@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.
- package/.ada/SYSTEM.md +81 -0
- package/.ada/agents/researcher.md +69 -0
- package/.ada/agents/reviewer.md +92 -0
- package/.ada/agents/verifier.md +45 -0
- package/.ada/agents/writer.md +54 -0
- package/.ada/settings.json +32 -0
- package/.ada/themes/ada.json +85 -0
- package/.env.example +31 -0
- package/AGENTS.md +79 -0
- package/LICENSE +191 -0
- package/README.md +188 -0
- package/bin/ada.js +26 -0
- package/dist/bootstrap/sync.js +143 -0
- package/dist/cli.js +404 -0
- package/dist/config/paths.js +32 -0
- package/dist/index.js +10 -0
- package/dist/model/catalog.js +255 -0
- package/dist/model/commands.js +180 -0
- package/dist/pi/launch.js +33 -0
- package/dist/pi/package-presets.js +55 -0
- package/dist/pi/runtime.js +81 -0
- package/dist/pi/settings.js +108 -0
- package/dist/pi/web-access.js +74 -0
- package/dist/search/commands.js +12 -0
- package/dist/setup/doctor.js +126 -0
- package/dist/setup/preview.js +117 -0
- package/dist/setup/prompts.js +34 -0
- package/dist/setup/setup.js +98 -0
- package/dist/setup/update.js +133 -0
- package/dist/system/executables.js +38 -0
- package/dist/system/node-version.js +31 -0
- package/dist/system/open-url.js +35 -0
- package/dist/system/promise-polyfill.js +12 -0
- package/dist/ui/terminal.js +64 -0
- package/dist/web/launch.js +48 -0
- package/dist/web-search.js +1 -0
- package/extensions/docparser/constants.ts +62 -0
- package/extensions/docparser/deps.ts +584 -0
- package/extensions/docparser/doctor.ts +353 -0
- package/extensions/docparser/index.ts +9 -0
- package/extensions/docparser/input.ts +230 -0
- package/extensions/docparser/request.ts +67 -0
- package/extensions/docparser/schema.ts +82 -0
- package/extensions/docparser/tool.ts +305 -0
- package/extensions/docparser/types.ts +99 -0
- package/extensions/research-tools/alpha.ts +107 -0
- package/extensions/research-tools/header.ts +284 -0
- package/extensions/research-tools/help.ts +93 -0
- package/extensions/research-tools/project-scaffold.ts +64 -0
- package/extensions/research-tools/project.ts +123 -0
- package/extensions/research-tools/shared.ts +16 -0
- package/extensions/research-tools.ts +42 -0
- package/logo.d.mts +3 -0
- package/logo.mjs +14 -0
- package/metadata/commands.d.mts +46 -0
- package/metadata/commands.mjs +133 -0
- package/package.json +80 -0
- package/prompts/audit.md +17 -0
- package/prompts/autoresearch.md +66 -0
- package/prompts/compare.md +18 -0
- package/prompts/deepresearch.md +189 -0
- package/prompts/draft.md +19 -0
- package/prompts/jobs.md +16 -0
- package/prompts/litreview.md +18 -0
- package/prompts/log.md +14 -0
- package/prompts/replicate.md +24 -0
- package/prompts/review.md +18 -0
- package/prompts/watch.md +16 -0
- package/scripts/build-native-bundle.mjs +349 -0
- package/scripts/check-node-version.mjs +35 -0
- package/scripts/patch-embedded-pi.mjs +588 -0
- package/scripts/prepare-runtime-workspace.mjs +162 -0
- package/scripts/prune-runtime-deps.mjs +131 -0
- package/scripts/release.sh +152 -0
- package/skills/adaptyv/SKILL.md +112 -0
- package/skills/adaptyv/reference/api_reference.md +308 -0
- package/skills/adaptyv/reference/examples.md +913 -0
- package/skills/adaptyv/reference/experiments.md +360 -0
- package/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/skills/aeon/SKILL.md +372 -0
- package/skills/aeon/references/anomaly_detection.md +154 -0
- package/skills/aeon/references/classification.md +144 -0
- package/skills/aeon/references/clustering.md +123 -0
- package/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/skills/aeon/references/distances.md +256 -0
- package/skills/aeon/references/forecasting.md +140 -0
- package/skills/aeon/references/networks.md +289 -0
- package/skills/aeon/references/regression.md +118 -0
- package/skills/aeon/references/segmentation.md +163 -0
- package/skills/aeon/references/similarity_search.md +187 -0
- package/skills/aeon/references/transformations.md +246 -0
- package/skills/alpha-research/SKILL.md +42 -0
- package/skills/alpha-vantage/SKILL.md +142 -0
- package/skills/alpha-vantage/references/commodities.md +153 -0
- package/skills/alpha-vantage/references/economic-indicators.md +158 -0
- package/skills/alpha-vantage/references/forex-crypto.md +154 -0
- package/skills/alpha-vantage/references/fundamentals.md +223 -0
- package/skills/alpha-vantage/references/intelligence.md +138 -0
- package/skills/alpha-vantage/references/options.md +93 -0
- package/skills/alpha-vantage/references/technical-indicators.md +374 -0
- package/skills/alpha-vantage/references/time-series.md +157 -0
- package/skills/alphafold-database/SKILL.md +511 -0
- package/skills/alphafold-database/references/api_reference.md +423 -0
- package/skills/anndata/SKILL.md +398 -0
- package/skills/anndata/references/best_practices.md +525 -0
- package/skills/anndata/references/concatenation.md +396 -0
- package/skills/anndata/references/data_structure.md +314 -0
- package/skills/anndata/references/io_operations.md +404 -0
- package/skills/anndata/references/manipulation.md +516 -0
- package/skills/arboreto/SKILL.md +241 -0
- package/skills/arboreto/references/algorithms.md +138 -0
- package/skills/arboreto/references/basic_inference.md +151 -0
- package/skills/arboreto/references/distributed_computing.md +242 -0
- package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/skills/arxiv-database/SKILL.md +362 -0
- package/skills/arxiv-database/references/api_reference.md +430 -0
- package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
- package/skills/astropy/SKILL.md +329 -0
- package/skills/astropy/references/coordinates.md +273 -0
- package/skills/astropy/references/cosmology.md +307 -0
- package/skills/astropy/references/fits.md +396 -0
- package/skills/astropy/references/tables.md +489 -0
- package/skills/astropy/references/time.md +404 -0
- package/skills/astropy/references/units.md +178 -0
- package/skills/astropy/references/wcs_and_other_modules.md +373 -0
- package/skills/autoresearch/SKILL.md +12 -0
- package/skills/benchling-integration/SKILL.md +478 -0
- package/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/skills/benchling-integration/references/authentication.md +379 -0
- package/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/skills/bgpt-paper-search/SKILL.md +81 -0
- package/skills/bindingdb-database/SKILL.md +332 -0
- package/skills/bindingdb-database/references/affinity_queries.md +178 -0
- package/skills/biopython/SKILL.md +441 -0
- package/skills/biopython/references/advanced.md +577 -0
- package/skills/biopython/references/alignment.md +362 -0
- package/skills/biopython/references/blast.md +455 -0
- package/skills/biopython/references/databases.md +484 -0
- package/skills/biopython/references/phylogenetics.md +566 -0
- package/skills/biopython/references/sequence_io.md +285 -0
- package/skills/biopython/references/structure.md +564 -0
- package/skills/biorxiv-database/SKILL.md +481 -0
- package/skills/biorxiv-database/references/api_reference.md +280 -0
- package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/skills/bioservices/SKILL.md +359 -0
- package/skills/bioservices/references/identifier_mapping.md +685 -0
- package/skills/bioservices/references/services_reference.md +636 -0
- package/skills/bioservices/references/workflow_patterns.md +811 -0
- package/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/skills/brenda-database/SKILL.md +717 -0
- package/skills/brenda-database/references/api_reference.md +537 -0
- package/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/skills/cbioportal-database/SKILL.md +367 -0
- package/skills/cbioportal-database/references/study_exploration.md +128 -0
- package/skills/cellxgene-census/SKILL.md +509 -0
- package/skills/cellxgene-census/references/census_schema.md +182 -0
- package/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/skills/chembl-database/SKILL.md +387 -0
- package/skills/chembl-database/references/api_reference.md +272 -0
- package/skills/chembl-database/scripts/example_queries.py +278 -0
- package/skills/cirq/SKILL.md +344 -0
- package/skills/cirq/references/building.md +307 -0
- package/skills/cirq/references/experiments.md +572 -0
- package/skills/cirq/references/hardware.md +515 -0
- package/skills/cirq/references/noise.md +515 -0
- package/skills/cirq/references/simulation.md +350 -0
- package/skills/cirq/references/transformation.md +416 -0
- package/skills/citation-management/SKILL.md +1113 -0
- package/skills/citation-management/assets/bibtex_template.bib +264 -0
- package/skills/citation-management/assets/citation_checklist.md +386 -0
- package/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/skills/citation-management/references/citation_validation.md +794 -0
- package/skills/citation-management/references/google_scholar_search.md +725 -0
- package/skills/citation-management/references/metadata_extraction.md +870 -0
- package/skills/citation-management/references/pubmed_search.md +839 -0
- package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/skills/citation-management/scripts/extract_metadata.py +569 -0
- package/skills/citation-management/scripts/format_bibtex.py +349 -0
- package/skills/citation-management/scripts/search_google_scholar.py +282 -0
- package/skills/citation-management/scripts/search_pubmed.py +398 -0
- package/skills/citation-management/scripts/validate_citations.py +497 -0
- package/skills/clinical-decision-support/SKILL.md +510 -0
- package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
- package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
- package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
- package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
- package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
- package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
- package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
- package/skills/clinical-decision-support/references/README.md +129 -0
- package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
- package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
- package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
- package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
- package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
- package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
- package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
- package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
- package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
- package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
- package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
- package/skills/clinical-reports/SKILL.md +1131 -0
- package/skills/clinical-reports/assets/case_report_template.md +352 -0
- package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
- package/skills/clinical-reports/assets/consult_note_template.md +305 -0
- package/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
- package/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
- package/skills/clinical-reports/assets/history_physical_template.md +305 -0
- package/skills/clinical-reports/assets/lab_report_template.md +309 -0
- package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
- package/skills/clinical-reports/assets/quality_checklist.md +338 -0
- package/skills/clinical-reports/assets/radiology_report_template.md +318 -0
- package/skills/clinical-reports/assets/soap_note_template.md +253 -0
- package/skills/clinical-reports/references/README.md +236 -0
- package/skills/clinical-reports/references/case_report_guidelines.md +570 -0
- package/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
- package/skills/clinical-reports/references/data_presentation.md +530 -0
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
- package/skills/clinical-reports/references/medical_terminology.md +588 -0
- package/skills/clinical-reports/references/patient_documentation.md +744 -0
- package/skills/clinical-reports/references/peer_review_standards.md +585 -0
- package/skills/clinical-reports/references/regulatory_compliance.md +577 -0
- package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
- package/skills/clinical-reports/scripts/compliance_checker.py +78 -0
- package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
- package/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
- package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
- package/skills/clinical-reports/scripts/validate_case_report.py +334 -0
- package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
- package/skills/clinicaltrials-database/SKILL.md +505 -0
- package/skills/clinicaltrials-database/references/api_reference.md +358 -0
- package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
- package/skills/clinpgx-database/SKILL.md +636 -0
- package/skills/clinpgx-database/references/api_reference.md +757 -0
- package/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
- package/skills/clinvar-database/SKILL.md +360 -0
- package/skills/clinvar-database/references/api_reference.md +227 -0
- package/skills/clinvar-database/references/clinical_significance.md +218 -0
- package/skills/clinvar-database/references/data_formats.md +358 -0
- package/skills/cobrapy/SKILL.md +461 -0
- package/skills/cobrapy/references/api_quick_reference.md +655 -0
- package/skills/cobrapy/references/workflows.md +593 -0
- package/skills/consciousness-council/SKILL.md +150 -0
- package/skills/consciousness-council/references/advanced-configurations.md +96 -0
- package/skills/cosmic-database/SKILL.md +334 -0
- package/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
- package/skills/cosmic-database/scripts/download_cosmic.py +231 -0
- package/skills/crawl4ai/SKILL.md +172 -0
- package/skills/dask/SKILL.md +454 -0
- package/skills/dask/references/arrays.md +497 -0
- package/skills/dask/references/bags.md +468 -0
- package/skills/dask/references/best-practices.md +277 -0
- package/skills/dask/references/dataframes.md +368 -0
- package/skills/dask/references/futures.md +541 -0
- package/skills/dask/references/schedulers.md +504 -0
- package/skills/datacommons-client/SKILL.md +253 -0
- package/skills/datacommons-client/references/getting_started.md +417 -0
- package/skills/datacommons-client/references/node.md +250 -0
- package/skills/datacommons-client/references/observation.md +185 -0
- package/skills/datacommons-client/references/resolve.md +246 -0
- package/skills/datamol/SKILL.md +704 -0
- package/skills/datamol/references/conformers_module.md +131 -0
- package/skills/datamol/references/core_api.md +130 -0
- package/skills/datamol/references/descriptors_viz.md +195 -0
- package/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/skills/datamol/references/io_module.md +109 -0
- package/skills/datamol/references/reactions_data.md +218 -0
- package/skills/deep-research/SKILL.md +12 -0
- package/skills/deepchem/SKILL.md +595 -0
- package/skills/deepchem/references/api_reference.md +303 -0
- package/skills/deepchem/references/workflows.md +491 -0
- package/skills/deepchem/scripts/graph_neural_network.py +338 -0
- package/skills/deepchem/scripts/predict_solubility.py +224 -0
- package/skills/deepchem/scripts/transfer_learning.py +375 -0
- package/skills/deeptools/SKILL.md +529 -0
- package/skills/deeptools/assets/quick_reference.md +58 -0
- package/skills/deeptools/references/effective_genome_sizes.md +116 -0
- package/skills/deeptools/references/normalization_methods.md +410 -0
- package/skills/deeptools/references/tools_reference.md +533 -0
- package/skills/deeptools/references/workflows.md +474 -0
- package/skills/deeptools/scripts/validate_files.py +195 -0
- package/skills/deeptools/scripts/workflow_generator.py +454 -0
- package/skills/denario/SKILL.md +213 -0
- package/skills/denario/references/examples.md +494 -0
- package/skills/denario/references/installation.md +213 -0
- package/skills/denario/references/llm_configuration.md +265 -0
