
706
+ **Presentation Environment**:
707
+ - Works in various lighting conditions
708
+ - Visible from distance (back of large room)
709
+ - Readable on different screens (laptop, projector, phone)
710
+ - Printable in grayscale if needed
711
+
712
+ ### Alternative Text and Descriptions
713
+
714
+ **For Figures**:
715
+ - Provide verbal description during talk
716
+ - Include detailed caption in notes
717
+ - Describe key patterns: "Notice the increasing trend..."
718
+
719
+ **For Complex Visuals**:
720
+ - Break into components
721
+ - Use progressive builds
722
+ - Provide interpretive context
723
+
724
+ ## Design Workflow
725
+
726
+ ### Step 1: Define Visual Identity
727
+
728
+ Before creating slides:
729
+ 1. **Color palette**: Choose 3-5 colors
730
+ 2. **Fonts**: Select 1-2 font families
731
+ 3. **Style**: Decide on overall aesthetic (minimal, bold, traditional)
732
+ 4. **Templates**: Create master slides for different types
733
+
734
+ ### Step 2: Create Master Templates
735
+
736
+ Design 4-6 slide layouts:
737
+ 1. **Title slide**: Name, title, affiliation
738
+ 2. **Section divider**: Major transitions
739
+ 3. **Content slide**: Standard text/bullets
740
+ 4. **Figure slide**: Large visual focus
741
+ 5. **Two-column**: Text + figure side-by-side
742
+ 6. **Closing**: Questions, contact, acknowledgments
743
+
744
+ ### Step 3: Apply Consistently
745
+
746
+ For each slide:
747
+ - Choose appropriate template
748
+ - Add content (text or visuals)
749
+ - Ensure alignment and spacing
750
+ - Check font sizes and contrast
751
+ - Verify consistency with other slides
752
+
753
+ ### Step 4: Review and Refine
754
+
755
+ Review checklist:
756
+ - [ ] Every slide has clear focus
757
+ - [ ] Text is minimal and readable
758
+ - [ ] Visual hierarchy is clear
759
+ - [ ] Colors are consistent and accessible
760
+ - [ ] Alignment is precise
761
+ - [ ] White space is adequate
762
+ - [ ] Animations are purposeful
763
+ - [ ] Overall flow is smooth
764
+
765
+ ## Tools and Resources
766
+
767
+ ### Design Software
768
+
769
+ **PowerPoint**:
770
+ - Master slides for templates
771
+ - Alignment guides and gridlines
772
+ - Design Ideas feature for inspiration
773
+ - Morph transition for smooth animations
774
+
775
+ **Keynote** (Mac):
776
+ - Beautiful default templates
777
+ - Smooth animations
778
+ - Magic Move for object transitions
779
+
780
+ **Google Slides**:
781
+ - Collaborative editing
782
+ - Cloud-based access
783
+ - Simple, clean interface
784
+
785
+ **LaTeX Beamer**:
786
+ - Consistent, professional appearance
787
+ - Excellent for equations and code
788
+ - Version control friendly
789
+ - Reproducible designs
790
+
791
+ ### Design Resources
792
+
793
+ **Color Tools**:
794
+ - Coolors.co: Palette generator
795
+ - Adobe Color: Color scheme creator
796
+ - WebAIM Contrast Checker: Accessibility testing
797
+ - Coblis: Color blindness simulator
798
+
799
+ **Icon Sources**:
800
+ - Font Awesome: General icons
801
+ - Noun Project: Specific concepts
802
+ - BioIcons: Science-specific graphics
803
+ - Flaticon: Large collection
804
+
805
+ **Inspiration**:
806
+ - Scientific presentation examples in your field
807
+ - TED talks for delivery style
808
+ - Conference websites for design trends
809
+ - Design portfolios (Behance, Dribbble)
810
+
811
+ ## Summary Checklist
812
+
813
+ Before finalizing your slide design:
814
+
815
+ **Typography**:
816
+ - [ ] Font size ≥18pt minimum, preferably 24pt+ for body
817
+ - [ ] Maximum 6 bullets per slide, 6 words per bullet
818
+ - [ ] Sans-serif fonts used throughout
819
+ - [ ] Consistent font family (1-2 max)
820
+
821
+ **Color**:
822
+ - [ ] High contrast text-background (4.5:1 minimum)
823
+ - [ ] Limited color palette (3-5 colors)
824
+ - [ ] Color-blind safe combinations
825
+ - [ ] Consistent color use throughout
826
+
827
+ **Layout**:
828
+ - [ ] One main idea per slide
829
+ - [ ] Generous white space (don't fill every pixel)
830
+ - [ ] Elements aligned precisely
831
+ - [ ] Consistent layouts for similar content
832
+
833
+ **Visual Elements**:
834
+ - [ ] High-resolution images (300 DPI)
835
+ - [ ] Consistent icon/graphic style
836
+ - [ ] Minimal decorative elements
837
+ - [ ] Clear visual hierarchy
838
+
839
+ **Accessibility**:
840
+ - [ ] Readable from back of room
841
+ - [ ] Works in various lighting conditions
842
+ - [ ] No reliance on color alone
843
+ - [ ] Clear without audio (for recorded talks)
844
+
845
+ **Professional Polish**:
846
+ - [ ] Consistent template throughout
847
+ - [ ] No typos or formatting errors
848
+ - [ ] Smooth animations (if any)
849
+ - [ ] Clean, uncluttered appearance