From 9a89e01aba4c2ed17382d3fa12a6a56c8ea71673 Mon Sep 17 00:00:00 2001 From: Timothy Kassis Date: Wed, 31 Dec 2025 15:10:41 -0800 Subject: [PATCH] Update license metadata field --- .claude-plugin/marketplace.json | 2 +- scientific-skills/adaptyv/SKILL.md | 1 + scientific-skills/aeon/SKILL.md | 1 + scientific-skills/alphafold-database/SKILL.md | 1 + scientific-skills/anndata/SKILL.md | 1 + scientific-skills/arboreto/SKILL.md | 1 + scientific-skills/astropy/SKILL.md | 1 + .../benchling-integration/SKILL.md | 1 + scientific-skills/biomni/SKILL.md | 1 + scientific-skills/biopython/SKILL.md | 1 + scientific-skills/biorxiv-database/SKILL.md | 1 + scientific-skills/bioservices/SKILL.md | 1 + scientific-skills/brenda-database/SKILL.md | 1 + scientific-skills/cellxgene-census/SKILL.md | 1 + scientific-skills/chembl-database/SKILL.md | 1 + scientific-skills/cirq/SKILL.md | 1 + .../citation-management/SKILL.md | 1 + .../clinical-decision-support/README.md | 129 ------------------ .../clinical-decision-support/SKILL.md | 1 + scientific-skills/clinical-reports/SKILL.md | 1 + .../clinicaltrials-database/SKILL.md | 1 + scientific-skills/clinpgx-database/SKILL.md | 1 + scientific-skills/clinvar-database/SKILL.md | 1 + scientific-skills/cobrapy/SKILL.md | 1 + scientific-skills/cosmic-database/SKILL.md | 1 + scientific-skills/dask/SKILL.md | 1 + scientific-skills/datacommons-client/SKILL.md | 1 + scientific-skills/datamol/SKILL.md | 1 + scientific-skills/deepchem/SKILL.md | 1 + scientific-skills/deeptools/SKILL.md | 1 + scientific-skills/denario/SKILL.md | 1 + scientific-skills/diffdock/SKILL.md | 1 + .../dnanexus-integration/SKILL.md | 1 + scientific-skills/drugbank-database/SKILL.md | 1 + scientific-skills/ena-database/SKILL.md | 1 + scientific-skills/ensembl-database/SKILL.md | 1 + scientific-skills/esm/SKILL.md | 1 + scientific-skills/etetoolkit/SKILL.md | 1 + .../exploratory-data-analysis/SKILL.md | 1 + scientific-skills/fda-database/SKILL.md | 1 + scientific-skills/flowio/SKILL.md | 1 + scientific-skills/fluidsim/SKILL.md | 1 + scientific-skills/gene-database/SKILL.md | 1 + scientific-skills/generate-image/SKILL.md | 1 + scientific-skills/geniml/SKILL.md | 1 + scientific-skills/geo-database/SKILL.md | 1 + scientific-skills/geopandas/SKILL.md | 1 + .../get-available-resources/SKILL.md | 1 + scientific-skills/gget/SKILL.md | 1 + scientific-skills/gtars/SKILL.md | 1 + scientific-skills/gwas-database/SKILL.md | 1 + scientific-skills/histolab/SKILL.md | 1 + scientific-skills/hmdb-database/SKILL.md | 1 + scientific-skills/hypogenic/SKILL.md | 1 + .../hypothesis-generation/SKILL.md | 1 + .../iso-13485-certification/SKILL.md | 1 + scientific-skills/kegg-database/SKILL.md | 1 + .../labarchive-integration/SKILL.md | 1 + scientific-skills/lamindb/SKILL.md | 1 + .../latchbio-integration/SKILL.md | 1 + scientific-skills/latex-posters/SKILL.md | 1 + scientific-skills/literature-review/SKILL.md | 1 + .../market-research-reports/SKILL.md | 1 + scientific-skills/markitdown/SKILL.md | 2 +- scientific-skills/matchms/SKILL.md | 1 + scientific-skills/matplotlib/SKILL.md | 1 + scientific-skills/medchem/SKILL.md | 1 + .../metabolomics-workbench-database/SKILL.md | 1 + scientific-skills/modal/SKILL.md | 1 + scientific-skills/molfeat/SKILL.md | 1 + scientific-skills/networkx/SKILL.md | 1 + scientific-skills/neurokit2/SKILL.md | 1 + .../neuropixels-analysis/SKILL.md | 2 +- scientific-skills/omero-integration/SKILL.md | 1 + scientific-skills/openalex-database/SKILL.md | 1 + .../opentargets-database/SKILL.md | 1 + .../opentrons-integration/SKILL.md | 1 + scientific-skills/paper-2-web/SKILL.md | 1 + scientific-skills/pathml/SKILL.md | 1 + scientific-skills/pdb-database/SKILL.md | 1 + scientific-skills/peer-review/SKILL.md | 1 + scientific-skills/pennylane/SKILL.md | 1 + scientific-skills/perplexity-search/SKILL.md | 1 + scientific-skills/plotly/SKILL.md | 1 + .../{reference => references}/chart-types.md | 0 .../export-interactivity.md | 0 .../graph-objects.md | 0 .../layouts-styling.md | 0 .../plotly-express.md | 0 scientific-skills/polars/SKILL.md | 1 + scientific-skills/pptx-posters/SKILL.md | 1 + .../protocolsio-integration/SKILL.md | 1 + scientific-skills/pubchem-database/SKILL.md | 1 + scientific-skills/pubmed-database/SKILL.md | 1 + scientific-skills/pufferlib/SKILL.md | 1 + scientific-skills/pydeseq2/SKILL.md | 1 + scientific-skills/pydicom/SKILL.md | 1 + scientific-skills/pyhealth/SKILL.md | 1 + scientific-skills/pylabrobot/SKILL.md | 1 + scientific-skills/pymatgen/SKILL.md | 1 + scientific-skills/pymc/SKILL.md | 1 + scientific-skills/pymoo/SKILL.md | 1 + scientific-skills/pyopenms/SKILL.md | 1 + scientific-skills/pysam/SKILL.md | 1 + scientific-skills/pytdc/SKILL.md | 1 + scientific-skills/pytorch-lightning/SKILL.md | 1 + scientific-skills/qiskit/SKILL.md | 1 + scientific-skills/qutip/SKILL.md | 1 + scientific-skills/rdkit/SKILL.md | 1 + scientific-skills/reactome-database/SKILL.md | 1 + scientific-skills/research-grants/SKILL.md | 1 + scientific-skills/research-lookup/SKILL.md | 1 + scientific-skills/scanpy/SKILL.md | 1 + scientific-skills/scholar-evaluation/SKILL.md | 1 + .../scientific-brainstorming/SKILL.md | 1 + .../scientific-critical-thinking/SKILL.md | 1 + .../scientific-schematics/SKILL.md | 1 + scientific-skills/scientific-slides/SKILL.md | 1 + .../scientific-visualization/SKILL.md | 1 + scientific-skills/scientific-writing/SKILL.md | 1 + scientific-skills/scikit-bio/SKILL.md | 1 + scientific-skills/scikit-learn/SKILL.md | 1 + scientific-skills/scikit-survival/SKILL.md | 1 + scientific-skills/scvi-tools/SKILL.md | 1 + scientific-skills/seaborn/SKILL.md | 1 + scientific-skills/shap/SKILL.md | 1 + scientific-skills/simpy/SKILL.md | 1 + scientific-skills/stable-baselines3/SKILL.md | 1 + .../statistical-analysis/SKILL.md | 1 + scientific-skills/statsmodels/SKILL.md | 1 + scientific-skills/string-database/SKILL.md | 1 + scientific-skills/sympy/SKILL.md | 1 + scientific-skills/torch_geometric/SKILL.md | 1 + scientific-skills/torchdrug/SKILL.md | 1 + scientific-skills/transformers/SKILL.md | 1 + scientific-skills/treatment-plans/SKILL.md | 1 + scientific-skills/umap-learn/SKILL.md | 1 + scientific-skills/uniprot-database/SKILL.md | 1 + scientific-skills/uspto-database/SKILL.md | 1 + scientific-skills/vaex/SKILL.md | 1 + scientific-skills/venue-templates/SKILL.md | 1 + scientific-skills/zarr-python/SKILL.md | 1 + scientific-skills/zinc-database/SKILL.md | 1 + 143 files changed, 137 insertions(+), 132 deletions(-) delete mode 100644 scientific-skills/clinical-decision-support/README.md rename scientific-skills/plotly/{reference => references}/chart-types.md (100%) rename scientific-skills/plotly/{reference => references}/export-interactivity.md (100%) rename scientific-skills/plotly/{reference => references}/graph-objects.md (100%) rename scientific-skills/plotly/{reference => references}/layouts-styling.md (100%) rename scientific-skills/plotly/{reference => references}/plotly-express.md (100%) diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json index 35d06e0..e79b199 100644 --- a/.claude-plugin/marketplace.json +++ b/.claude-plugin/marketplace.json @@ -6,7 +6,7 @@ }, "metadata": { "description": "Claude scientific skills from K-Dense Inc", - "version": "2.11.1" + "version": "2.11.2" }, "plugins": [ { diff --git a/scientific-skills/adaptyv/SKILL.md b/scientific-skills/adaptyv/SKILL.md index 1e694de..3b78415 100644 --- a/scientific-skills/adaptyv/SKILL.md +++ b/scientific-skills/adaptyv/SKILL.md @@ -1,6 +1,7 @@ --- name: adaptyv description: Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/aeon/SKILL.md b/scientific-skills/aeon/SKILL.md index dda56ff..15a783a 100644 --- a/scientific-skills/aeon/SKILL.md +++ b/scientific-skills/aeon/SKILL.md @@ -1,6 +1,7 @@ --- name: aeon description: This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/alphafold-database/SKILL.md b/scientific-skills/alphafold-database/SKILL.md index d7269d4..78d316a 100644 --- a/scientific-skills/alphafold-database/SKILL.md +++ b/scientific-skills/alphafold-database/SKILL.md @@ -1,6 +1,7 @@ --- name: alphafold-database description: "Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/anndata/SKILL.md b/scientific-skills/anndata/SKILL.md index 44957e7..61de572 100644 --- a/scientific-skills/anndata/SKILL.md +++ b/scientific-skills/anndata/SKILL.md @@ -1,6 +1,7 @@ --- name: anndata description: This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/arboreto/SKILL.md b/scientific-skills/arboreto/SKILL.md index 1545099..5a0086f 100644 --- a/scientific-skills/arboreto/SKILL.md +++ b/scientific-skills/arboreto/SKILL.md @@ -1,6 +1,7 @@ --- name: arboreto description: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/astropy/SKILL.md b/scientific-skills/astropy/SKILL.md index e1fa05d..41e77b7 100644 --- a/scientific-skills/astropy/SKILL.md +++ b/scientific-skills/astropy/SKILL.md @@ -1,6 +1,7 @@ --- name: astropy description: Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/benchling-integration/SKILL.md b/scientific-skills/benchling-integration/SKILL.md index 062d691..8362311 100644 --- a/scientific-skills/benchling-integration/SKILL.md +++ b/scientific-skills/benchling-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: benchling-integration description: "Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/biomni/SKILL.md b/scientific-skills/biomni/SKILL.md index 6ee5671..5ef8eb9 100644 --- a/scientific-skills/biomni/SKILL.md +++ b/scientific-skills/biomni/SKILL.md @@ -1,6 +1,7 @@ --- name: biomni description: Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/biopython/SKILL.md b/scientific-skills/biopython/SKILL.md index b721261..6eb88bf 100644 --- a/scientific-skills/biopython/SKILL.md +++ b/scientific-skills/biopython/SKILL.md @@ -1,6 +1,7 @@ --- name: biopython description: "Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/biorxiv-database/SKILL.md b/scientific-skills/biorxiv-database/SKILL.md index 206a262..7765c29 100644 --- a/scientific-skills/biorxiv-database/SKILL.md +++ b/scientific-skills/biorxiv-database/SKILL.md @@ -1,6 +1,7 @@ --- name: biorxiv-database description: Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/bioservices/SKILL.md b/scientific-skills/bioservices/SKILL.md index 95c9993..76ca36d 100644 --- a/scientific-skills/bioservices/SKILL.md +++ b/scientific-skills/bioservices/SKILL.md @@ -1,6 +1,7 @@ --- name: bioservices description: "Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database)." +license: GPLv3 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/brenda-database/SKILL.md b/scientific-skills/brenda-database/SKILL.md index e5b053e..adb3115 100644 --- a/scientific-skills/brenda-database/SKILL.md +++ b/scientific-skills/brenda-database/SKILL.md @@ -1,6 +1,7 @@ --- name: brenda-database description: "Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/cellxgene-census/SKILL.md b/scientific-skills/cellxgene-census/SKILL.md index e0e77a5..ceed59c 100644 --- a/scientific-skills/cellxgene-census/SKILL.md +++ b/scientific-skills/cellxgene-census/SKILL.md @@ -1,6 +1,7 @@ --- name: cellxgene-census description: "Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/chembl-database/SKILL.md b/scientific-skills/chembl-database/SKILL.md index ce938f6..b11fcec 100644 --- a/scientific-skills/chembl-database/SKILL.md +++ b/scientific-skills/chembl-database/SKILL.md @@ -1,6 +1,7 @@ --- name: chembl-database description: "Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/cirq/SKILL.md b/scientific-skills/cirq/SKILL.md index 2decb69..ac5a108 100644 --- a/scientific-skills/cirq/SKILL.md +++ b/scientific-skills/cirq/SKILL.md @@ -1,6 +1,7 @@ --- name: cirq description: Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking). +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/citation-management/SKILL.md b/scientific-skills/citation-management/SKILL.md index 5fb75e8..7d0baa8 100644 --- a/scientific-skills/citation-management/SKILL.md +++ b/scientific-skills/citation-management/SKILL.md @@ -2,6 +2,7 @@ name: citation-management description: Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing. allowed-tools: [Read, Write, Edit, Bash] +license: MIT License metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/clinical-decision-support/README.md b/scientific-skills/clinical-decision-support/README.md deleted file mode 100644 index c96faf7..0000000 --- a/scientific-skills/clinical-decision-support/README.md +++ /dev/null @@ -1,129 +0,0 @@ -# Clinical Decision Support Skill - -Professional clinical decision support documents for medical professionals in pharmaceutical and clinical research settings. - -## Quick Start - -This skill enables generation of three types of clinical documents: - -1. **Individual Patient Treatment Plans** - Personalized protocols for specific patients -2. **Patient Cohort