- package/skills/denario/references/research_pipeline.md +471 -0
- package/skills/depmap/SKILL.md +300 -0
- package/skills/depmap/references/dependency_analysis.md +178 -0
- package/skills/dhdna-profiler/SKILL.md +162 -0
- package/skills/dhdna-profiler/references/advanced-profiling.md +72 -0
- package/skills/diffdock/SKILL.md +481 -0
- package/skills/diffdock/assets/batch_template.csv +4 -0
- package/skills/diffdock/assets/custom_inference_config.yaml +90 -0
- package/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/skills/diffdock/references/parameters_reference.md +163 -0
- package/skills/diffdock/references/workflows_examples.md +392 -0
- package/skills/diffdock/scripts/analyze_results.py +334 -0
- package/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
- package/skills/diffdock/scripts/setup_check.py +278 -0
- package/skills/dnanexus-integration/SKILL.md +381 -0
- package/skills/dnanexus-integration/references/app-development.md +247 -0
- package/skills/dnanexus-integration/references/configuration.md +646 -0
- package/skills/dnanexus-integration/references/data-operations.md +400 -0
- package/skills/dnanexus-integration/references/job-execution.md +412 -0
- package/skills/dnanexus-integration/references/python-sdk.md +523 -0
- package/skills/docker/SKILL.md +84 -0
- package/skills/docx/LICENSE.txt +30 -0
- package/skills/docx/SKILL.md +590 -0
- package/skills/docx/scripts/__init__.py +1 -0
- package/skills/docx/scripts/accept_changes.py +135 -0
- package/skills/docx/scripts/comment.py +318 -0
- package/skills/docx/scripts/office/helpers/__init__.py +0 -0
- package/skills/docx/scripts/office/helpers/merge_runs.py +199 -0
- package/skills/docx/scripts/office/helpers/simplify_redlines.py +197 -0
- package/skills/docx/scripts/office/pack.py +159 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/docx/scripts/office/soffice.py +183 -0
- package/skills/docx/scripts/office/unpack.py +132 -0
- package/skills/docx/scripts/office/validate.py +111 -0
- package/skills/docx/scripts/office/validators/__init__.py +15 -0
- package/skills/docx/scripts/office/validators/base.py +847 -0
- package/skills/docx/scripts/office/validators/docx.py +446 -0
- package/skills/docx/scripts/office/validators/pptx.py +275 -0
- package/skills/docx/scripts/office/validators/redlining.py +247 -0
- package/skills/docx/scripts/templates/comments.xml +3 -0
- package/skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/skills/docx/scripts/templates/people.xml +3 -0
- package/skills/drugbank-database/SKILL.md +188 -0
- package/skills/drugbank-database/references/chemical-analysis.md +590 -0
- package/skills/drugbank-database/references/data-access.md +242 -0
- package/skills/drugbank-database/references/drug-queries.md +386 -0
- package/skills/drugbank-database/references/interactions.md +425 -0
- package/skills/drugbank-database/references/targets-pathways.md +518 -0
- package/skills/drugbank-database/scripts/drugbank_helper.py +350 -0
- package/skills/edgartools/SKILL.md +136 -0
- package/skills/edgartools/references/ai-integration.md +274 -0
- package/skills/edgartools/references/companies.md +268 -0
- package/skills/edgartools/references/data-objects.md +237 -0
- package/skills/edgartools/references/entity-facts.md +372 -0
- package/skills/edgartools/references/filings.md +387 -0
- package/skills/edgartools/references/financial-data.md +274 -0
- package/skills/edgartools/references/xbrl.md +373 -0
- package/skills/eli5/SKILL.md +25 -0
- package/skills/ena-database/SKILL.md +202 -0
- package/skills/ena-database/references/api_reference.md +490 -0
- package/skills/ensembl-database/SKILL.md +309 -0
- package/skills/ensembl-database/references/api_endpoints.md +346 -0
- package/skills/ensembl-database/scripts/ensembl_query.py +427 -0
- package/skills/esm/SKILL.md +304 -0
- package/skills/esm/references/esm-c-api.md +583 -0
- package/skills/esm/references/esm3-api.md +452 -0
- package/skills/esm/references/forge-api.md +657 -0
- package/skills/esm/references/workflows.md +685 -0
- package/skills/etetoolkit/SKILL.md +621 -0
- package/skills/etetoolkit/references/api_reference.md +583 -0
- package/skills/etetoolkit/references/visualization.md +783 -0
- package/skills/etetoolkit/references/workflows.md +774 -0
- package/skills/etetoolkit/scripts/quick_visualize.py +214 -0
- package/skills/etetoolkit/scripts/tree_operations.py +229 -0
- package/skills/exploratory-data-analysis/SKILL.md +444 -0
- package/skills/exploratory-data-analysis/assets/report_template.md +196 -0
- package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
- package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
- package/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
- package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
- package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
- package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
- package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
- package/skills/fda-database/SKILL.md +516 -0
- package/skills/fda-database/references/animal_veterinary.md +377 -0
- package/skills/fda-database/references/api_basics.md +687 -0
- package/skills/fda-database/references/devices.md +632 -0
- package/skills/fda-database/references/drugs.md +468 -0
- package/skills/fda-database/references/foods.md +374 -0
- package/skills/fda-database/references/other.md +472 -0
- package/skills/fda-database/scripts/fda_examples.py +335 -0
- package/skills/fda-database/scripts/fda_query.py +440 -0
- package/skills/flowio/SKILL.md +606 -0
- package/skills/flowio/references/api_reference.md +372 -0
- package/skills/fluidsim/SKILL.md +347 -0
- package/skills/fluidsim/references/advanced_features.md +398 -0
- package/skills/fluidsim/references/installation.md +68 -0
- package/skills/fluidsim/references/output_analysis.md +283 -0
- package/skills/fluidsim/references/parameters.md +198 -0
- package/skills/fluidsim/references/simulation_workflow.md +172 -0
- package/skills/fluidsim/references/solvers.md +94 -0
- package/skills/fred-economic-data/SKILL.md +433 -0
- package/skills/fred-economic-data/references/api_basics.md +212 -0
- package/skills/fred-economic-data/references/categories.md +442 -0
- package/skills/fred-economic-data/references/geofred.md +588 -0
- package/skills/fred-economic-data/references/releases.md +642 -0
- package/skills/fred-economic-data/references/series.md +584 -0
- package/skills/fred-economic-data/references/sources.md +423 -0
- package/skills/fred-economic-data/references/tags.md +485 -0
- package/skills/fred-economic-data/scripts/fred_examples.py +354 -0
- package/skills/fred-economic-data/scripts/fred_query.py +590 -0
- package/skills/gene-database/SKILL.md +177 -0
- package/skills/gene-database/references/api_reference.md +404 -0
- package/skills/gene-database/references/common_workflows.md +428 -0
- package/skills/gene-database/scripts/batch_gene_lookup.py +298 -0
- package/skills/gene-database/scripts/fetch_gene_data.py +277 -0
- package/skills/gene-database/scripts/query_gene.py +251 -0
- package/skills/generate-image/SKILL.md +183 -0
- package/skills/generate-image/scripts/generate_image.py +281 -0
- package/skills/geniml/SKILL.md +316 -0
- package/skills/geniml/references/bedspace.md +127 -0
- package/skills/geniml/references/consensus_peaks.md +238 -0
- package/skills/geniml/references/region2vec.md +90 -0
- package/skills/geniml/references/scembed.md +197 -0
- package/skills/geniml/references/utilities.md +385 -0
- package/skills/geo-database/SKILL.md +813 -0
- package/skills/geo-database/references/geo_reference.md +829 -0
- package/skills/geomaster/README.md +105 -0
- package/skills/geomaster/SKILL.md +365 -0
- package/skills/geomaster/references/advanced-gis.md +376 -0
- package/skills/geomaster/references/big-data.md +363 -0
- package/skills/geomaster/references/code-examples.md +531 -0
- package/skills/geomaster/references/coordinate-systems.md +364 -0
- package/skills/geomaster/references/core-libraries.md +273 -0
- package/skills/geomaster/references/data-sources.md +330 -0
- package/skills/geomaster/references/gis-software.md +369 -0
- package/skills/geomaster/references/industry-applications.md +420 -0
- package/skills/geomaster/references/machine-learning.md +462 -0
- package/skills/geomaster/references/programming-languages.md +456 -0
- package/skills/geomaster/references/remote-sensing.md +370 -0
- package/skills/geomaster/references/scientific-domains.md +416 -0
- package/skills/geomaster/references/specialized-topics.md +428 -0
- package/skills/geomaster/references/troubleshooting.md +439 -0
- package/skills/geopandas/SKILL.md +249 -0
- package/skills/geopandas/references/crs-management.md +243 -0
- package/skills/geopandas/references/data-io.md +165 -0
- package/skills/geopandas/references/data-structures.md +70 -0
- package/skills/geopandas/references/geometric-operations.md +221 -0
- package/skills/geopandas/references/spatial-analysis.md +184 -0
- package/skills/geopandas/references/visualization.md +243 -0
- package/skills/get-available-resources/SKILL.md +275 -0
- package/skills/get-available-resources/scripts/detect_resources.py +401 -0
- package/skills/gget/SKILL.md +869 -0
- package/skills/gget/references/database_info.md +300 -0
- package/skills/gget/references/module_reference.md +467 -0
- package/skills/gget/references/workflows.md +814 -0
- package/skills/gget/scripts/batch_sequence_analysis.py +191 -0
- package/skills/gget/scripts/enrichment_pipeline.py +235 -0
- package/skills/gget/scripts/gene_analysis.py +161 -0
- package/skills/ginkgo-cloud-lab/SKILL.md +56 -0
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +85 -0
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +71 -0
- package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +87 -0
- package/skills/glycoengineering/SKILL.md +338 -0
- package/skills/glycoengineering/references/glycan_databases.md +165 -0
- package/skills/gnomad-database/SKILL.md +395 -0
- package/skills/gnomad-database/references/graphql_queries.md +219 -0
- package/skills/gnomad-database/references/variant_interpretation.md +85 -0
- package/skills/gtars/SKILL.md +283 -0
- package/skills/gtars/references/cli.md +222 -0
- package/skills/gtars/references/coverage.md +172 -0
- package/skills/gtars/references/overlap.md +156 -0
- package/skills/gtars/references/python-api.md +211 -0
- package/skills/gtars/references/refget.md +147 -0
- package/skills/gtars/references/tokenizers.md +103 -0
- package/skills/gtex-database/SKILL.md +315 -0
- package/skills/gtex-database/references/api_reference.md +191 -0
- package/skills/gwas-database/SKILL.md +606 -0
- package/skills/gwas-database/references/api_reference.md +793 -0
- package/skills/hedgefundmonitor/SKILL.md +128 -0
- package/skills/hedgefundmonitor/references/api-overview.md +93 -0
- package/skills/hedgefundmonitor/references/datasets.md +150 -0
- package/skills/hedgefundmonitor/references/endpoints-combined.md +196 -0
- package/skills/hedgefundmonitor/references/endpoints-metadata.md +136 -0
- package/skills/hedgefundmonitor/references/endpoints-series-data.md +126 -0
- package/skills/hedgefundmonitor/references/examples.md +287 -0
- package/skills/hedgefundmonitor/references/parameters.md +104 -0
- package/skills/histolab/SKILL.md +676 -0
- package/skills/histolab/references/filters_preprocessing.md +514 -0
- package/skills/histolab/references/slide_management.md +172 -0
- package/skills/histolab/references/tile_extraction.md +421 -0
- package/skills/histolab/references/tissue_masks.md +251 -0
- package/skills/histolab/references/visualization.md +547 -0
- package/skills/hmdb-database/SKILL.md +194 -0
- package/skills/hmdb-database/references/hmdb_data_fields.md +267 -0
- package/skills/hypogenic/SKILL.md +653 -0
- package/skills/hypogenic/references/config_template.yaml +150 -0
- package/skills/hypothesis-generation/SKILL.md +297 -0
- package/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
- package/skills/hypothesis-generation/assets/hypothesis_generation.sty +307 -0
- package/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
- package/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
- package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
- package/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
- package/skills/imaging-data-commons/SKILL.md +843 -0
- package/skills/imaging-data-commons/references/bigquery_guide.md +556 -0
- package/skills/imaging-data-commons/references/cli_guide.md +272 -0
- package/skills/imaging-data-commons/references/clinical_data_guide.md +324 -0
- package/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
- package/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
- package/skills/imaging-data-commons/references/digital_pathology_guide.md +403 -0
- package/skills/imaging-data-commons/references/index_tables_guide.md +146 -0
- package/skills/imaging-data-commons/references/sql_patterns.md +207 -0
- package/skills/imaging-data-commons/references/use_cases.md +186 -0
- package/skills/infographics/SKILL.md +563 -0
- package/skills/infographics/references/color_palettes.md +496 -0
- package/skills/infographics/references/design_principles.md +636 -0
- package/skills/infographics/references/infographic_types.md +907 -0
- package/skills/infographics/scripts/generate_infographic.py +234 -0
- package/skills/infographics/scripts/generate_infographic_ai.py +1290 -0
- package/skills/interpro-database/SKILL.md +305 -0
- package/skills/interpro-database/references/domain_analysis.md +159 -0
- package/skills/iso-13485-certification/SKILL.md +678 -0
- package/skills/iso-13485-certification/assets/templates/procedures/CAPA-procedure-template.md +453 -0
- package/skills/iso-13485-certification/assets/templates/procedures/document-control-procedure-template.md +567 -0
- package/skills/iso-13485-certification/assets/templates/quality-manual-template.md +521 -0
- package/skills/iso-13485-certification/references/gap-analysis-checklist.md +568 -0
- package/skills/iso-13485-certification/references/iso-13485-requirements.md +610 -0
- package/skills/iso-13485-certification/references/mandatory-documents.md +606 -0
- package/skills/iso-13485-certification/references/quality-manual-guide.md +688 -0
- package/skills/iso-13485-certification/scripts/gap_analyzer.py +440 -0
- package/skills/jaspar-database/SKILL.md +351 -0
- package/skills/jaspar-database/references/api_reference.md +182 -0
- package/skills/jobs/SKILL.md +10 -0
- package/skills/kegg-database/SKILL.md +375 -0
- package/skills/kegg-database/references/kegg_reference.md +326 -0
- package/skills/kegg-database/scripts/kegg_api.py +251 -0
- package/skills/labarchive-integration/SKILL.md +266 -0
- package/skills/labarchive-integration/references/api_reference.md +342 -0
- package/skills/labarchive-integration/references/authentication_guide.md +357 -0
- package/skills/labarchive-integration/references/integrations.md +425 -0
- package/skills/labarchive-integration/scripts/entry_operations.py +334 -0
- package/skills/labarchive-integration/scripts/notebook_operations.py +269 -0
- package/skills/labarchive-integration/scripts/setup_config.py +205 -0
- package/skills/lamindb/SKILL.md +388 -0
- package/skills/lamindb/references/annotation-validation.md +513 -0
- package/skills/lamindb/references/core-concepts.md +380 -0
- package/skills/lamindb/references/data-management.md +433 -0
- package/skills/lamindb/references/integrations.md +642 -0
- package/skills/lamindb/references/ontologies.md +497 -0
- package/skills/lamindb/references/setup-deployment.md +733 -0
- package/skills/latchbio-integration/SKILL.md +351 -0
- package/skills/latchbio-integration/references/data-management.md +427 -0
- package/skills/latchbio-integration/references/resource-configuration.md +429 -0
- package/skills/latchbio-integration/references/verified-workflows.md +487 -0
- package/skills/latchbio-integration/references/workflow-creation.md +254 -0
- package/skills/latex-posters/SKILL.md +1602 -0
- package/skills/latex-posters/assets/baposter_template.tex +257 -0
- package/skills/latex-posters/assets/beamerposter_template.tex +244 -0
- package/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
- package/skills/latex-posters/assets/tikzposter_template.tex +251 -0
- package/skills/latex-posters/references/README.md +417 -0
- package/skills/latex-posters/references/latex_poster_packages.md +745 -0
- package/skills/latex-posters/references/poster_content_guide.md +748 -0
- package/skills/latex-posters/references/poster_design_principles.md +806 -0
- package/skills/latex-posters/references/poster_layout_design.md +900 -0
- package/skills/latex-posters/scripts/review_poster.sh +214 -0
- package/skills/literature-review/SKILL.md +637 -0
- package/skills/literature-review/assets/review_template.md +412 -0
- package/skills/literature-review/references/citation_styles.md +166 -0
- package/skills/literature-review/references/database_strategies.md +455 -0
- package/skills/literature-review/scripts/generate_pdf.py +176 -0
- package/skills/literature-review/scripts/search_databases.py +303 -0
- package/skills/literature-review/scripts/verify_citations.py +222 -0
- package/skills/markdown-mermaid-writing/SKILL.md +327 -0
- package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +221 -0
- package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +108 -0
- package/skills/markdown-mermaid-writing/references/diagrams/block.md +177 -0
- package/skills/markdown-mermaid-writing/references/diagrams/c4.md +136 -0
- package/skills/markdown-mermaid-writing/references/diagrams/class.md +246 -0
- package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +384 -0
- package/skills/markdown-mermaid-writing/references/diagrams/er.md +222 -0
- package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +177 -0
- package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +138 -0
- package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +74 -0
- package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +107 -0
- package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +74 -0
- package/skills/markdown-mermaid-writing/references/diagrams/packet.md +55 -0
- package/skills/markdown-mermaid-writing/references/diagrams/pie.md +52 -0
- package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +66 -0
- package/skills/markdown-mermaid-writing/references/diagrams/radar.md +59 -0
- package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +88 -0
- package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +71 -0
- package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +174 -0
- package/skills/markdown-mermaid-writing/references/diagrams/state.md +150 -0
- package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +96 -0
- package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +66 -0
- package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +108 -0
- package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +53 -0
- package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +71 -0
- package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +733 -0
- package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +458 -0
- package/skills/markdown-mermaid-writing/templates/decision_record.md +211 -0
- package/skills/markdown-mermaid-writing/templates/how_to_guide.md +275 -0
- package/skills/markdown-mermaid-writing/templates/issue.md +303 -0
- package/skills/markdown-mermaid-writing/templates/kanban.md +223 -0
- package/skills/markdown-mermaid-writing/templates/presentation.md +312 -0
- package/skills/markdown-mermaid-writing/templates/project_documentation.md +412 -0
- package/skills/markdown-mermaid-writing/templates/pull_request.md +319 -0
- package/skills/markdown-mermaid-writing/templates/research_paper.md +304 -0
- package/skills/markdown-mermaid-writing/templates/status_report.md +185 -0
- package/skills/market-research-reports/SKILL.md +905 -0
- package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
- package/skills/market-research-reports/assets/market_report_template.tex +1380 -0
- package/skills/market-research-reports/assets/market_research.sty +564 -0
- package/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
- package/skills/market-research-reports/references/report_structure_guide.md +999 -0
- package/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
- package/skills/market-research-reports/scripts/generate_market_visuals.py +529 -0
- package/skills/markitdown/SKILL.md +488 -0
- package/skills/markitdown/assets/example_usage.md +463 -0
- package/skills/markitdown/references/api_reference.md +396 -0
- package/skills/markitdown/references/file_formats.md +542 -0
- package/skills/markitdown/scripts/batch_convert.py +228 -0
- package/skills/markitdown/scripts/convert_literature.py +283 -0
- package/skills/markitdown/scripts/convert_with_ai.py +240 -0
- package/skills/matchms/SKILL.md +201 -0
- package/skills/matchms/references/filtering.md +288 -0
- package/skills/matchms/references/importing_exporting.md +416 -0
- package/skills/matchms/references/similarity.md +380 -0
- package/skills/matchms/references/workflows.md +647 -0
- package/skills/matlab/SKILL.md +376 -0
- package/skills/matlab/references/data-import-export.md +479 -0
- package/skills/matlab/references/executing-scripts.md +444 -0
- package/skills/matlab/references/graphics-visualization.md +579 -0
- package/skills/matlab/references/mathematics.md +553 -0
- package/skills/matlab/references/matrices-arrays.md +349 -0
- package/skills/matlab/references/octave-compatibility.md +544 -0
- package/skills/matlab/references/programming.md +672 -0
- package/skills/matlab/references/python-integration.md +433 -0
- package/skills/matplotlib/SKILL.md +359 -0
- package/skills/matplotlib/references/api_reference.md +412 -0
- package/skills/matplotlib/references/common_issues.md +563 -0
- package/skills/matplotlib/references/plot_types.md +476 -0
- package/skills/matplotlib/references/styling_guide.md +589 -0
- package/skills/matplotlib/scripts/plot_template.py +401 -0
- package/skills/matplotlib/scripts/style_configurator.py +409 -0
- package/skills/medchem/SKILL.md +404 -0
- package/skills/medchem/references/api_guide.md +600 -0
- package/skills/medchem/references/rules_catalog.md +604 -0
- package/skills/medchem/scripts/filter_molecules.py +418 -0
- package/skills/metabolomics-workbench-database/SKILL.md +257 -0
- package/skills/metabolomics-workbench-database/references/api_reference.md +494 -0
- package/skills/modal/SKILL.md +406 -0
- package/skills/modal/references/api_reference.md +187 -0
- package/skills/modal/references/examples.md +266 -0
- package/skills/modal/references/functions.md +260 -0
- package/skills/modal/references/getting-started.md +175 -0
- package/skills/modal/references/gpu.md +174 -0
- package/skills/modal/references/images.md +259 -0
- package/skills/modal/references/resources.md +117 -0
- package/skills/modal/references/scaling.md +173 -0
- package/skills/modal/references/scheduled-jobs.md +143 -0
- package/skills/modal/references/secrets.md +119 -0
- package/skills/modal/references/volumes.md +247 -0
- package/skills/modal/references/web-endpoints.md +254 -0
- package/skills/modal-compute/SKILL.md +56 -0
- package/skills/molecular-dynamics/SKILL.md +457 -0
- package/skills/molecular-dynamics/references/mdanalysis_analysis.md +208 -0
- package/skills/molfeat/SKILL.md +509 -0
- package/skills/molfeat/references/api_reference.md +428 -0
- package/skills/molfeat/references/available_featurizers.md +333 -0
- package/skills/molfeat/references/examples.md +723 -0
- package/skills/monarch-database/SKILL.md +372 -0
- package/skills/monarch-database/references/phenotype_ontology.md +160 -0
- package/skills/networkx/SKILL.md +435 -0
- package/skills/networkx/references/algorithms.md +383 -0
- package/skills/networkx/references/generators.md +378 -0
- package/skills/networkx/references/graph-basics.md +283 -0
- package/skills/networkx/references/io.md +441 -0
- package/skills/networkx/references/visualization.md +529 -0
- package/skills/neurokit2/SKILL.md +354 -0
- package/skills/neurokit2/references/bio_module.md +417 -0
- package/skills/neurokit2/references/complexity.md +715 -0
- package/skills/neurokit2/references/ecg_cardiac.md +355 -0
- package/skills/neurokit2/references/eda.md +497 -0
- package/skills/neurokit2/references/eeg.md +506 -0
- package/skills/neurokit2/references/emg.md +408 -0
- package/skills/neurokit2/references/eog.md +407 -0
- package/skills/neurokit2/references/epochs_events.md +471 -0
- package/skills/neurokit2/references/hrv.md +480 -0
- package/skills/neurokit2/references/ppg.md +413 -0
- package/skills/neurokit2/references/rsp.md +510 -0
- package/skills/neurokit2/references/signal_processing.md +648 -0
- package/skills/neuropixels-analysis/SKILL.md +348 -0
- package/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
- package/skills/neuropixels-analysis/references/AI_CURATION.md +345 -0
- package/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
- package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +358 -0
- package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
- package/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
- package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
- package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
- package/skills/neuropixels-analysis/references/api_reference.md +415 -0
- package/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
- package/skills/neuropixels-analysis/references/standard_workflow.md +385 -0
- package/skills/neuropixels-analysis/scripts/compute_metrics.py +178 -0
- package/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
- package/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
- package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +432 -0
- package/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
- package/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
- package/skills/offer-k-dense-web/SKILL.md +21 -0
- package/skills/omero-integration/SKILL.md +249 -0
- package/skills/omero-integration/references/advanced.md +631 -0
- package/skills/omero-integration/references/connection.md +369 -0
- package/skills/omero-integration/references/data_access.md +544 -0
- package/skills/omero-integration/references/image_processing.md +665 -0
- package/skills/omero-integration/references/metadata.md +688 -0
- package/skills/omero-integration/references/rois.md +648 -0
- package/skills/omero-integration/references/scripts.md +637 -0
- package/skills/omero-integration/references/tables.md +532 -0
- package/skills/open-notebook/SKILL.md +289 -0
- package/skills/open-notebook/references/api_reference.md +715 -0
- package/skills/open-notebook/references/architecture.md +163 -0
- package/skills/open-notebook/references/configuration.md +226 -0
- package/skills/open-notebook/references/examples.md +290 -0
- package/skills/open-notebook/scripts/chat_interaction.py +190 -0
- package/skills/open-notebook/scripts/notebook_management.py +142 -0
- package/skills/open-notebook/scripts/source_ingestion.py +160 -0
- package/skills/open-notebook/scripts/test_open_notebook_skill.py +423 -0
- package/skills/openalex-database/SKILL.md +496 -0
- package/skills/openalex-database/references/api_guide.md +371 -0
- package/skills/openalex-database/references/common_queries.md +381 -0
- package/skills/openalex-database/scripts/openalex_client.py +337 -0
- package/skills/openalex-database/scripts/query_helpers.py +306 -0
- package/skills/opentargets-database/SKILL.md +371 -0
- package/skills/opentargets-database/references/api_reference.md +249 -0
- package/skills/opentargets-database/references/evidence_types.md +306 -0
- package/skills/opentargets-database/references/target_annotations.md +401 -0
- package/skills/opentargets-database/scripts/query_opentargets.py +403 -0
- package/skills/opentrons-integration/SKILL.md +571 -0
- package/skills/opentrons-integration/references/api_reference.md +366 -0
- package/skills/opentrons-integration/scripts/basic_protocol_template.py +67 -0
- package/skills/opentrons-integration/scripts/pcr_setup_template.py +154 -0
- package/skills/opentrons-integration/scripts/serial_dilution_template.py +96 -0
- package/skills/paper-2-web/SKILL.md +495 -0
- package/skills/paper-2-web/references/installation.md +141 -0
- package/skills/paper-2-web/references/paper2poster.md +346 -0
- package/skills/paper-2-web/references/paper2video.md +305 -0
- package/skills/paper-2-web/references/paper2web.md +187 -0
- package/skills/paper-2-web/references/usage_examples.md +436 -0
- package/skills/paper-code-audit/SKILL.md +12 -0
- package/skills/paper-writing/SKILL.md +12 -0
- package/skills/parallel-web/SKILL.md +314 -0
- package/skills/parallel-web/references/api_reference.md +244 -0
- package/skills/parallel-web/references/deep_research_guide.md +362 -0
- package/skills/parallel-web/references/extraction_patterns.md +338 -0
- package/skills/parallel-web/references/search_best_practices.md +297 -0
- package/skills/parallel-web/references/workflow_recipes.md +456 -0
- package/skills/parallel-web/scripts/parallel_web.py +568 -0
- package/skills/parse-document/SKILL.md +139 -0
- package/skills/pathml/SKILL.md +164 -0
- package/skills/pathml/references/data_management.md +742 -0
- package/skills/pathml/references/graphs.md +653 -0
- package/skills/pathml/references/image_loading.md +448 -0
- package/skills/pathml/references/machine_learning.md +725 -0
- package/skills/pathml/references/multiparametric.md +686 -0
- package/skills/pathml/references/preprocessing.md +722 -0
- package/skills/pdb-database/SKILL.md +307 -0
- package/skills/pdb-database/references/api_reference.md +617 -0
- package/skills/pdf/LICENSE.txt +30 -0
- package/skills/pdf/SKILL.md +314 -0
- package/skills/pdf/forms.md +294 -0
- package/skills/pdf/reference.md +612 -0
- package/skills/pdf/scripts/check_bounding_boxes.py +65 -0
- package/skills/pdf/scripts/check_fillable_fields.py +11 -0
- package/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
- package/skills/pdf/scripts/create_validation_image.py +37 -0
- package/skills/pdf/scripts/extract_form_field_info.py +122 -0
- package/skills/pdf/scripts/extract_form_structure.py +115 -0
- package/skills/pdf/scripts/fill_fillable_fields.py +98 -0
- package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
- package/skills/peer-review/SKILL.md +569 -0
- package/skills/peer-review/references/common_issues.md +552 -0
- package/skills/peer-review/references/reporting_standards.md +290 -0
- package/skills/pennylane/SKILL.md +224 -0
- package/skills/pennylane/references/advanced_features.md +667 -0
- package/skills/pennylane/references/devices_backends.md +596 -0
- package/skills/pennylane/references/getting_started.md +227 -0
- package/skills/pennylane/references/optimization.md +671 -0
- package/skills/pennylane/references/quantum_chemistry.md +567 -0
- package/skills/pennylane/references/quantum_circuits.md +437 -0
- package/skills/pennylane/references/quantum_ml.md +571 -0
- package/skills/perplexity-search/SKILL.md +446 -0
- package/skills/perplexity-search/assets/.env.example +16 -0
- package/skills/perplexity-search/references/model_comparison.md +386 -0
- package/skills/perplexity-search/references/openrouter_setup.md +454 -0
- package/skills/perplexity-search/references/search_strategies.md +258 -0
- package/skills/perplexity-search/scripts/perplexity_search.py +277 -0
- package/skills/perplexity-search/scripts/setup_env.py +171 -0
- package/skills/phylogenetics/SKILL.md +404 -0
- package/skills/phylogenetics/references/iqtree_inference.md +181 -0
- package/skills/phylogenetics/scripts/phylogenetic_analysis.py +270 -0
- package/skills/plotly/SKILL.md +265 -0
- package/skills/plotly/references/chart-types.md +488 -0
- package/skills/plotly/references/export-interactivity.md +453 -0
- package/skills/plotly/references/graph-objects.md +302 -0
- package/skills/plotly/references/layouts-styling.md +457 -0