Analysis** - Biomarker-stratified group analyses with outcomes -3. **Treatment Recommendation Reports** - Evidence-based clinical guidelines - -All documents are generated as compact, professional LaTeX/PDF files. - -## Directory Structure - -``` -clinical-decision-support/ -├── SKILL.md # Main skill definition -├── README.md # This file -│ -├── references/ # Clinical guidance documents -│ ├── patient_cohort_analysis.md -│ ├── treatment_recommendations.md -│ ├── clinical_decision_algorithms.md -│ ├── biomarker_classification.md -│ ├── outcome_analysis.md -│ └── evidence_synthesis.md -│ -├── assets/ # Templates and examples -│ ├── cohort_analysis_template.tex -│ ├── treatment_recommendation_template.tex -│ ├── clinical_pathway_template.tex -│ ├── biomarker_report_template.tex -│ ├── example_gbm_cohort.md -│ ├── recommendation_strength_guide.md -│ └── color_schemes.tex -│ -└── scripts/ # Analysis and generation tools - ├── generate_survival_analysis.py - ├── create_cohort_tables.py - ├── build_decision_tree.py - ├── biomarker_classifier.py - └── validate_cds_document.py -``` - -## Example Use Cases - -### Create a Patient Cohort Analysis -``` -> Analyze a cohort of 45 NSCLC patients stratified by PD-L1 expression - (<1%, 1-49%, ≥50%) including ORR, PFS, and OS outcomes -``` - -### Generate Treatment Recommendations -``` -> Create evidence-based treatment recommendations for HER2-positive - metastatic breast cancer with GRADE methodology -``` - -### Build Clinical Pathway -``` -> Generate a clinical decision algorithm for acute chest pain - management with TIMI risk score -``` - -## Key Features - -- **GRADE Methodology**: Evidence quality grading (High/Moderate/Low/Very Low) -- **Recommendation Strength**: Strong (Grade 1) vs Conditional (Grade 2) -- **Biomarker Integration**: Genomic, expression, and molecular subtype classification -- **Statistical Analysis**: Kaplan-Meier, Cox regression, log-rank tests -- **Guideline Concordance**: NCCN, ASCO, ESMO, AHA/ACC integration -- **Professional Output**: 0.5in margins, color-coded boxes, publication-ready - -## Dependencies - -Python scripts require: -- `pandas`, `numpy`, `scipy`: Data analysis and statistics -- `lifelines`: Survival analysis (Kaplan-Meier, Cox regression) -- `matplotlib`: Visualization -- `pyyaml` (optional): YAML input for decision trees - -Install with: -```bash -pip install pandas numpy scipy lifelines matplotlib pyyaml -``` - -## References Included - -1. **Patient Cohort Analysis**: Stratification methods, biomarker correlations, statistical comparisons -2. **Treatment Recommendations**: Evidence grading, treatment sequencing, special populations -3. **Clinical Decision Algorithms**: Risk scores, decision trees, TikZ flowcharts -4. **Biomarker Classification**: Genomic alterations, molecular subtypes, companion diagnostics -5. **Outcome Analysis**: Survival methods, response criteria (RECIST), effect sizes -6. **Evidence Synthesis**: Guideline integration, systematic reviews, meta-analysis - -## Templates Provided - -1. **Cohort Analysis**: Demographics table, biomarker profile, outcomes, statistics, recommendations -2. **Treatment Recommendations**: Evidence review, GRADE-graded options, monitoring, decision algorithm -3. **Clinical Pathway**: TikZ flowchart with risk stratification and urgency-coded actions -4. **Biomarker Report**: Genomic profiling with tier-based actionability and therapy matching - -## Scripts Included - -1. **`generate_survival_analysis.py`**: Create Kaplan-Meier curves with hazard ratios -2. **`create_cohort_tables.py`**: Generate baseline, efficacy, and safety tables -3. **`build_decision_tree.py`**: Convert text/JSON to TikZ flowcharts -4. **`biomarker_classifier.py`**: Stratify patients by PD-L1, HER2, molecular subtypes -5. **`validate_cds_document.py`**: Quality checks for completeness and compliance - -## Integration - -Integrates with existing skills: -- **scientific-writing**: Citation management, statistical reporting -- **clinical-reports**: Medical terminology, HIPAA compliance -- **scientific-schematics**: TikZ flowcharts - -## Version - -Version 1.0 - Initial release -Created: November 2024 -Last Updated: November 5, 2024 - -## Questions or Feedback - -This skill was designed for pharmaceutical and clinical research professionals creating clinical decision support documents. For questions about usage or suggestions for improvements, contact the Scientific Writer development team. - diff --git a/scientific-skills/clinical-decision-support/SKILL.md b/scientific-skills/clinical-decision-support/SKILL.md index 0fab080..0abfe95 100644 --- a/scientific-skills/clinical-decision-support/SKILL.md +++ b/scientific-skills/clinical-decision-support/SKILL.md @@ -2,6 +2,7 @@ name: clinical-decision-support description: "Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis." allowed-tools: [Read, Write, Edit, Bash] +license: MIT License metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/clinical-reports/SKILL.md b/scientific-skills/clinical-reports/SKILL.md index c8b6259..09e2a3a 100644 --- a/scientific-skills/clinical-reports/SKILL.md +++ b/scientific-skills/clinical-reports/SKILL.md @@ -2,6 +2,7 @@ name: clinical-reports description: "Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools." allowed-tools: [Read, Write, Edit, Bash] +license: MIT License metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/clinicaltrials-database/SKILL.md b/scientific-skills/clinicaltrials-database/SKILL.md index c9e57f9..5e98c25 100644 --- a/scientific-skills/clinicaltrials-database/SKILL.md +++ b/scientific-skills/clinicaltrials-database/SKILL.md @@ -1,6 +1,7 @@ --- name: clinicaltrials-database description: "Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/clinpgx-database/SKILL.md b/scientific-skills/clinpgx-database/SKILL.md index baeca06..c6d103d 100644 --- a/scientific-skills/clinpgx-database/SKILL.md +++ b/scientific-skills/clinpgx-database/SKILL.md @@ -1,6 +1,7 @@ --- name: clinpgx-database description: "Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/clinvar-database/SKILL.md b/scientific-skills/clinvar-database/SKILL.md index f959f69..c2fb77a 100644 --- a/scientific-skills/clinvar-database/SKILL.md +++ b/scientific-skills/clinvar-database/SKILL.md @@ -1,6 +1,7 @@ --- name: clinvar-database description: "Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/cobrapy/SKILL.md b/scientific-skills/cobrapy/SKILL.md index 