- package/skills/plotly/references/plotly-express.md +213 -0
- package/skills/polars/SKILL.md +385 -0
- package/skills/polars/references/best_practices.md +649 -0
- package/skills/polars/references/core_concepts.md +378 -0
- package/skills/polars/references/io_guide.md +557 -0
- package/skills/polars/references/operations.md +602 -0
- package/skills/polars/references/pandas_migration.md +417 -0
- package/skills/polars/references/transformations.md +549 -0
- package/skills/polars-bio/SKILL.md +374 -0
- package/skills/polars-bio/references/bioframe_migration.md +250 -0
- package/skills/polars-bio/references/configuration.md +175 -0
- package/skills/polars-bio/references/file_io.md +414 -0
- package/skills/polars-bio/references/interval_operations.md +362 -0
- package/skills/polars-bio/references/pileup_operations.md +176 -0
- package/skills/polars-bio/references/sql_processing.md +224 -0
- package/skills/pptx/LICENSE.txt +30 -0
- package/skills/pptx/SKILL.md +232 -0
- package/skills/pptx/editing.md +205 -0
- package/skills/pptx/pptxgenjs.md +420 -0
- package/skills/pptx/scripts/__init__.py +0 -0
- package/skills/pptx/scripts/add_slide.py +195 -0
- package/skills/pptx/scripts/clean.py +286 -0
- package/skills/pptx/scripts/office/helpers/__init__.py +0 -0
- package/skills/pptx/scripts/office/helpers/merge_runs.py +199 -0
- package/skills/pptx/scripts/office/helpers/simplify_redlines.py +197 -0
- package/skills/pptx/scripts/office/pack.py +159 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/pptx/scripts/office/soffice.py +183 -0
- package/skills/pptx/scripts/office/unpack.py +132 -0
- package/skills/pptx/scripts/office/validate.py +111 -0
- package/skills/pptx/scripts/office/validators/__init__.py +15 -0
- package/skills/pptx/scripts/office/validators/base.py +847 -0
- package/skills/pptx/scripts/office/validators/docx.py +446 -0
- package/skills/pptx/scripts/office/validators/pptx.py +275 -0
- package/skills/pptx/scripts/office/validators/redlining.py +247 -0
- package/skills/pptx/scripts/thumbnail.py +289 -0
- package/skills/pptx-posters/SKILL.md +414 -0
- package/skills/pptx-posters/assets/poster_html_template.html +257 -0
- package/skills/pptx-posters/assets/poster_quality_checklist.md +358 -0
- package/skills/pptx-posters/references/poster_content_guide.md +748 -0
- package/skills/pptx-posters/references/poster_design_principles.md +806 -0
- package/skills/pptx-posters/references/poster_layout_design.md +900 -0
- package/skills/preview/SKILL.md +27 -0
- package/skills/primekg/SKILL.md +97 -0
- package/skills/primekg/scripts/query_primekg.py +123 -0
- package/skills/protocolsio-integration/SKILL.md +419 -0
- package/skills/protocolsio-integration/references/additional_features.md +387 -0
- package/skills/protocolsio-integration/references/authentication.md +100 -0
- package/skills/protocolsio-integration/references/discussions.md +225 -0
- package/skills/protocolsio-integration/references/file_manager.md +412 -0
- package/skills/protocolsio-integration/references/protocols_api.md +294 -0
- package/skills/protocolsio-integration/references/workspaces.md +293 -0
- package/skills/pubchem-database/SKILL.md +572 -0
- package/skills/pubchem-database/references/api_reference.md +440 -0
- package/skills/pubchem-database/scripts/bioactivity_query.py +367 -0
- package/skills/pubchem-database/scripts/compound_search.py +297 -0
- package/skills/pubmed-database/SKILL.md +458 -0
- package/skills/pubmed-database/references/api_reference.md +298 -0
- package/skills/pubmed-database/references/common_queries.md +453 -0
- package/skills/pubmed-database/references/search_syntax.md +436 -0
- package/skills/pufferlib/SKILL.md +434 -0
- package/skills/pufferlib/references/environments.md +508 -0
- package/skills/pufferlib/references/integration.md +621 -0
- package/skills/pufferlib/references/policies.md +653 -0
- package/skills/pufferlib/references/training.md +360 -0
- package/skills/pufferlib/references/vectorization.md +557 -0
- package/skills/pufferlib/scripts/env_template.py +340 -0
- package/skills/pufferlib/scripts/train_template.py +239 -0
- package/skills/pydeseq2/SKILL.md +557 -0
- package/skills/pydeseq2/references/api_reference.md +228 -0
- package/skills/pydeseq2/references/workflow_guide.md +582 -0
- package/skills/pydeseq2/scripts/run_deseq2_analysis.py +353 -0
- package/skills/pydicom/SKILL.md +432 -0
- package/skills/pydicom/references/common_tags.md +228 -0
- package/skills/pydicom/references/transfer_syntaxes.md +352 -0
- package/skills/pydicom/scripts/anonymize_dicom.py +137 -0
- package/skills/pydicom/scripts/dicom_to_image.py +172 -0
- package/skills/pydicom/scripts/extract_metadata.py +173 -0
- package/skills/pyhealth/SKILL.md +489 -0
- package/skills/pyhealth/references/datasets.md +178 -0
- package/skills/pyhealth/references/medical_coding.md +284 -0
- package/skills/pyhealth/references/models.md +594 -0
- package/skills/pyhealth/references/preprocessing.md +638 -0
- package/skills/pyhealth/references/tasks.md +379 -0
- package/skills/pyhealth/references/training_evaluation.md +648 -0
- package/skills/pylabrobot/SKILL.md +183 -0
- package/skills/pylabrobot/references/analytical-equipment.md +464 -0
- package/skills/pylabrobot/references/hardware-backends.md +480 -0
- package/skills/pylabrobot/references/liquid-handling.md +403 -0
- package/skills/pylabrobot/references/material-handling.md +620 -0
- package/skills/pylabrobot/references/resources.md +489 -0
- package/skills/pylabrobot/references/visualization.md +532 -0
- package/skills/pymatgen/SKILL.md +689 -0
- package/skills/pymatgen/references/analysis_modules.md +530 -0
- package/skills/pymatgen/references/core_classes.md +318 -0
- package/skills/pymatgen/references/io_formats.md +469 -0
- package/skills/pymatgen/references/materials_project_api.md +517 -0
- package/skills/pymatgen/references/transformations_workflows.md +591 -0
- package/skills/pymatgen/scripts/phase_diagram_generator.py +233 -0
- package/skills/pymatgen/scripts/structure_analyzer.py +266 -0
- package/skills/pymatgen/scripts/structure_converter.py +169 -0
- package/skills/pymc/SKILL.md +570 -0
- package/skills/pymc/assets/hierarchical_model_template.py +333 -0
- package/skills/pymc/assets/linear_regression_template.py +241 -0
- package/skills/pymc/references/distributions.md +320 -0
- package/skills/pymc/references/sampling_inference.md +424 -0
- package/skills/pymc/references/workflows.md +526 -0
- package/skills/pymc/scripts/model_comparison.py +387 -0
- package/skills/pymc/scripts/model_diagnostics.py +350 -0
- package/skills/pymoo/SKILL.md +569 -0
- package/skills/pymoo/references/algorithms.md +180 -0
- package/skills/pymoo/references/constraints_mcdm.md +417 -0
- package/skills/pymoo/references/operators.md +345 -0
- package/skills/pymoo/references/problems.md +265 -0
- package/skills/pymoo/references/visualization.md +353 -0
- package/skills/pymoo/scripts/custom_problem_example.py +181 -0
- package/skills/pymoo/scripts/decision_making_example.py +161 -0
- package/skills/pymoo/scripts/many_objective_example.py +72 -0
- package/skills/pymoo/scripts/multi_objective_example.py +63 -0
- package/skills/pymoo/scripts/single_objective_example.py +59 -0
- package/skills/pyopenms/SKILL.md +215 -0
- package/skills/pyopenms/references/data_structures.md +497 -0
- package/skills/pyopenms/references/feature_detection.md +410 -0
- package/skills/pyopenms/references/file_io.md +349 -0
- package/skills/pyopenms/references/identification.md +422 -0
- package/skills/pyopenms/references/metabolomics.md +482 -0
- package/skills/pyopenms/references/signal_processing.md +433 -0
- package/skills/pysam/SKILL.md +263 -0
- package/skills/pysam/references/alignment_files.md +280 -0
- package/skills/pysam/references/common_workflows.md +520 -0
- package/skills/pysam/references/sequence_files.md +407 -0
- package/skills/pysam/references/variant_files.md +365 -0
- package/skills/pytdc/SKILL.md +458 -0
- package/skills/pytdc/references/datasets.md +246 -0
- package/skills/pytdc/references/oracles.md +400 -0
- package/skills/pytdc/references/utilities.md +684 -0
- package/skills/pytdc/scripts/benchmark_evaluation.py +327 -0
- package/skills/pytdc/scripts/load_and_split_data.py +214 -0
- package/skills/pytdc/scripts/molecular_generation.py +404 -0
- package/skills/pytorch-lightning/SKILL.md +172 -0
- package/skills/pytorch-lightning/references/best_practices.md +724 -0
- package/skills/pytorch-lightning/references/callbacks.md +564 -0
- package/skills/pytorch-lightning/references/data_module.md +565 -0
- package/skills/pytorch-lightning/references/distributed_training.md +643 -0
- package/skills/pytorch-lightning/references/lightning_module.md +487 -0
- package/skills/pytorch-lightning/references/logging.md +654 -0
- package/skills/pytorch-lightning/references/trainer.md +641 -0
- package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +454 -0
- package/skills/pytorch-lightning/scripts/template_datamodule.py +328 -0
- package/skills/pytorch-lightning/scripts/template_lightning_module.py +219 -0
- package/skills/pyzotero/SKILL.md +111 -0
- package/skills/pyzotero/references/authentication.md +90 -0
- package/skills/pyzotero/references/cli.md +100 -0
- package/skills/pyzotero/references/collections.md +113 -0
- package/skills/pyzotero/references/error-handling.md +103 -0
- package/skills/pyzotero/references/exports.md +102 -0
- package/skills/pyzotero/references/files-attachments.md +97 -0
- package/skills/pyzotero/references/full-text.md +68 -0
- package/skills/pyzotero/references/pagination.md +79 -0
- package/skills/pyzotero/references/read-api.md +137 -0
- package/skills/pyzotero/references/saved-searches.md +77 -0
- package/skills/pyzotero/references/search-params.md +90 -0
- package/skills/pyzotero/references/tags.md +87 -0
- package/skills/pyzotero/references/write-api.md +123 -0
- package/skills/qiskit/SKILL.md +273 -0
- package/skills/qiskit/references/algorithms.md +607 -0
- package/skills/qiskit/references/backends.md +433 -0
- package/skills/qiskit/references/circuits.md +197 -0
- package/skills/qiskit/references/patterns.md +533 -0
- package/skills/qiskit/references/primitives.md +277 -0
- package/skills/qiskit/references/setup.md +99 -0
- package/skills/qiskit/references/transpilation.md +286 -0
- package/skills/qiskit/references/visualization.md +415 -0
- package/skills/qutip/SKILL.md +316 -0
- package/skills/qutip/references/advanced.md +555 -0
- package/skills/qutip/references/analysis.md +523 -0
- package/skills/qutip/references/core_concepts.md +293 -0
- package/skills/qutip/references/time_evolution.md +348 -0
- package/skills/qutip/references/visualization.md +431 -0
- package/skills/rdkit/SKILL.md +778 -0
- package/skills/rdkit/references/api_reference.md +432 -0
- package/skills/rdkit/references/descriptors_reference.md +595 -0
- package/skills/rdkit/references/smarts_patterns.md +668 -0
- package/skills/rdkit/scripts/molecular_properties.py +243 -0
- package/skills/rdkit/scripts/similarity_search.py +297 -0
- package/skills/rdkit/scripts/substructure_filter.py +386 -0
- package/skills/reactome-database/SKILL.md +276 -0
- package/skills/reactome-database/references/api_reference.md +465 -0
- package/skills/reactome-database/scripts/reactome_query.py +286 -0
- package/skills/replication/SKILL.md +14 -0
- package/skills/research-grants/SKILL.md +955 -0
- package/skills/research-grants/assets/budget_justification_template.md +453 -0
- package/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
- package/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
- package/skills/research-grants/references/README.md +285 -0
- package/skills/research-grants/references/broader_impacts.md +392 -0
- package/skills/research-grants/references/darpa_guidelines.md +636 -0
- package/skills/research-grants/references/doe_guidelines.md +586 -0
- package/skills/research-grants/references/nih_guidelines.md +851 -0
- package/skills/research-grants/references/nsf_guidelines.md +570 -0
- package/skills/research-grants/references/nstc_guidelines.md +733 -0
- package/skills/research-grants/references/specific_aims_guide.md +458 -0
- package/skills/research-lookup/README.md +156 -0
- package/skills/research-lookup/SKILL.md +413 -0
- package/skills/research-lookup/examples.py +174 -0
- package/skills/research-lookup/lookup.py +187 -0
- package/skills/research-lookup/research_lookup.py +566 -0
- package/skills/research-lookup/scripts/research_lookup.py +566 -0
- package/skills/rowan/SKILL.md +427 -0
- package/skills/rowan/references/api_reference.md +413 -0
- package/skills/rowan/references/molecule_handling.md +429 -0
- package/skills/rowan/references/proteins_and_organization.md +499 -0
- package/skills/rowan/references/rdkit_native.md +438 -0
- package/skills/rowan/references/results_interpretation.md +481 -0
- package/skills/rowan/references/workflow_types.md +591 -0
- package/skills/runpod-compute/SKILL.md +48 -0
- package/skills/scanpy/SKILL.md +384 -0
- package/skills/scanpy/assets/analysis_template.py +295 -0
- package/skills/scanpy/references/api_reference.md +251 -0
- package/skills/scanpy/references/plotting_guide.md +352 -0
- package/skills/scanpy/references/standard_workflow.md +206 -0
- package/skills/scanpy/scripts/qc_analysis.py +200 -0
- package/skills/scholar-evaluation/SKILL.md +298 -0
- package/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
- package/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
- package/skills/scientific-brainstorming/SKILL.md +189 -0
- package/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
- package/skills/scientific-critical-thinking/SKILL.md +570 -0
- package/skills/scientific-critical-thinking/references/common_biases.md +364 -0
- package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
- package/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
- package/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
- package/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
- package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
- package/skills/scientific-schematics/SKILL.md +619 -0
- package/skills/scientific-schematics/references/QUICK_REFERENCE.md +207 -0
- package/skills/scientific-schematics/references/README.md +327 -0
- package/skills/scientific-schematics/references/best_practices.md +560 -0
- package/skills/scientific-schematics/scripts/example_usage.sh +89 -0
- package/skills/scientific-schematics/scripts/generate_schematic.py +139 -0
- package/skills/scientific-schematics/scripts/generate_schematic_ai.py +844 -0
- package/skills/scientific-slides/SKILL.md +1154 -0
- package/skills/scientific-slides/assets/beamer_template_conference.tex +407 -0
- package/skills/scientific-slides/assets/beamer_template_defense.tex +906 -0
- package/skills/scientific-slides/assets/beamer_template_seminar.tex +870 -0
- package/skills/scientific-slides/assets/powerpoint_design_guide.md +662 -0
- package/skills/scientific-slides/assets/timing_guidelines.md +597 -0
- package/skills/scientific-slides/references/beamer_guide.md +1019 -0
- package/skills/scientific-slides/references/data_visualization_slides.md +708 -0
- package/skills/scientific-slides/references/presentation_structure.md +642 -0
- package/skills/scientific-slides/references/slide_design_principles.md +849 -0
- package/skills/scientific-slides/references/talk_types_guide.md +687 -0
- package/skills/scientific-slides/references/visual_review_workflow.md +775 -0
- package/skills/scientific-slides/scripts/generate_slide_image.py +140 -0
- package/skills/scientific-slides/scripts/generate_slide_image_ai.py +763 -0
- package/skills/scientific-slides/scripts/pdf_to_images.py +221 -0
- package/skills/scientific-slides/scripts/slides_to_pdf.py +235 -0
- package/skills/scientific-slides/scripts/validate_presentation.py +403 -0
- package/skills/scientific-visualization/SKILL.md +777 -0
- package/skills/scientific-visualization/assets/color_palettes.py +197 -0
- package/skills/scientific-visualization/assets/nature.mplstyle +63 -0
- package/skills/scientific-visualization/assets/presentation.mplstyle +61 -0
- package/skills/scientific-visualization/assets/publication.mplstyle +68 -0
- package/skills/scientific-visualization/references/color_palettes.md +348 -0
- package/skills/scientific-visualization/references/journal_requirements.md +320 -0
- package/skills/scientific-visualization/references/matplotlib_examples.md +620 -0
- package/skills/scientific-visualization/references/publication_guidelines.md +205 -0
- package/skills/scientific-visualization/scripts/figure_export.py +343 -0
- package/skills/scientific-visualization/scripts/style_presets.py +416 -0
- package/skills/scientific-workflows/SKILL.md +1684 -0
- package/skills/scientific-writing/SKILL.md +718 -0
- package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +574 -0
- package/skills/scientific-writing/assets/scientific_report.sty +606 -0
- package/skills/scientific-writing/assets/scientific_report_template.tex +449 -0
- package/skills/scientific-writing/references/citation_styles.md +720 -0
- package/skills/scientific-writing/references/figures_tables.md +806 -0
- package/skills/scientific-writing/references/imrad_structure.md +686 -0
- package/skills/scientific-writing/references/professional_report_formatting.md +664 -0
- package/skills/scientific-writing/references/reporting_guidelines.md +748 -0
- package/skills/scientific-writing/references/writing_principles.md +824 -0
- package/skills/scikit-bio/SKILL.md +435 -0
- package/skills/scikit-bio/references/api_reference.md +749 -0
- package/skills/scikit-learn/SKILL.md +519 -0
- package/skills/scikit-learn/references/model_evaluation.md +592 -0
- package/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
- package/skills/scikit-learn/references/preprocessing.md +606 -0
- package/skills/scikit-learn/references/quick_reference.md +433 -0
- package/skills/scikit-learn/references/supervised_learning.md +378 -0
- package/skills/scikit-learn/references/unsupervised_learning.md +505 -0
- package/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
- package/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
- package/skills/scikit-survival/SKILL.md +397 -0
- package/skills/scikit-survival/references/competing-risks.md +397 -0
- package/skills/scikit-survival/references/cox-models.md +182 -0
- package/skills/scikit-survival/references/data-handling.md +494 -0
- package/skills/scikit-survival/references/ensemble-models.md +327 -0
- package/skills/scikit-survival/references/evaluation-metrics.md +378 -0
- package/skills/scikit-survival/references/svm-models.md +411 -0
- package/skills/scvelo/SKILL.md +321 -0
- package/skills/scvelo/references/velocity_models.md +168 -0
- package/skills/scvelo/scripts/rna_velocity_workflow.py +232 -0
- package/skills/scvi-tools/SKILL.md +188 -0
- package/skills/scvi-tools/references/differential-expression.md +581 -0
- package/skills/scvi-tools/references/models-atac-seq.md +321 -0
- package/skills/scvi-tools/references/models-multimodal.md +367 -0
- package/skills/scvi-tools/references/models-scrna-seq.md +330 -0
- package/skills/scvi-tools/references/models-spatial.md +438 -0
- package/skills/scvi-tools/references/models-specialized.md +408 -0
- package/skills/scvi-tools/references/theoretical-foundations.md +438 -0
- package/skills/scvi-tools/references/workflows.md +546 -0
- package/skills/seaborn/SKILL.md +671 -0
- package/skills/seaborn/references/examples.md +822 -0
- package/skills/seaborn/references/function_reference.md +770 -0
- package/skills/seaborn/references/objects_interface.md +964 -0
- package/skills/semantic-scholar/SKILL.md +123 -0
- package/skills/session-log/SKILL.md +10 -0
- package/skills/session-search/SKILL.md +26 -0
- package/skills/setup/SKILL.md +216 -0
- package/skills/shap/SKILL.md +564 -0
- package/skills/shap/references/explainers.md +339 -0
- package/skills/shap/references/plots.md +507 -0
- package/skills/shap/references/theory.md +449 -0
- package/skills/shap/references/workflows.md +605 -0
- package/skills/simpy/SKILL.md +427 -0
- package/skills/simpy/references/events.md +374 -0
- package/skills/simpy/references/monitoring.md +475 -0
- package/skills/simpy/references/process-interaction.md +424 -0
- package/skills/simpy/references/real-time.md +395 -0
- package/skills/simpy/references/resources.md +275 -0
- package/skills/simpy/scripts/basic_simulation_template.py +193 -0
- package/skills/simpy/scripts/resource_monitor.py +345 -0
- package/skills/source-comparison/SKILL.md +12 -0
- package/skills/stable-baselines3/SKILL.md +297 -0
- package/skills/stable-baselines3/references/algorithms.md +333 -0
- package/skills/stable-baselines3/references/callbacks.md +556 -0
- package/skills/stable-baselines3/references/custom_environments.md +526 -0
- package/skills/stable-baselines3/references/vectorized_envs.md +568 -0
- package/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
- package/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
- package/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
- package/skills/statistical-analysis/SKILL.md +630 -0
- package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
- package/skills/statistical-analysis/references/bayesian_statistics.md +661 -0
- package/skills/statistical-analysis/references/effect_sizes_and_power.md +581 -0
- package/skills/statistical-analysis/references/reporting_standards.md +469 -0
- package/skills/statistical-analysis/references/test_selection_guide.md +129 -0
- package/skills/statistical-analysis/scripts/assumption_checks.py +539 -0
- package/skills/statsmodels/SKILL.md +612 -0
- package/skills/statsmodels/references/discrete_choice.md +669 -0
- package/skills/statsmodels/references/glm.md +619 -0
- package/skills/statsmodels/references/linear_models.md +447 -0
- package/skills/statsmodels/references/stats_diagnostics.md +859 -0
- package/skills/statsmodels/references/time_series.md +716 -0
- package/skills/string-database/SKILL.md +532 -0
- package/skills/string-database/references/string_reference.md +455 -0
- package/skills/string-database/scripts/string_api.py +369 -0
- package/skills/sympy/SKILL.md +498 -0
- package/skills/sympy/references/advanced-topics.md +635 -0
- package/skills/sympy/references/code-generation-printing.md +599 -0
- package/skills/sympy/references/core-capabilities.md +348 -0
- package/skills/sympy/references/matrices-linear-algebra.md +526 -0
- package/skills/sympy/references/physics-mechanics.md +592 -0
- package/skills/tiledbvcf/SKILL.md +459 -0
- package/skills/timesfm-forecasting/SKILL.md +785 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +524 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +448 -0
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +568 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +59 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +109 -0
- package/skills/timesfm-forecasting/examples/global-temperature/README.md +178 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +147 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +248 -0
- package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +544 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +5441 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +13 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +188 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +5939 -0
- package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +53 -0
- package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +167 -0
- package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +37 -0
- package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +123 -0
- package/skills/timesfm-forecasting/references/api_reference.md +231 -0
- package/skills/timesfm-forecasting/references/data_preparation.md +272 -0
- package/skills/timesfm-forecasting/references/system_requirements.md +201 -0
- package/skills/timesfm-forecasting/scripts/check_system.py +520 -0
- package/skills/timesfm-forecasting/scripts/forecast_csv.py +269 -0
- package/skills/torch-geometric/SKILL.md +674 -0
- package/skills/torch-geometric/references/datasets_reference.md +574 -0
- package/skills/torch-geometric/references/layers_reference.md +485 -0
- package/skills/torch-geometric/references/transforms_reference.md +679 -0
- package/skills/torch-geometric/scripts/benchmark_model.py +309 -0
- package/skills/torch-geometric/scripts/create_gnn_template.py +529 -0
- package/skills/torch-geometric/scripts/visualize_graph.py +313 -0
- package/skills/torchdrug/SKILL.md +448 -0
- package/skills/torchdrug/references/core_concepts.md +565 -0
- package/skills/torchdrug/references/datasets.md +380 -0
- package/skills/torchdrug/references/knowledge_graphs.md +320 -0
- package/skills/torchdrug/references/models_architectures.md +541 -0
- package/skills/torchdrug/references/molecular_generation.md +352 -0
- package/skills/torchdrug/references/molecular_property_prediction.md +169 -0
- package/skills/torchdrug/references/protein_modeling.md +272 -0
- package/skills/torchdrug/references/retrosynthesis.md +436 -0
- package/skills/transformers/SKILL.md +162 -0
- package/skills/transformers/references/generation.md +467 -0
- package/skills/transformers/references/models.md +361 -0
- package/skills/transformers/references/pipelines.md +335 -0
- package/skills/transformers/references/tokenizers.md +447 -0
- package/skills/transformers/references/training.md +500 -0
- package/skills/treatment-plans/SKILL.md +1580 -0
- package/skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md +185 -0
- package/skills/treatment-plans/assets/chronic_disease_management_plan.tex +665 -0
- package/skills/treatment-plans/assets/general_medical_treatment_plan.tex +547 -0
- package/skills/treatment-plans/assets/medical_treatment_plan.sty +222 -0
- package/skills/treatment-plans/assets/mental_health_treatment_plan.tex +774 -0
- package/skills/treatment-plans/assets/one_page_treatment_plan.tex +193 -0
- package/skills/treatment-plans/assets/pain_management_plan.tex +799 -0
- package/skills/treatment-plans/assets/perioperative_care_plan.tex +753 -0
- package/skills/treatment-plans/assets/quality_checklist.md +471 -0
- package/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
- package/skills/treatment-plans/references/README.md +488 -0
- package/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
- package/skills/treatment-plans/references/intervention_guidelines.md +507 -0
- package/skills/treatment-plans/references/regulatory_compliance.md +476 -0
- package/skills/treatment-plans/references/specialty_specific_guidelines.md +655 -0
- package/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
- package/skills/treatment-plans/scripts/check_completeness.py +318 -0
- package/skills/treatment-plans/scripts/generate_template.py +244 -0
- package/skills/treatment-plans/scripts/timeline_generator.py +369 -0
- package/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
- package/skills/umap-learn/SKILL.md +477 -0
- package/skills/umap-learn/references/api_reference.md +532 -0
- package/skills/uniprot-database/SKILL.md +193 -0
- package/skills/uniprot-database/references/api_examples.md +413 -0
- package/skills/uniprot-database/references/api_fields.md +275 -0
- package/skills/uniprot-database/references/id_mapping_databases.md +285 -0
- package/skills/uniprot-database/references/query_syntax.md +256 -0
- package/skills/uniprot-database/scripts/uniprot_client.py +341 -0
- package/skills/usfiscaldata/SKILL.md +163 -0
- package/skills/usfiscaldata/references/api-basics.md +86 -0
- package/skills/usfiscaldata/references/datasets-debt.md +163 -0
- package/skills/usfiscaldata/references/datasets-fiscal.md +196 -0
- package/skills/usfiscaldata/references/datasets-interest-rates.md +182 -0
- package/skills/usfiscaldata/references/datasets-securities.md +216 -0
- package/skills/usfiscaldata/references/examples.md +258 -0
- package/skills/usfiscaldata/references/parameters.md +155 -0
- package/skills/usfiscaldata/references/response-format.md +176 -0
- package/skills/uspto-database/SKILL.md +605 -0
- package/skills/uspto-database/references/additional_apis.md +394 -0
- package/skills/uspto-database/references/patentsearch_api.md +266 -0
- package/skills/uspto-database/references/peds_api.md +212 -0
- package/skills/uspto-database/references/trademark_api.md +358 -0
- package/skills/uspto-database/scripts/patent_search.py +290 -0
- package/skills/uspto-database/scripts/peds_client.py +285 -0
- package/skills/uspto-database/scripts/trademark_client.py +311 -0
- package/skills/vaex/SKILL.md +180 -0
- package/skills/vaex/references/core_dataframes.md +367 -0
- package/skills/vaex/references/data_processing.md +555 -0
- package/skills/vaex/references/io_operations.md +703 -0
- package/skills/vaex/references/machine_learning.md +728 -0
- package/skills/vaex/references/performance.md +571 -0
- package/skills/vaex/references/visualization.md +613 -0
- package/skills/venue-templates/SKILL.md +688 -0
- package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
- package/skills/venue-templates/assets/journals/nature_article.tex +171 -0
- package/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
- package/skills/venue-templates/assets/journals/plos_one.tex +317 -0
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
- package/skills/venue-templates/references/cell_press_style.md +483 -0
- package/skills/venue-templates/references/conferences_formatting.md +564 -0
- package/skills/venue-templates/references/cs_conference_style.md +463 -0
- package/skills/venue-templates/references/grants_requirements.md +787 -0
- package/skills/venue-templates/references/journals_formatting.md +486 -0
- package/skills/venue-templates/references/medical_journal_styles.md +535 -0
- package/skills/venue-templates/references/ml_conference_style.md +556 -0
- package/skills/venue-templates/references/nature_science_style.md +405 -0
- package/skills/venue-templates/references/posters_guidelines.md +628 -0
- package/skills/venue-templates/references/reviewer_expectations.md +417 -0
- package/skills/venue-templates/references/venue_writing_styles.md +321 -0
- package/skills/venue-templates/scripts/customize_template.py +206 -0
- package/skills/venue-templates/scripts/query_template.py +260 -0
- package/skills/venue-templates/scripts/validate_format.py +255 -0
- package/skills/watch/SKILL.md +12 -0
- package/skills/what-if-oracle/SKILL.md +168 -0
- package/skills/what-if-oracle/references/scenario-templates.md +137 -0
- package/skills/writing/SKILL.md +414 -0
- package/skills/xlsx/LICENSE.txt +30 -0
- package/skills/xlsx/SKILL.md +292 -0
- package/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
- package/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
- package/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
- package/skills/xlsx/scripts/office/pack.py +159 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/xlsx/scripts/office/soffice.py +183 -0
- package/skills/xlsx/scripts/office/unpack.py +132 -0
- package/skills/xlsx/scripts/office/validate.py +111 -0
- package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
- package/skills/xlsx/scripts/office/validators/base.py +847 -0
- package/skills/xlsx/scripts/office/validators/docx.py +446 -0
- package/skills/xlsx/scripts/office/validators/pptx.py +275 -0
- package/skills/xlsx/scripts/office/validators/redlining.py +247 -0
- package/skills/xlsx/scripts/recalc.py +184 -0
- package/skills/zarr-python/SKILL.md +777 -0
- package/skills/zarr-python/references/api_reference.md +515 -0
- package/skills/zinc-database/SKILL.md +402 -0
- package/skills/zinc-database/references/api_reference.md +692 -0
|
@@ -0,0 +1,213 @@
|
|
|
1
|
+
# Nature/Science Abstract Examples
|
|
2
|
+
|
|
3
|
+
Examples of well-crafted abstracts for high-impact multidisciplinary journals. These demonstrate the flowing paragraph style with broad accessibility expected at Nature, Science, and related venues.