140aeaa..3091d2a 100644 --- a/scientific-skills/cobrapy/SKILL.md +++ b/scientific-skills/cobrapy/SKILL.md @@ -1,6 +1,7 @@ --- name: cobrapy description: "Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis." +license: GPL-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/cosmic-database/SKILL.md b/scientific-skills/cosmic-database/SKILL.md index daa71ca..f5b3bc0 100644 --- a/scientific-skills/cosmic-database/SKILL.md +++ b/scientific-skills/cosmic-database/SKILL.md @@ -1,6 +1,7 @@ --- name: cosmic-database description: "Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/dask/SKILL.md b/scientific-skills/dask/SKILL.md index ba921a6..e8bc6c9 100644 --- a/scientific-skills/dask/SKILL.md +++ b/scientific-skills/dask/SKILL.md @@ -1,6 +1,7 @@ --- name: dask description: "Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/datacommons-client/SKILL.md b/scientific-skills/datacommons-client/SKILL.md index 34b7f1a..711f912 100644 --- a/scientific-skills/datacommons-client/SKILL.md +++ b/scientific-skills/datacommons-client/SKILL.md @@ -1,6 +1,7 @@ --- name: datacommons-client description: Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/datamol/SKILL.md b/scientific-skills/datamol/SKILL.md index 873eea8..611439e 100644 --- a/scientific-skills/datamol/SKILL.md +++ b/scientific-skills/datamol/SKILL.md @@ -1,6 +1,7 @@ --- name: datamol description: "Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/deepchem/SKILL.md b/scientific-skills/deepchem/SKILL.md index 25e5d7f..51fac22 100644 --- a/scientific-skills/deepchem/SKILL.md +++ b/scientific-skills/deepchem/SKILL.md @@ -1,6 +1,7 @@ --- name: deepchem description: "Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/deeptools/SKILL.md b/scientific-skills/deeptools/SKILL.md index 78f4af8..f9968a6 100644 --- a/scientific-skills/deeptools/SKILL.md +++ b/scientific-skills/deeptools/SKILL.md @@ -1,6 +1,7 @@ --- name: deeptools description: "NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization." +license: BSD license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/denario/SKILL.md b/scientific-skills/denario/SKILL.md index 073d3a2..fa31753 100644 --- a/scientific-skills/denario/SKILL.md +++ b/scientific-skills/denario/SKILL.md @@ -1,6 +1,7 @@ --- name: denario description: Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration. +license: GPL-3.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/diffdock/SKILL.md b/scientific-skills/diffdock/SKILL.md index 5b1e668..377b288 100644 --- a/scientific-skills/diffdock/SKILL.md +++ b/scientific-skills/diffdock/SKILL.md @@ -1,6 +1,7 @@ --- name: diffdock description: "Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/dnanexus-integration/SKILL.md b/scientific-skills/dnanexus-integration/SKILL.md index c638089..1ecd184 100644 --- a/scientific-skills/dnanexus-integration/SKILL.md +++ b/scientific-skills/dnanexus-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: dnanexus-integration description: "DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/drugbank-database/SKILL.md b/scientific-skills/drugbank-database/SKILL.md index 78fa9f8..28e9907 100644 --- a/scientific-skills/drugbank-database/SKILL.md +++ b/scientific-skills/drugbank-database/SKILL.md @@ -1,6 +1,7 @@ --- name: drugbank-database description: Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/ena-database/SKILL.md b/scientific-skills/ena-database/SKILL.md index a68cf32..6db4ce9 100644 --- a/scientific-skills/ena-database/SKILL.md +++ b/scientific-skills/ena-database/SKILL.md @@ -1,6 +1,7 @@ --- name: ena-database description: "Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/ensembl-database/SKILL.md b/scientific-skills/ensembl-database/SKILL.md index 796e8f3..7b7c2f1 100644 --- a/scientific-skills/ensembl-database/SKILL.md +++ b/scientific-skills/ensembl-database/SKILL.md @@ -1,6 +1,7 @@ --- name: ensembl-database description: "Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/esm/SKILL.md b/scientific-skills/esm/SKILL.md index f6f06a9..e43d4a1 100644 --- a/scientific-skills/esm/SKILL.md +++ b/scientific-skills/esm/SKILL.md @@ -1,6 +1,7 @@ --- name: esm description: Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/etetoolkit/SKILL.md b/scientific-skills/etetoolkit/SKILL.md index 1dd8314..ca75e3a 100644 --- a/scientific-skills/etetoolkit/SKILL.md +++ b/scientific-skills/etetoolkit/SKILL.md @@ -1,6 +1,7 @@ --- name: etetoolkit description: "Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics." +license: GPL-3.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/exploratory-data-analysis/SKILL.md b/scientific-skills/exploratory-data-analysis/SKILL.md index a5d93bb..44bc4bc 100644 --- a/scientific-skills/exploratory-data-analysis/SKILL.md +++ b/scientific-skills/exploratory-data-analysis/SKILL.md @@ -1,6 +1,7 @@ --- name: exploratory-data-analysis description: Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/fda-database/SKILL.md b/scientific-skills/fda-database/SKILL.md index 9e999ea..3a6c83f 100644 --- a/scientific-skills/fda-database/SKILL.md +++ b/scientific-skills/fda-database/SKILL.md @@ -1,6 +1,7 @@ --- name: fda-database description: "Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/flowio/SKILL.md b/scientific-skills/flowio/SKILL.md index 9985da9..48f1bb1 100644 --- a/scientific-skills/flowio/SKILL.md +++ b/scientific-skills/flowio/SKILL.md @@ -1,6 +1,7 @@ --- name: flowio description: "Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/fluidsim/SKILL.md b/scientific-skills/fluidsim/SKILL.md index f689a09..3268878 100644 --- a/scientific-skills/fluidsim/SKILL.md +++ b/scientific-skills/fluidsim/SKILL.md @@ -1,6 +1,7 @@ --- name: fluidsim description: Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis. +license: CeCILL FREE SOFTWARE LICENSE AGREEMENT metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/gene-database/SKILL.md b/scientific-skills/gene-database/SKILL.md index 8c09d76..df57ac5 100644 --- a/scientific-skills/gene-database/SKILL.md +++ b/scientific-skills/gene-database/SKILL.md @@ -1,6 +1,7 @@ --- name: gene-database description: "Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/generate-image/SKILL.md b/scientific-skills/generate-image/SKILL.md index 862410e..2d669d6 100644 --- a/scientific-skills/generate-image/SKILL.md +++ b/scientific-skills/generate-image/SKILL.md @@ -1,6 +1,7 @@ --- name: generate-image description: Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that