|
|
4
|
+
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
## Example 1: Molecular Biology / Cell Biology
|
|
8
|
+
|
|
9
|
+
**Topic**: CRISPR gene editing discovery
|
|
10
|
+
|
|
11
|
+
```
|
|
12
|
+
The ability to precisely edit DNA sequences in living cells has transformed
|
|
13
|
+
biological research and holds promise for treating genetic diseases. However,
|
|
14
|
+
current genome editing tools can introduce unwanted mutations at off-target
|
|
15
|
+
sites, limiting their clinical potential. Here we describe prime editing, a
|
|
16
|
+
versatile and precise genome editing method that directly writes new genetic
|
|
17
|
+
information into a specified DNA site using a reverse transcriptase fused to a
|
|
18
|
+
CRISPR nickase. Prime editing can make all 12 types of point mutations, as
|
|
19
|
+
well as small insertions and deletions, with minimal off-target editing and
|
|
20
|
+
without requiring double-strand breaks or donor DNA templates. In human cells,
|
|
21
|
+
we used prime editing to correct the primary genetic causes of sickle cell
|
|
22
|
+
disease and Tay-Sachs disease, and to install protective mutations that
|
|
23
|
+
reduce risk of prion disease. Prime editing expands the scope and capabilities
|
|
24
|
+
of genome editing and may address approximately 89% of known human genetic
|
|
25
|
+
disease variants.
|
|
26
|
+
```
|
|
27
|
+
|
|
28
|
+
**Why this works**:
|
|
29
|
+
- Opens with broad significance (genetic disease treatment)
|
|
30
|
+
- States the problem clearly (off-target mutations)
|
|
31
|
+
- Describes the approach accessibly ("writes new genetic information")
|
|
32
|
+
- Includes specific results (all 12 point mutations, specific diseases)
|
|
33
|
+
- Ends with quantified impact (89% of variants)
|
|
34
|
+
|
|
35
|
+
---
|
|
36
|
+
|
|
37
|
+
## Example 2: Neuroscience
|
|
38
|
+
|
|
39
|
+
**Topic**: Memory consolidation mechanism
|
|
40
|
+
|
|
41
|
+
```
|
|
42
|
+
Sleep is essential for memory consolidation, yet how the sleeping brain
|
|
43
|
+
transforms labile memories into stable long-term representations remains
|
|
44
|
+
poorly understood. We used multi-site electrophysiology in freely behaving
|
|
45
|
+
mice to record the activity of thousands of neurons across hippocampus and
|
|
46
|
+
cortex during learning and subsequent sleep. We discovered that specific
|
|
47
|
+
neurons that encode a newly learned memory reactivate in precisely timed
|
|
48
|
+
sequences during slow-wave sleep, with hippocampal reactivation preceding
|
|
49
|
+
cortical reactivation by 10-15 milliseconds. Optogenetic disruption of this
|
|
50
|
+
temporal coordination impaired memory retention by 78%, whereas artificial
|
|
51
|
+
enhancement of the temporal relationship strengthened memories beyond normal
|
|
52
|
+
levels. These results reveal that the temporal ordering of hippocampal-cortical
|
|
53
|
+
replay is not merely correlative but causally necessary for memory
|
|
54
|
+
consolidation. Our findings suggest new therapeutic approaches for memory
|
|
55
|
+
disorders based on optimizing the temporal dynamics of sleep.
|
|
56
|
+
```
|
|
57
|
+
|
|
58
|
+
**Why this works**:
|
|
59
|
+
- Connects to well-known phenomenon (sleep and memory)
|
|
60
|
+
- States what was unknown
|
|
61
|
+
- Describes approach (multi-site recordings)
|
|
62
|
+
- Key finding with specific number (10-15 ms)
|
|
63
|
+
- Causal evidence (disruption and enhancement experiments)
|
|
64
|
+
- Broader implications (therapeutic approaches)
|
|
65
|
+
|
|
66
|
+
---
|
|
67
|
+
|
|
68
|
+
## Example 3: Climate Science
|
|
69
|
+
|
|
70
|
+
**Topic**: Carbon cycle feedback
|
|
71
|
+
|
|
72
|
+
```
|
|
73
|
+
Arctic permafrost contains approximately 1,500 billion tonnes of organic
|
|
74
|
+
carbon—twice the amount currently in the atmosphere. As the Arctic warms,
|
|
75
|
+
this carbon may be released to the atmosphere, accelerating global warming
|
|
76
|
+
through a positive feedback loop. However, the magnitude and timing of this
|
|
77
|
+
feedback remain highly uncertain because microbial decomposition rates in
|
|
78
|
+
thawing permafrost are poorly constrained. Here we present a 15-year
|
|
79
|
+
field experiment across 25 sites spanning the Arctic, tracking carbon
|
|
80
|
+
fluxes in warming permafrost under natural conditions. We find that
|
|
81
|
+
microbial respiration increases exponentially with temperature until soils
|
|
82
|
+
reach 3°C, then plateaus due to substrate limitation—a threshold effect
|
|
83
|
+
not captured by current Earth system models. Our results suggest that
|
|
84
|
+
permafrost carbon feedback will be 30-50% lower than current projections
|
|
85
|
+
during this century, providing more time to limit warming, but will
|
|
86
|
+
accelerate dramatically if deep permafrost begins to thaw.
|
|
87
|
+
```
|
|
88
|
+
|
|
89
|
+
**Why this works**:
|
|
90
|
+
- Opens with striking number (1,500 billion tonnes)
|
|
91
|
+
- Clear problem statement (feedback uncertainty)
|
|
92
|
+
- Specific methodology (15 years, 25 sites)
|
|
93
|
+
- Novel finding (threshold at 3°C)
|
|
94
|
+
- Implications both reassuring and cautionary
|
|
95
|
+
|
|
96
|
+
---
|
|
97
|
+
|
|
98
|
+
## Example 4: Physics / Materials Science
|
|
99
|
+
|
|
100
|
+
**Topic**: Room-temperature superconductivity
|
|
101
|
+
|
|
102
|
+
```
|
|
103
|
+
Superconductivity—the flow of electricity without resistance—has been
|
|
104
|
+
confined to extremely low temperatures since its discovery over a century
|
|
105
|
+
ago, limiting practical applications. The recent demonstration of
|
|
106
|
+
superconductivity in hydrogen-rich materials at high pressure has raised
|
|
107
|
+
hopes for higher transition temperatures, but achieving room-temperature
|
|
108
|
+
superconductivity at ambient pressure has remained elusive. Here we report
|
|
109
|
+
superconductivity at 21°C (294 K) in a nitrogen-doped lutetium hydride
|
|
110
|
+
(Lu-N-H) compound at pressures of approximately 1 GPa—nearly ambient
|
|
111
|
+
conditions. Electrical resistance drops to zero below the transition
|
|
112
|
+
temperature with a sharp transition width of 2 K, and we observe the Meissner
|
|
113
|
+
effect confirming bulk superconductivity. Density functional theory
|
|
114
|
+
calculations suggest that nitrogen incorporation stabilizes the high-symmetry
|
|
115
|
+
structure that enables strong electron-phonon coupling. These results
|
|
116
|
+
establish a pathway toward practical room-temperature superconductors.
|
|
117
|
+
```
|
|
118
|
+
|
|
119
|
+
**Why this works**:
|
|
120
|
+
- Opens with accessible explanation of significance
|
|
121
|
+
- Historical context (century-old limitation)
|
|
122
|
+
- Precise results (21°C, 1 GPa, 2 K transition width)
|
|
123
|
+
- Multiple lines of evidence (resistance + Meissner effect)
|
|
124
|
+
- Theoretical explanation briefly included
|
|
125
|
+
- Forward-looking conclusion
|
|
126
|
+
|
|
127
|
+
---
|
|
128
|
+
|
|
129
|
+
## Example 5: Evolution / Ecology
|
|
130
|
+
|
|
131
|
+
**Topic**: Rapid evolution in response to climate
|
|
132
|
+
|
|
133
|
+
```
|
|
134
|
+
Climate change is driving rapid shifts in the geographic distributions of
|
|
135
|
+
species, but whether organisms can adapt quickly enough to keep pace with
|
|
136
|
+
warming remains a critical question for biodiversity conservation. Here we
|
|
137
|
+
document real-time evolution in wild populations of a widespread forest tree,
|
|
138
|
+
Scots pine, along a 1,000 km latitudinal gradient in Scandinavia. By combining
|
|
139
|
+
whole-genome sequencing with phenotypic measurements across 25 common gardens,
|
|
140
|
+
we detect signatures of selection at 47 loci associated with cold tolerance,
|
|
141
|
+
phenology, and drought resistance over just 50 years—approximately
|
|
142
|
+
five tree generations. Alleles conferring warmer-adapted phenotypes have
|
|
143
|
+
increased in frequency by 4-12% across northern populations, matching
|
|
144
|
+
predictions from models of climate-driven selection. However, migration of
|
|
145
|
+
warm-adapted genotypes from the south appears limited by geographic barriers.
|
|
146
|
+
These results demonstrate that trees can evolve rapidly in response to
|
|
147
|
+
climate change but suggest that assisted gene flow may be necessary to
|
|
148
|
+
prevent local maladaptation.
|
|
149
|
+
```
|
|
150
|
+
|
|
151
|
+
**Why this works**:
|
|
152
|
+
- Opens with pressing question (climate adaptation)
|
|
153
|
+
- Specific system (Scots pine) and scale (1,000 km)
|
|
154
|
+
- Methods described briefly (genomics + common gardens)
|
|
155
|
+
- Quantitative results (47 loci, 4-12% frequency shift, 5 generations)
|
|
156
|
+
- Mechanism identified (limited migration)
|
|
157
|
+
- Conservation implications stated
|
|
158
|
+
|
|
159
|
+
---
|
|
160
|
+
|
|
161
|
+
## Common Elements Across Examples
|
|
162
|
+
|
|
163
|
+
### Structure (Implicit)
|
|
164
|
+
1. **Hook**: Why this matters broadly (1-2 sentences)
|
|
165
|
+
2. **Gap**: What was unknown or problematic (1 sentence)
|
|
166
|
+
3. **Approach**: What was done (1 sentence)
|
|
167
|
+
4. **Findings**: Key results with numbers (2-3 sentences)
|
|
168
|
+
5. **Significance**: Why this matters going forward (1 sentence)
|
|
169
|
+
|
|
170
|
+
### Style Features
|
|
171
|
+
- **Active voice**: "We discovered," "We find," "We report"
|
|
172
|
+
- **Specific numbers**: Exact values, not vague quantities
|
|
173
|
+
- **Accessible language**: Minimal jargon, explained when needed
|
|
174
|
+
- **Compelling opening**: Broad hook before technical details
|
|
175
|
+
- **Strong close**: Implications or future directions
|
|
176
|
+
|
|
177
|
+
### Word Count
|
|
178
|
+
- Nature: 150-200 words (examples above: 185-210 words)
|
|
179
|
+
- Science: ≤125 words (would need tightening)
|
|
180
|
+
|
|
181
|
+
---
|
|
182
|
+
|
|
183
|
+
## What to Avoid
|
|
184
|
+
|
|
185
|
+
❌ **Too technical opening**:
|
|
186
|
+
> "The CRISPR-Cas9 system with guide RNA targeting PAM sequences..."
|
|
187
|
+
|
|
188
|
+
✅ **Better opening**:
|
|
189
|
+
> "The ability to precisely edit DNA in living cells..."
|
|
190
|
+
|
|
191
|
+
---
|
|
192
|
+
|
|
193
|
+
❌ **Vague results**:
|
|
194
|
+
> "Our method significantly outperformed existing approaches..."
|
|
195
|
+
|
|
196
|
+
✅ **Better results**:
|
|
197
|
+
> "Our method reduced off-target editing by 78% compared to standard Cas9..."
|
|
198
|
+
|
|
199
|
+
---
|
|
200
|
+
|
|
201
|
+
❌ **Weak significance statement**:
|
|
202
|
+
> "These findings may have implications for the field..."
|
|
203
|
+
|
|
204
|
+
✅ **Better significance**:
|
|
205
|
+
> "These findings suggest new therapeutic approaches for memory disorders..."
|
|
206
|
+
|
|
207
|
+
---
|
|
208
|
+
|
|
209
|
+
## See Also
|
|
210
|
+
|
|
211
|
+
- `nature_science_style.md` - Comprehensive Nature/Science writing guide
|
|
212
|
+
- `venue_writing_styles.md` - Style comparison across venues
|
|
213
|
+
|
|
@@ -0,0 +1,245 @@
|
|
|
1
|
+
# NeurIPS/ICML Introduction Example
|
|
2
|
+
|
|
3
|
+
This example demonstrates the distinctive ML conference introduction structure with numbered contributions and technical precision.
|
|
4
|
+
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
## Full Introduction Example
|
|
8
|
+
|
|
9
|
+
**Paper Topic**: Efficient Long-Context Transformers
|
|
10
|
+
|
|
11
|
+
---
|
|
12
|
+
|
|
13
|
+
### Paragraph 1: Problem Motivation
|
|
14
|
+
|
|
15
|
+
```
|
|
16
|
+
Large language models (LLMs) have demonstrated remarkable capabilities in
|
|
17
|
+
natural language understanding, code generation, and reasoning tasks [1, 2, 3].
|
|
18
|
+
These capabilities scale with both model size and context length—longer
|
|
19
|
+
contexts enable processing of entire documents, multi-turn conversations,
|
|
20
|
+
and complex reasoning chains that span many steps [4, 5]. However, the
|
|
21
|
+
standard Transformer attention mechanism [6] has O(N²) time and memory
|
|
22
|
+
complexity with respect to sequence length N, creating a fundamental
|
|
23
|
+
bottleneck for processing long sequences. For a context window of 100K
|
|
24
|
+
tokens, computing full attention requires 10 billion scalar operations
|
|
25
|
+
and 40 GB of memory for the attention matrix alone, making training and
|
|
26
|
+
inference prohibitively expensive on current hardware.
|
|
27
|
+
```
|
|
28
|
+
|
|
29
|
+
**Key features**:
|
|
30
|
+
- States why this matters (LLM capabilities)
|
|
31
|
+
- Connects to scaling (longer contexts = better performance)
|
|
32
|
+
- Specific numbers (O(N²), 100K tokens, 10 billion ops, 40 GB)
|
|
33
|
+
- Citations to establish credibility
|
|
34
|
+
|
|
35
|
+
---
|
|
36
|
+
|
|
37
|
+
### Paragraph 2: Limitations of Existing Approaches
|
|
38
|
+
|
|
39
|
+
```
|
|
40
|
+
Prior work has addressed attention efficiency through three main approaches.
|
|
41
|
+
Sparse attention patterns [7, 8, 9] reduce complexity to O(N√N) or O(N log N)
|
|
42
|
+
by restricting attention to local windows, fixed stride patterns, or learned
|
|
43
|
+
sparse masks. Linear attention approximations [10, 11, 12] reformulate
|
|
44
|
+
attention using kernel feature maps that enable O(N) computation, but
|
|
45
|
+
sacrifice the ability to model arbitrary pairwise interactions. Low-rank
|
|
46
|
+
factorizations [13, 14] approximate the attention matrix as a product of
|
|
47
|
+
smaller matrices, achieving efficiency at the cost of expressivity. While
|
|
48
|
+
these methods reduce theoretical complexity, they introduce approximation
|
|
49
|
+
errors that compound in deep networks, often resulting in 2-5% accuracy
|
|
50
|
+
degradation on long-range modeling benchmarks [15]. Perhaps more importantly,
|
|
51
|
+
they fundamentally change the attention mechanism, making it difficult to
|
|
52
|
+
apply advances in standard attention (e.g., rotary positional embeddings,
|
|
53
|
+
grouped-query attention) to efficient variants.
|
|
54
|
+
```
|
|
55
|
+
|
|
56
|
+
**Key features**:
|
|
57
|
+
- Organized categorization of prior work
|
|
58
|
+
- Complexity stated for each approach
|
|
59
|
+
- Limitations clearly identified
|
|
60
|
+
- Quantified shortcomings (2-5% degradation)
|
|
61
|
+
- Deeper issue identified (incompatibility with advances)
|
|
62
|
+
|
|
63
|
+
---
|
|
64
|
+
|
|
65
|
+
### Paragraph 3: Your Approach (High-Level)
|
|
66
|
+
|
|
67
|
+
```
|
|
68
|
+
We take a different approach: rather than approximating attention, we
|
|
69
|
+
accelerate exact attention by optimizing memory access patterns. Our key
|
|
70
|
+
observation is that on modern GPUs, attention is bottlenecked by memory
|
|
71
|
+
bandwidth, not compute. Reading and writing the N × N attention matrix to
|
|
72
|
+
and from GPU high-bandwidth memory (HBM) dominates runtime, while the GPU's
|
|
73
|
+
tensor cores remain underutilized. We propose LongFlash, an IO-aware exact
|
|
74
|
+
attention algorithm that computes attention block-by-block in fast on-chip
|
|
75
|
+
SRAM, never materializing the full attention matrix in HBM. By carefully
|
|
76
|
+
orchestrating the tiling pattern and fusing the softmax computation with
|
|
77
|
+
matrix multiplications, LongFlash reduces HBM accesses from O(N²) to
|
|
78
|
+
O(N²d/M) where d is the head dimension and M is the SRAM size, achieving
|
|
79
|
+
asymptotically optimal IO complexity.
|
|
80
|
+
```
|
|
81
|
+
|
|
82
|
+
**Key features**:
|
|
83
|
+
- Clear differentiation from prior work ("different approach")
|
|
84
|
+
- Key insight stated explicitly
|
|
85
|
+
- Technical mechanism explained
|
|
86
|
+
- Complexity improvement quantified
|
|
87
|
+
- Method name introduced
|
|
88
|
+
|
|
89
|
+
---
|
|
90
|
+
|
|
91
|
+
### Paragraph 4: Contributions (CRITICAL)
|
|
92
|
+
|
|
93
|
+
```
|
|
94
|
+
Our contributions are as follows:
|
|
95
|
+
|
|
96
|
+
• We propose LongFlash, an IO-aware exact attention algorithm that achieves
|
|
97
|
+
2-4× speedup over FlashAttention [16] and up to 9× over standard PyTorch
|
|
98
|
+
attention on sequences from 1K to 128K tokens (Section 3).
|
|
99
|
+
|
|
100
|
+
• We provide theoretical analysis proving that LongFlash achieves optimal
|
|
101
|
+
IO complexity of O(N²d/M) among all algorithms that compute exact
|
|
102
|
+
attention, and analyze the regime where our algorithm provides maximum
|
|
103
|
+
benefit (Section 3.3).
|
|
104
|
+
|
|
105
|
+
• We introduce sequence parallelism techniques that enable LongFlash to
|
|
106
|
+
scale to sequences of 1M+ tokens across multiple GPUs with near-linear
|
|
107
|
+
weak scaling efficiency (Section 4).
|
|
108
|
+
|
|
109
|
+
• We demonstrate that LongFlash enables training with 8× longer contexts
|
|
110
|
+
on the same hardware: we train a 7B parameter model on 128K token
|
|
111
|
+
contexts using the same memory that previously limited us to 16K tokens
|
|
112
|
+
(Section 5).
|
|
113
|
+
|
|
114
|
+
• We release optimized CUDA kernels achieving 80% of theoretical peak
|
|
115
|
+
FLOPS on A100 and H100 GPUs, along with PyTorch and JAX bindings, at
|
|
116
|
+
[anonymous URL] (Section 6).
|
|
117
|
+
```
|
|
118
|
+
|
|
119
|
+
**Key features**:
|
|
120
|
+
- Numbered/bulleted format
|
|
121
|
+
- Each contribution is specific and quantified
|
|
122
|
+
- Section references for each claim
|
|
123
|
+
- Both methodological and empirical contributions
|
|
124
|
+
- Code release mentioned
|
|
125
|
+
- Self-contained bullets (each makes sense alone)
|
|
126
|
+
|
|
127
|
+
---
|
|
128
|
+
|
|
129
|
+
## Alternative Opening Paragraphs
|
|
130
|
+
|
|
131
|
+
### For a Methods Paper
|
|
132
|
+
|
|
133
|
+
```
|
|
134
|
+
Scalable optimization algorithms are fundamental to modern machine learning.
|
|
135
|
+
Stochastic gradient descent (SGD) and its variants [1, 2, 3] have enabled
|
|
136
|
+
training of models with billions of parameters on massive datasets. However,
|
|
137
|
+
these first-order methods exhibit slow convergence on ill-conditioned
|
|
138
|
+
problems, often requiring thousands of iterations to converge on tasks
|
|
139
|
+
where second-order methods would converge in tens of iterations [4, 5].
|
|
140
|
+
```
|
|
141
|
+
|
|
142
|
+
### For an Applications Paper
|
|
143
|
+
|
|
144
|
+
```
|
|
145
|
+
Drug discovery is a costly and time-consuming process, with the average new
|
|
146
|
+
drug requiring 10-15 years and $2.6 billion to develop [1]. Machine learning
|
|
147
|
+
offers the potential to accelerate this process by predicting molecular
|
|
148
|
+
properties, identifying promising candidates, and optimizing lead compounds
|
|
149
|
+
computationally [2, 3]. Recent successes in protein structure prediction [4]
|
|
150
|
+
and molecular generation [5] have demonstrated that deep learning can
|
|
151
|
+
capture complex chemical patterns, raising hopes for ML-driven drug discovery.
|
|
152
|
+
```
|
|
153
|
+
|
|
154
|
+
### For a Theory Paper
|
|
155
|
+
|
|
156
|
+
```
|
|
157
|
+
Understanding why deep neural networks generalize well despite having more
|
|
158
|
+
parameters than training examples remains one of the central puzzles of
|
|
159
|
+
modern machine learning [1, 2]. Classical statistical learning theory
|
|
160
|
+
predicts that such overparameterized models should overfit dramatically,
|
|
161
|
+
yet in practice, large networks trained with SGD achieve excellent test
|
|
162
|
+
accuracy [3]. This gap between theory and practice has motivated a rich
|
|
163
|
+
literature on implicit regularization [4], neural tangent kernels [5],
|
|
164
|
+
and feature learning [6], but a complete theoretical picture remains elusive.
|
|
165
|
+
```
|
|
166
|
+
|
|
167
|
+
---
|
|
168
|
+
|
|
169
|
+
## Contribution Bullet Templates
|
|
170
|
+
|
|
171
|
+
### For a New Method
|
|
172
|
+
|
|
173
|
+
```
|
|
174
|
+
• We propose [Method Name], a novel [type of method] that [key innovation]
|
|
175
|
+
achieving [performance improvement] over [baseline] on [benchmark].
|
|
176
|
+
```
|
|
177
|
+
|
|
178
|
+
### For Theoretical Analysis
|
|
179
|
+
|
|
180
|
+
```
|
|
181
|
+
• We prove that [statement], providing the first [type of result] for
|
|
182
|
+
[problem setting]. This resolves an open question from [prior work].
|
|
183
|
+
```
|
|
184
|
+
|
|
185
|
+
### For Empirical Study
|
|
186
|
+
|
|
187
|
+
```
|
|
188
|
+
• We conduct a comprehensive evaluation of [N] methods across [M] datasets,
|
|
189
|
+
revealing that [key finding] and identifying [failure mode/best practice].
|
|
190
|
+
```
|
|
191
|
+
|
|
192
|
+
### For Code/Data Release
|
|
193
|
+
|
|
194
|
+
```
|
|
195
|
+
• We release [resource name], a [description] containing [scale/scope],
|
|
196
|
+
available at [URL]. This enables [future work/reproducibility].
|
|
197
|
+
```
|
|
198
|
+
|
|
199
|
+
---
|
|
200
|
+
|
|
201
|
+
## Common Mistakes to Avoid
|
|
202
|
+
|
|
203
|
+
### Vague Contributions
|
|
204
|
+
|
|
205
|
+
❌ **Bad**:
|
|
206
|
+
```
|
|
207
|
+
• We propose a novel method for attention
|
|
208
|
+
• We show our method is better than baselines
|
|
209
|
+
• We provide theoretical analysis
|
|
210
|
+
```
|
|
211
|
+
|
|
212
|
+
✅ **Good**:
|
|
213
|
+
```
|
|
214
|
+
• We propose LongFlash, achieving 2-4× speedup over FlashAttention
|
|
215
|
+
• We prove LongFlash achieves optimal O(N²d/M) IO complexity
|
|
216
|
+
• We enable 8× longer context training on fixed hardware budget
|
|
217
|
+
```
|
|
218
|
+
|
|
219
|
+
### Missing Quantification
|
|
220
|
+
|
|
221
|
+
❌ **Bad**: "Our method significantly outperforms prior work"
|
|
222
|
+
✅ **Good**: "Our method improves accuracy by 3.2% on GLUE and 4.1% on SuperGLUE"
|
|
223
|
+
|
|
224
|
+
### Overlapping Bullets
|
|
225
|
+
|
|
226
|
+
❌ **Bad**:
|
|
227
|
+
```
|
|
228
|
+
• We propose a new attention mechanism
|
|
229
|
+
• We introduce LongFlash attention
|
|
230
|
+
• Our novel attention approach...
|
|
231
|
+
```
|
|
232
|
+
(These say the same thing three times)
|
|
233
|
+
|
|
234
|
+
### Buried Contributions
|
|
235
|
+
|
|
236
|
+
❌ **Bad**: Contribution bullets at the end of page 2
|
|
237
|
+
✅ **Good**: Contribution bullets clearly visible by end of page 1
|
|
238
|
+
|
|
239
|
+
---
|
|
240
|
+
|
|
241
|
+
## See Also
|
|
242
|
+
|
|
243
|
+
- `ml_conference_style.md` - Comprehensive ML conference guide
|
|
244
|
+
- `venue_writing_styles.md` - Style comparison across venues
|
|
245
|
+
|
|
@@ -0,0 +1,235 @@
|
|
|
1
|
+
% NIH Specific Aims Page Template
|
|
2
|
+
% THE MOST CRITICAL PAGE OF YOUR NIH PROPOSAL
|
|
3
|
+
% 1 page maximum - strictly enforced
|
|
4
|
+
% Last updated: 2024
|
|
5
|
+
|
|
6
|
+
\documentclass[11pt,letterpaper]{article}
|
|
7
|
+
|
|
8
|
+
% Formatting
|
|
9
|
+
\usepackage[margin=0.5in]{geometry} % 0.5 inch minimum margins
|
|
10
|
+
\usepackage{helvet} % Arial-like font
|
|
11
|
+
\renewcommand{\familydefault}{\sfdefault}
|
|
12
|
+
|
|
13
|
+
\usepackage{setspace}
|
|
14
|
+
\usepackage{color}
|
|
15
|
+
\usepackage{soul} % For highlighting (remove in final version)
|
|
16
|
+
|
|
17
|
+
% Remove page numbers (optional)
|
|
18
|
+
\pagestyle{empty}
|
|
19
|
+
|
|
20
|
+
\begin{document}
|
|
21
|
+
|
|
22
|
+
% Optional: Highlight template text to remind yourself to replace
|
|
23
|
+
% Remove \hl{} and color in final version
|
|
24
|
+
\definecolor{highlight}{RGB}{255,255,200}
|
|
25
|
+
\sethlcolor{highlight}
|
|
26
|
+
|
|
27
|
+
% ====================
|
|
28
|
+
% SPECIFIC AIMS PAGE
|
|
29
|
+
% ====================
|
|
30
|
+
|
|
31
|
+
\begin{center}
|
|
32
|
+
\textbf{\large Your Project Title Here: Concise and Descriptive}
|
|
33
|
+
\end{center}
|
|
34
|
+
|
|
35
|
+
\vspace{0.3cm}
|
|
36
|
+
|
|
37
|
+
% OPENING PARAGRAPH: The Hook and Gap
|
|
38
|
+
% 2-3 sentences establishing significance and the knowledge gap
|
|
39
|
+
|
|
40
|
+
\textbf{[Disease/condition]} affects \textbf{[number]} people worldwide and results in \textbf{[burden: mortality, morbidity, cost]}. \textbf{[Current treatment/understanding]} has improved outcomes, but \textbf{[limitation/gap]} remains a critical barrier to \textbf{[desired outcome]}. Understanding \textbf{[specific mechanism/relationship]} is essential for \textbf{[future advance: therapy, prevention, diagnosis]}.
|
|
41
|
+
|
|
42
|
+
\vspace{0.2cm}
|
|
43
|
+
|
|
44
|
+
% LONG-TERM GOAL
|
|
45
|
+
% 1 sentence on your overarching research vision
|
|
46
|
+
|
|
47
|
+
Our \textbf{long-term goal} is to \textbf{[overarching vision: develop cure, understand mechanism, improve treatment]} for \textbf{[disease/population]}.
|
|
48
|
+
|
|
49
|
+
\vspace{0.2cm}
|
|
50
|
+
|
|
51
|
+
% OBJECTIVE AND CENTRAL HYPOTHESIS
|
|
52
|
+
% 1-2 sentences on what THIS proposal will accomplish
|
|
53
|
+
|
|
54
|
+
The \textbf{objective} of this proposal is to \textbf{[specific objective for this project]}. Our \textbf{central hypothesis} is that \textbf{[clearly stated, testable hypothesis]}.
|
|
55
|
+
|
|
56
|
+
\vspace{0.2cm}
|
|
57
|
+
|
|
58
|
+
% RATIONALE
|
|
59
|
+
% 2-3 sentences explaining WHY you expect success (preliminary data!)
|
|
60
|
+
|
|
61
|
+
This hypothesis is based on our \textbf{preliminary data} showing that \textbf{[key preliminary finding 1]} and \textbf{[key preliminary finding 2]}. These findings suggest that \textbf{[mechanistic explanation or expected outcome]}.
|
|
62
|
+
|
|
63
|
+
\vspace{0.2cm}
|
|
64
|
+
|
|
65
|
+
% TRANSITION TO AIMS
|
|
66
|
+
% 1 sentence introducing the specific aims
|
|
67
|
+
|
|
68
|
+
To test this hypothesis and achieve our objective, we will pursue the following \textbf{Specific Aims}:
|
|
69
|
+
|
|
70
|
+
\vspace{0.3cm}
|
|
71
|
+
|
|
72
|
+
% ====================
|
|
73
|
+
% SPECIFIC AIM 1
|
|
74
|
+
% ====================
|
|
75
|
+
|
|
76
|
+
\noindent\textbf{Specific Aim 1: [Concise, active verb title describing what you'll do].}
|
|
77
|
+
|
|
78
|
+
\textit{Working Hypothesis:} \hl{State testable hypothesis for this aim.}
|
|
79
|
+
|
|
80
|
+
We will \textbf{[approach/method]} to determine \textbf{[what you'll learn]}. We will use \textbf{[model system/approach]} to test whether \textbf{[specific prediction]}.
|
|
81
|
+
|
|
82
|
+
\textbf{Expected Outcome:} We expect to find that \textbf{[predicted result]}. This outcome will demonstrate that \textbf{[significance of finding]} and will be \textbf{[positive/negative/innovative/transformative]} because \textbf{[why it matters]}.
|
|
83
|
+
|
|
84
|
+
\vspace{0.3cm}
|
|
85
|
+
|
|
86
|
+
% ====================
|
|
87
|
+
% SPECIFIC AIM 2
|
|
88
|
+
% ====================
|
|
89
|
+
|
|
90
|
+
\noindent\textbf{Specific Aim 2: [Title of second aim].}
|
|
91
|
+
|
|
92
|
+
\textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 2.}
|
|
93
|
+
|
|
94
|
+
Building on Aim 1, we will \textbf{[approach]} to \textbf{[objective]}. We will employ \textbf{[method/technique]} in \textbf{[model/population]} to test the hypothesis that \textbf{[specific prediction]}.
|
|
95
|
+
|
|
96
|
+
\textbf{Expected Outcome:} These studies will reveal \textbf{[predicted finding]}. This is significant because \textbf{[impact on field/understanding]}.
|
|
97
|
+
|
|
98
|
+
\vspace{0.3cm}
|
|
99
|
+
|
|
100
|
+
% ====================
|
|
101
|
+
% SPECIFIC AIM 3 (OPTIONAL)
|
|
102
|
+
% ====================
|
|
103
|
+
|
|
104
|
+
\noindent\textbf{Specific Aim 3: [Title of third aim].}
|
|
105
|
+
|
|
106
|
+
\textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 3.}
|
|
107
|
+
|
|
108
|
+
To translate findings from Aims 1-2, we will \textbf{[approach]} to determine \textbf{[translational objective]}. We will \textbf{[method]} using \textbf{[clinically relevant model/patient samples]} to test whether \textbf{[translational prediction]}.
|
|
109
|
+
|
|
110
|
+
\textbf{Expected Outcome:} We anticipate that \textbf{[result]}, which will provide \textbf{[proof-of-concept/validation/mechanism]} for \textbf{[therapeutic/diagnostic/preventive strategy]}.
|
|
111
|
+
|
|
112
|
+
\vspace{0.3cm}
|
|
113
|
+
|
|
114
|
+
% ====================
|
|
115
|
+
% PAYOFF PARAGRAPH
|
|
116
|
+
% ====================
|
|
117
|
+
|
|
118
|
+
% 2-3 sentences on IMPACT, INNOVATION, and FUTURE DIRECTIONS
|
|
119
|
+
|
|
120
|
+
\textbf{Impact and Innovation:} This project is \textbf{innovative} because it \textbf{[novel aspect: new concept, method, approach, application]}. The proposed research is \textbf{significant} because it will \textbf{[advance the field by...]} and will ultimately lead to \textbf{[long-term impact: improved treatment, new therapeutic target, diagnostic tool]}. Upon completion of these studies, we will be positioned to \textbf{[next steps: clinical trial, mechanistic studies, therapeutic development]}.
|
|
121
|
+
|
|
122
|
+
\vspace{0.5cm}
|
|
123
|
+
|
|
124
|
+
% ====================
|
|
125
|
+
% ALTERNATIVE STRUCTURE (if preferred)
|
|
126
|
+
% ====================
|
|
127
|
+
|
|
128
|
+
% Some successful Specific Aims pages use this alternative structure:
|
|
129
|
+
% - Open with hook (same as above)
|
|
130
|
+
% - State long-term goal and objective (same)
|
|
131
|
+
% - Present central hypothesis with 2-3 supporting pieces of preliminary data
|
|
132
|
+
% - Then state: "We will test this hypothesis through three Specific Aims:"
|
|
133
|
+
% - List aims more concisely (1-2 sentences each, plus expected outcome)
|
|
134
|
+
% - Conclude with payoff paragraph emphasizing innovation, significance, impact
|
|
135
|
+
|
|
136
|
+
\end{document}
|
|
137
|
+
|
|
138
|
+
% ====================
|
|
139
|
+
% TIPS FOR WRITING SPECIFIC AIMS
|
|
140
|
+
% ====================
|
|
141
|
+
|
|
142
|
+
% 1. START WITH A HOOK
|
|
143
|
+
% - Open with the big picture: disease burden, societal cost, mortality
|
|
144
|
+
% - Use compelling statistics
|
|
145
|
+
% - Make it clear why anyone should care
|
|
146
|
+
|
|
147
|
+
% 2. IDENTIFY THE GAP
|
|
148
|
+
% - What's currently known?
|
|
149
|
+
% - What's the critical barrier or unknown?
|
|
150
|
+
% - Why does it matter?
|
|
151
|
+
|
|
152
|
+
% 3. STATE YOUR HYPOTHESIS EXPLICITLY
|
|
153
|
+
% - Clear, testable hypothesis
|
|
154
|
+
% - Not "We hypothesize that we will study..." (that's not a hypothesis!)
|
|
155
|
+
% - "We hypothesize that [mechanism] causes [outcome]"
|
|
156
|
+
|
|
157
|
+
% 4. SHOW PRELIMINARY DATA
|
|
158
|
+
% - Demonstrate feasibility
|
|
159
|
+
% - Prove you're not starting from scratch
|
|
160
|
+
% - Build confidence in your approach
|
|
161
|
+
|
|
162
|
+
% 5. THREE AIMS (TYPICALLY)
|
|
163
|
+
% - Can be 2 or 4, but 3 is most common
|
|
164
|
+
% - Aims should be related but somewhat independent
|
|
165
|
+
% - Failure of one aim shouldn't sink the whole project
|
|
166
|
+
% - Aims can build on each other (Aim 1 → Aim 2 → Aim 3)
|
|
167
|
+
|
|
168
|
+
% 6. EACH AIM SHOULD HAVE:
|
|
169
|
+
% - Clear title (active verb)
|
|
170
|
+
% - Working hypothesis
|
|
171
|
+
% - Approach/method
|
|
172
|
+
% - Expected outcome
|
|
173
|
+
% - Significance/impact
|
|
174
|
+
|
|
175
|
+
% 7. END WITH PAYOFF
|
|
176
|
+
% - Innovation: What's new/different?
|
|
177
|
+
% - Significance: Why does it matter?
|
|
178
|
+
% - Impact: What will change?
|
|
179
|
+
% - Future: Where does this lead?
|
|
180
|
+
|
|
181
|
+
% 8. COMMON MISTAKES TO AVOID
|
|
182
|
+
% - Too much background (this is not a mini-review)
|
|
183
|
+
% - Vague hypotheses or objectives
|
|
184
|
+
% - Missing expected outcomes
|
|
185
|
+
% - No preliminary data mentioned
|
|
186
|
+
% - Too ambitious (can't do it all in 5 years)
|
|
187
|
+
% - Not addressing innovation and significance
|
|
188
|
+
% - Poor logical flow between aims
|
|
189
|
+
% - Exceeding 1 page (auto-reject!)
|
|
190
|
+
|
|
191
|
+
% 9. FORMATTING RULES (STRICTLY ENFORCED)
|
|
192
|
+
% - 1 page maximum (including all text, no figures typically)
|
|
193
|
+
% - Arial 11pt minimum (or equivalent)
|
|
194
|
+
% - 0.5 inch margins minimum
|
|
195
|
+
% - Any spacing (single, 1.5, double acceptable)
|
|
196
|
+
% - No smaller fonts allowed (even for superscripts/subscripts)
|
|
197
|
+
|
|
198
|
+
% 10. REVISION STRATEGY
|
|
199
|
+
% - Write, get feedback, revise 10+ times
|
|
200
|
+
% - Every word must earn its place
|
|
201
|
+
% - Test on non-specialist colleagues
|
|
202
|
+
% - Read aloud to check flow
|
|
203
|
+
% - Have it reviewed by successful R01 holders
|
|
204
|
+
% - Mock study section review
|
|
205
|
+
|
|
206
|
+
% ====================
|
|
207
|
+
% EXAMPLES OF STRONG OPENING SENTENCES
|
|
208
|
+
% ====================
|
|
209
|
+
|
|
210
|
+
% DISEASE BURDEN APPROACH:
|
|
211
|
+
% "Alzheimer's disease (AD) affects 6.7 million Americans and will cost $345 billion in 2023,
|
|
212
|
+
% yet no disease-modifying therapies exist."
|
|
213
|
+
|
|
214
|
+
% MECHANISTIC GAP APPROACH:
|
|
215
|
+
% "Despite decades of research, the molecular mechanisms driving metastasis remain poorly understood,
|
|
216
|
+
% limiting our ability to develop effective therapies for the 90% of cancer deaths caused by metastatic disease."
|
|
217
|
+
|
|
218
|
+
% TRANSLATIONAL APPROACH:
|
|
219
|
+
% "Current immunotherapies fail in 70% of patients with melanoma, largely because we cannot predict
|
|
220
|
+
% who will respond, highlighting an urgent need for biomarkers of treatment response."
|
|
221
|
+
|
|
222
|
+
% ====================
|
|
223
|
+
% REMEMBER
|
|
224
|
+
% ====================
|
|
225
|
+
|
|
226
|
+
% The Specific Aims page is often the ONLY page reviewers read carefully before
|
|
227
|
+
% forming their initial opinion. A weak Specific Aims page can doom an otherwise
|
|
228
|
+
% excellent proposal. Invest the time to make it compelling, clear, and concise.
|
|
229
|
+
|
|
230
|
+
% Get feedback from:
|
|
231
|
+
% - Successful R01 awardees in your field
|
|
232
|
+
% - Grant writing office at your institution
|
|
233
|
+
% - Colleagues who've served on NIH study sections
|
|
234
|
+
% - Non-specialists (if they can't understand it, reviewers may struggle too)
|
|
235
|
+
|