isn't a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/geniml/SKILL.md b/scientific-skills/geniml/SKILL.md index 5efa878..36788ea 100644 --- a/scientific-skills/geniml/SKILL.md +++ b/scientific-skills/geniml/SKILL.md @@ -1,6 +1,7 @@ --- name: geniml description: This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning. +license: BSD-2-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/geo-database/SKILL.md b/scientific-skills/geo-database/SKILL.md index 655d374..98bdff6 100644 --- a/scientific-skills/geo-database/SKILL.md +++ b/scientific-skills/geo-database/SKILL.md @@ -1,6 +1,7 @@ --- name: geo-database description: "Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/geopandas/SKILL.md b/scientific-skills/geopandas/SKILL.md index 6d01f2c..88af48d 100644 --- a/scientific-skills/geopandas/SKILL.md +++ b/scientific-skills/geopandas/SKILL.md @@ -1,6 +1,7 @@ --- name: geopandas description: Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/get-available-resources/SKILL.md b/scientific-skills/get-available-resources/SKILL.md index 38e9b33..9110ae3 100644 --- a/scientific-skills/get-available-resources/SKILL.md +++ b/scientific-skills/get-available-resources/SKILL.md @@ -1,6 +1,7 @@ --- name: get-available-resources description: This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/gget/SKILL.md b/scientific-skills/gget/SKILL.md index 812cf6c..b5a9a19 100644 --- a/scientific-skills/gget/SKILL.md +++ b/scientific-skills/gget/SKILL.md @@ -1,6 +1,7 @@ --- name: gget description: "CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices." +license: BSD-2-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/gtars/SKILL.md b/scientific-skills/gtars/SKILL.md index d3fd2a7..77d70ab 100644 --- a/scientific-skills/gtars/SKILL.md +++ b/scientific-skills/gtars/SKILL.md @@ -1,6 +1,7 @@ --- name: gtars description: High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/gwas-database/SKILL.md b/scientific-skills/gwas-database/SKILL.md index d4abcd3..dfa0250 100644 --- a/scientific-skills/gwas-database/SKILL.md +++ b/scientific-skills/gwas-database/SKILL.md @@ -1,6 +1,7 @@ --- name: gwas-database description: "Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/histolab/SKILL.md b/scientific-skills/histolab/SKILL.md index d907ee0..6b608c7 100644 --- a/scientific-skills/histolab/SKILL.md +++ b/scientific-skills/histolab/SKILL.md @@ -1,6 +1,7 @@ --- name: histolab description: Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/hmdb-database/SKILL.md b/scientific-skills/hmdb-database/SKILL.md index 6f292a4..7497a46 100644 --- a/scientific-skills/hmdb-database/SKILL.md +++ b/scientific-skills/hmdb-database/SKILL.md @@ -1,6 +1,7 @@ --- name: hmdb-database description: "Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification." +license: HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications. metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/hypogenic/SKILL.md b/scientific-skills/hypogenic/SKILL.md index d4674fd..1ae466b 100644 --- a/scientific-skills/hypogenic/SKILL.md +++ b/scientific-skills/hypogenic/SKILL.md @@ -1,6 +1,7 @@ --- name: hypogenic description: Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/hypothesis-generation/SKILL.md b/scientific-skills/hypothesis-generation/SKILL.md index 9342b05..eef0333 100644 --- a/scientific-skills/hypothesis-generation/SKILL.md +++ b/scientific-skills/hypothesis-generation/SKILL.md @@ -2,6 +2,7 @@ name: hypothesis-generation description: "Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/iso-13485-certification/SKILL.md b/scientific-skills/iso-13485-certification/SKILL.md index 5006043..d733400 100644 --- a/scientific-skills/iso-13485-certification/SKILL.md +++ b/scientific-skills/iso-13485-certification/SKILL.md @@ -1,6 +1,7 @@ --- name: iso-13485-certification description: Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/kegg-database/SKILL.md b/scientific-skills/kegg-database/SKILL.md index b6a9e03..c19c4ea 100644 --- a/scientific-skills/kegg-database/SKILL.md +++ b/scientific-skills/kegg-database/SKILL.md @@ -1,6 +1,7 @@ --- name: kegg-database description: "Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control." +license: Non-academic use of KEGG requires a commercial license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/labarchive-integration/SKILL.md b/scientific-skills/labarchive-integration/SKILL.md index 3d4a4eb..88a1b19 100644 --- a/scientific-skills/labarchive-integration/SKILL.md +++ b/scientific-skills/labarchive-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: labarchive-integration description: "Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/lamindb/SKILL.md b/scientific-skills/lamindb/SKILL.md index 2b4ff01..4278b18 100644 --- a/scientific-skills/lamindb/SKILL.md +++ b/scientific-skills/lamindb/SKILL.md @@ -1,6 +1,7 @@ --- name: lamindb description: This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/latchbio-integration/SKILL.md b/scientific-skills/latchbio-integration/SKILL.md index 39f866d..1207b20 100644 --- a/scientific-skills/latchbio-integration/SKILL.md +++ b/scientific-skills/latchbio-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: latchbio-integration description: "Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/latex-posters/SKILL.md b/scientific-skills/latex-posters/SKILL.md index b3d3e2a..ce89260 100644 --- a/scientific-skills/latex-posters/SKILL.md +++ b/scientific-skills/latex-posters/SKILL.md @@ -2,6 +2,7 @@ name: latex-posters description: "Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/literature-review/SKILL.md b/scientific-skills/literature-review/SKILL.md index 70979c0..e705b56 100644 --- a/scientific-skills/literature-review/SKILL.md +++ b/scientific-skills/literature-review/SKILL.md @@ -2,6 +2,7 @@ name: literature-review description: Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.). allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/market-research-reports/SKILL.md b/scientific-skills/market-research-reports/SKILL.md index c4e3848..04e8e12 100644 --- a/scientific-skills/market-research-reports/SKILL.md +++ b/scientific-skills/market-research-reports/SKILL.md @@ -2,6 +2,7 @@ name: market-research-reports description: "Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/markitdown/SKILL.md b/scientific-skills/markitdown/SKILL.md index 2ea0d57..6a4da63 100644 --- a/scientific-skills/markitdown/SKILL.md +++ b/scientific-skills/markitdown/SKILL.md @@ -2,7 +2,7 @@ name: markitdown description: "Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more." allowed-tools: [Read, Write, Edit, Bash] -license: MIT +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/matchms/SKILL.md b/scientific-skills/matchms/SKILL.md index afd73a3..c172934 100644 --- a/scientific-skills/matchms/SKILL.md +++ b/scientific-skills/matchms/SKILL.md @@ -1,6 +1,7 @@ --- name: matchms description: "Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/matplotlib/SKILL.md b/scientific-skills/matplotlib/SKILL.md index b650bef..88c0b8c 100644 --- a/scientific-skills/matplotlib/SKILL.md +++ b/scientific-skills/matplotlib/SKILL.md @@ -1,6 +1,7 @@ --- name: matplotlib description: "Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures." +license: https://github.com/matplotlib/matplotlib/tree/main/LICENSE metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/medchem/SKILL.md b/scientific-skills/medchem/SKILL.md index f45d98c..e994b95 100644 --- a/scientific-skills/medchem/SKILL.md +++ b/scientific-skills/medchem/SKILL.md @@ -1,6 +1,7 @@ --- name: medchem description: "Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/metabolomics-workbench-database/SKILL.md b/scientific-skills/metabolomics-workbench-database/SKILL.md index 375ab3f..0043f2b 100644 --- a/scientific-skills/metabolomics-workbench-database/SKILL.md +++ b/scientific-skills/metabolomics-workbench-database/SKILL.md @@ -1,6 +1,7 @@ --- name: metabolomics-workbench-database description: "Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/modal/SKILL.md b/scientific-skills/modal/SKILL.md index 0bfe58b..e585665 100644 --- a/scientific-skills/modal/SKILL.md +++ b/scientific-skills/modal/SKILL.md @@ -1,6 +1,7 @@ --- name: modal description: Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/molfeat/SKILL.md b/scientific-skills/molfeat/SKILL.md index 136fc2f..2ee9bb8 100644 --- a/scientific-skills/molfeat/SKILL.md +++ b/scientific-skills/molfeat/SKILL.md @@ -1,6 +1,7 @@ --- name: molfeat description: "Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/networkx/SKILL.md b/scientific-skills/networkx/SKILL.md index 3cd36a0..0572f69 100644 --- a/scientific-skills/networkx/SKILL.md +++ b/scientific-skills/networkx/SKILL.md @@ -1,6 +1,7 @@ --- name: networkx description: Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships. +license: 3-clause BSD license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/neurokit2/SKILL.md b/scientific-skills/neurokit2/SKILL.md index 2503669..5d97650 100644 --- a/scientific-skills/neurokit2/SKILL.md +++ b/scientific-skills/neurokit2/SKILL.md @@ -1,6 +1,7 @@ --- name: neurokit2 description: Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/neuropixels-analysis/SKILL.md b/scientific-skills/neuropixels-analysis/SKILL.md index b81599a..0d6ba60 100644 --- a/scientific-skills/neuropixels-analysis/SKILL.md +++ b/scientific-skills/neuropixels-analysis/SKILL.md @@ -1,7 +1,7 @@ --- name: neuropixels-analysis description: "Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation." -license: MIT License +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/omero-integration/SKILL.md b/scientific-skills/omero-integration/SKILL.md index b9fe445..7ae44b8 100644 --- a/scientific-skills/omero-integration/SKILL.md +++ b/scientific-skills/omero-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: omero-integration description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/openalex-database/SKILL.md b/scientific-skills/openalex-database/SKILL.md index 939a994..eee806f 100644 --- a/scientific-skills/openalex-database/SKILL.md +++ b/scientific-skills/openalex-database/SKILL.md @@ -1,6 +1,7 @@ --- name: openalex-database description: Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/opentargets-database/SKILL.md b/scientific-skills/opentargets-database/SKILL.md index 10c6f0b..7feabb3 100644 --- a/scientific-skills/opentargets-database/SKILL.md +++ b/scientific-skills/opentargets-database/SKILL.md @@ -1,6 +1,7 @@ --- name: opentargets-database description: "Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/opentrons-integration/SKILL.md b/scientific-skills/opentrons-integration/SKILL.md index c1b3dff..6b2f551 100644 --- a/scientific-skills/opentrons-integration/SKILL.md +++ b/scientific-skills/opentrons-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: opentrons-integration description: "Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/paper-2-web/SKILL.md b/scientific-skills/paper-2-web/SKILL.md index e358370..b7095ef 100644 --- a/scientific-skills/paper-2-web/SKILL.md +++ b/scientific-skills/paper-2-web/SKILL.md @@ -2,6 +2,7 @@ name: paper-2-web description: This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources. allowed-tools: [Read, Write, Edit, Bash] +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pathml/SKILL.md b/scientific-skills/pathml/SKILL.md index 8dbf7e9..d9da884 100644 --- a/scientific-skills/pathml/SKILL.md +++ b/scientific-skills/pathml/SKILL.md @@ -1,6 +1,7 @@ --- name: pathml description: Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows. +license: GPL-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pdb-database/SKILL.md b/scientific-skills/pdb-database/SKILL.md index 3e2aed9..153183c 100644 --- a/scientific-skills/pdb-database/SKILL.md +++ b/scientific-skills/pdb-database/SKILL.md @@ -1,6 +1,7 @@ --- name: pdb-database description: "Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/peer-review/SKILL.md b/scientific-skills/peer-review/SKILL.md index 7f99313..ff5bf9d 100644 --- a/scientific-skills/peer-review/SKILL.md +++ b/scientific-skills/peer-review/SKILL.md @@ -2,6 +2,7 @@ name: peer-review description: "Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pennylane/SKILL.md b/scientific-skills/pennylane/SKILL.md index 2db54de..831a3c0 100644 --- a/scientific-skills/pennylane/SKILL.md +++ b/scientific-skills/pennylane/SKILL.md @@ -1,6 +1,7 @@ --- name: pennylane description: Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables building and training quantum circuits with automatic differentiation, seamless integration with PyTorch/JAX/TensorFlow, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ, etc.). Use when working with quantum circuits, variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, molecular simulations, quantum chemistry calculations, or any quantum computing tasks requiring gradient-based optimization, hardware-agnostic programming, or quantum machine learning workflows. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/perplexity-search/SKILL.md b/scientific-skills/perplexity-search/SKILL.md index 77ac1bf..c489ba6 100644 --- a/scientific-skills/perplexity-search/SKILL.md +++ b/scientific-skills/perplexity-search/SKILL.md @@ -1,6 +1,7 @@ --- name: perplexity-search description: Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model's knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/plotly/SKILL.md b/scientific-skills/plotly/SKILL.md index bcd8af1..e714270 100644 --- a/scientific-skills/plotly/SKILL.md +++ b/scientific-skills/plotly/SKILL.md @@ -1,6 +1,7 @@ --- name: plotly description: Interactive scientific and statistical data visualization library for Python. Use when creating charts, plots, or visualizations including scatter plots, line charts, bar charts, heatmaps, 3D plots, geographic maps, statistical distributions, financial charts, and dashboards. Supports both quick visualizations (Plotly Express) and fine-grained customization (graph objects). Outputs interactive HTML or static images (PNG, PDF, SVG). +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/plotly/reference/chart-types.md b/scientific-skills/plotly/references/chart-types.md similarity index 100% rename from scientific-skills/plotly/reference/chart-types.md rename to scientific-skills/plotly/references/chart-types.md diff --git a/scientific-skills/plotly/reference/export-interactivity.md b/scientific-skills/plotly/references/export-interactivity.md similarity index 100% rename from scientific-skills/plotly/reference/export-interactivity.md rename to scientific-skills/plotly/references/export-interactivity.md diff --git a/scientific-skills/plotly/reference/graph-objects.md b/scientific-skills/plotly/references/graph-objects.md similarity index 100% rename from scientific-skills/plotly/reference/graph-objects.md rename to scientific-skills/plotly/references/graph-objects.md diff --git a/scientific-skills/plotly/reference/layouts-styling.md b/scientific-skills/plotly/references/layouts-styling.md similarity index 100% rename from scientific-skills/plotly/reference/layouts-styling.md rename to scientific-skills/plotly/references/layouts-styling.md diff --git a/scientific-skills/plotly/reference/plotly-express.md b/scientific-skills/plotly/references/plotly-express.md similarity index 100% rename from scientific-skills/plotly/reference/plotly-express.md rename to scientific-skills/plotly/references/plotly-express.md diff --git a/scientific-skills/polars/SKILL.md b/scientific-skills/polars/SKILL.md index 42a4627..2bd0f06 100644 --- a/scientific-skills/polars/SKILL.md +++ b/scientific-skills/polars/SKILL.md @@ -1,6 +1,7 @@ --- name: polars description: "Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows." +license: https://github.com/pola-rs/polars/blob/main/LICENSE metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pptx-posters/SKILL.md b/scientific-skills/pptx-posters/SKILL.md index b3d3e2a..ce89260 100644 --- a/scientific-skills/pptx-posters/SKILL.md +++ b/scientific-skills/pptx-posters/SKILL.md @@ -2,6 +2,7 @@ name: latex-posters description: "Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/protocolsio-integration/SKILL.md b/scientific-skills/protocolsio-integration/SKILL.md index 3f76701..20ef3cd 100644 --- a/scientific-skills/protocolsio-integration/SKILL.md +++ b/scientific-skills/protocolsio-integration/SKILL.md @@ -1,6 +1,7 @@ --- name: protocolsio-integration description: Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation. +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pubchem-database/SKILL.md b/scientific-skills/pubchem-database/SKILL.md index 3ded1bc..542fb77 100644 --- a/scientific-skills/pubchem-database/SKILL.md +++ b/scientific-skills/pubchem-database/SKILL.md @@ -1,6 +1,7 @@ --- name: pubchem-database description: "Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pubmed-database/SKILL.md b/scientific-skills/pubmed-database/SKILL.md index 2416f1b..f89f7c0 100644 --- a/scientific-skills/pubmed-database/SKILL.md +++ b/scientific-skills/pubmed-database/SKILL.md @@ -1,6 +1,7 @@ --- name: pubmed-database description: "Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pufferlib/SKILL.md b/scientific-skills/pufferlib/SKILL.md index 8813495..dbaf08f 100644 --- a/scientific-skills/pufferlib/SKILL.md +++ b/scientific-skills/pufferlib/SKILL.md @@ -1,6 +1,7 @@ --- name: pufferlib description: This skill should be used when working with reinforcement learning tasks including high-performance RL training, custom environment development, vectorized parallel simulation, multi-agent systems, or integration with existing RL environments (Gymnasium, PettingZoo, Atari, Procgen, etc.). Use this skill for implementing PPO training, creating PufferEnv environments, optimizing RL performance, or developing policies with CNNs/LSTMs. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pydeseq2/SKILL.md b/scientific-skills/pydeseq2/SKILL.md index 1edde56..bd2be16 100644 --- a/scientific-skills/pydeseq2/SKILL.md +++ b/scientific-skills/pydeseq2/SKILL.md @@ -1,6 +1,7 @@ --- name: pydeseq2 description: "Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pydicom/SKILL.md b/scientific-skills/pydicom/SKILL.md index 54a2f4c..5701c9e 100644 --- a/scientific-skills/pydicom/SKILL.md +++ b/scientific-skills/pydicom/SKILL.md @@ -1,6 +1,7 @@ --- name: pydicom description: Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications. +license: https://github.com/pydicom/pydicom/blob/main/LICENSE metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pyhealth/SKILL.md b/scientific-skills/pyhealth/SKILL.md index 2aad3b8..59a120a 100644 --- a/scientific-skills/pyhealth/SKILL.md +++ b/scientific-skills/pyhealth/SKILL.md @@ -1,6 +1,7 @@ --- name: pyhealth description: Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN). +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pylabrobot/SKILL.md b/scientific-skills/pylabrobot/SKILL.md index 5c709b4..21895b7 100644 --- a/scientific-skills/pylabrobot/SKILL.md +++ b/scientific-skills/pylabrobot/SKILL.md @@ -1,6 +1,7 @@ --- name: pylabrobot description: Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR, Opentrons OT-2, Tecan EVO), integrating lab equipment, managing deck layouts and resources (plates, tips, containers), reading plates, or creating reproducible laboratory protocols. Applicable for both simulated protocols and physical hardware control. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pymatgen/SKILL.md b/scientific-skills/pymatgen/SKILL.md index b50ad04..22d23c5 100644 --- a/scientific-skills/pymatgen/SKILL.md +++ b/scientific-skills/pymatgen/SKILL.md @@ -1,6 +1,7 @@ --- name: pymatgen description: "Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pymc/SKILL.md b/scientific-skills/pymc/SKILL.md index 6acbcc8..014ab81 100644 --- a/scientific-skills/pymc/SKILL.md +++ b/scientific-skills/pymc/SKILL.md @@ -1,6 +1,7 @@ --- name: pymc-bayesian-modeling description: "Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference." +license: Apache License, Version 2.0 metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pymoo/SKILL.md b/scientific-skills/pymoo/SKILL.md index fc946de..9f40d2a 100644 --- a/scientific-skills/pymoo/SKILL.md +++ b/scientific-skills/pymoo/SKILL.md @@ -1,6 +1,7 @@ --- name: pymoo description: "Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pyopenms/SKILL.md b/scientific-skills/pyopenms/SKILL.md index 68d4e20..581f0a1 100644 --- a/scientific-skills/pyopenms/SKILL.md +++ b/scientific-skills/pyopenms/SKILL.md @@ -1,6 +1,7 @@ --- name: pyopenms description: Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets. +license: 3 clause BSD license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pysam/SKILL.md b/scientific-skills/pysam/SKILL.md index 02491f6..88d93bb 100644 --- a/scientific-skills/pysam/SKILL.md +++ b/scientific-skills/pysam/SKILL.md @@ -1,6 +1,7 @@ --- name: pysam description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pytdc/SKILL.md b/scientific-skills/pytdc/SKILL.md index 6f1d66c..6cebe72 100644 --- a/scientific-skills/pytdc/SKILL.md +++ b/scientific-skills/pytdc/SKILL.md @@ -1,6 +1,7 @@ --- name: pytdc description: "Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/pytorch-lightning/SKILL.md b/scientific-skills/pytorch-lightning/SKILL.md index 921d0e7..dd6ff97 100644 --- a/scientific-skills/pytorch-lightning/SKILL.md +++ b/scientific-skills/pytorch-lightning/SKILL.md @@ -1,6 +1,7 @@ --- name: pytorch-lightning description: "Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/qiskit/SKILL.md b/scientific-skills/qiskit/SKILL.md index a866fbc..6f10642 100644 --- a/scientific-skills/qiskit/SKILL.md +++ b/scientific-skills/qiskit/SKILL.md @@ -1,6 +1,7 @@ --- name: qiskit description: Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/qutip/SKILL.md b/scientific-skills/qutip/SKILL.md index 0fe6e37..a4bbc28 100644 --- a/scientific-skills/qutip/SKILL.md +++ b/scientific-skills/qutip/SKILL.md @@ -1,6 +1,7 @@ --- name: qutip description: "Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/rdkit/SKILL.md b/scientific-skills/rdkit/SKILL.md index 460ea15..48efbe5 100644 --- a/scientific-skills/rdkit/SKILL.md +++ b/scientific-skills/rdkit/SKILL.md @@ -1,6 +1,7 @@ --- name: rdkit description: "Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/reactome-database/SKILL.md b/scientific-skills/reactome-database/SKILL.md index f63c3ca..3a0ee8b 100644 --- a/scientific-skills/reactome-database/SKILL.md +++ b/scientific-skills/reactome-database/SKILL.md @@ -1,6 +1,7 @@ --- name: reactome-database description: "Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/research-grants/SKILL.md b/scientific-skills/research-grants/SKILL.md index 66e6720..8a150ee 100644 --- a/scientific-skills/research-grants/SKILL.md +++ b/scientific-skills/research-grants/SKILL.md @@ -2,6 +2,7 @@ name: research-grants description: "Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/research-lookup/SKILL.md b/scientific-skills/research-lookup/SKILL.md index b31284e..f5ddd6e 100644 --- a/scientific-skills/research-lookup/SKILL.md +++ b/scientific-skills/research-lookup/SKILL.md @@ -2,6 +2,7 @@ name: research-lookup description: "Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scanpy/SKILL.md b/scientific-skills/scanpy/SKILL.md index dc3264c..2ec3b84 100644 --- a/scientific-skills/scanpy/SKILL.md +++ b/scientific-skills/scanpy/SKILL.md @@ -1,6 +1,7 @@ --- name: scanpy description: "Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis." +license: SD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scholar-evaluation/SKILL.md b/scientific-skills/scholar-evaluation/SKILL.md index d960f86..a44a176 100644 --- a/scientific-skills/scholar-evaluation/SKILL.md +++ b/scientific-skills/scholar-evaluation/SKILL.md @@ -1,6 +1,7 @@ --- name: scholar-evaluation description: Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-brainstorming/SKILL.md b/scientific-skills/scientific-brainstorming/SKILL.md index 54d9d24..f18d16e 100644 --- a/scientific-skills/scientific-brainstorming/SKILL.md +++ b/scientific-skills/scientific-brainstorming/SKILL.md @@ -1,6 +1,7 @@ --- name: scientific-brainstorming description: "Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-critical-thinking/SKILL.md b/scientific-skills/scientific-critical-thinking/SKILL.md index 6caa824..ab69690 100644 --- a/scientific-skills/scientific-critical-thinking/SKILL.md +++ b/scientific-skills/scientific-critical-thinking/SKILL.md @@ -2,6 +2,7 @@ name: scientific-critical-thinking description: "Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-schematics/SKILL.md b/scientific-skills/scientific-schematics/SKILL.md index 191c711..6435911 100644 --- a/scientific-skills/scientific-schematics/SKILL.md +++ b/scientific-skills/scientific-schematics/SKILL.md @@ -2,6 +2,7 @@ name: scientific-schematics description: "Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-slides/SKILL.md b/scientific-skills/scientific-slides/SKILL.md index b8afe68..c2092b5 100644 --- a/scientific-skills/scientific-slides/SKILL.md +++ b/scientific-skills/scientific-slides/SKILL.md @@ -2,6 +2,7 @@ name: scientific-slides description: "Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-visualization/SKILL.md b/scientific-skills/scientific-visualization/SKILL.md index e6a5038..ff2551d 100644 --- a/scientific-skills/scientific-visualization/SKILL.md +++ b/scientific-skills/scientific-visualization/SKILL.md @@ -1,6 +1,7 @@ --- name: scientific-visualization description: "Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scientific-writing/SKILL.md b/scientific-skills/scientific-writing/SKILL.md index a5c2138..ab8e9ab 100644 --- a/scientific-skills/scientific-writing/SKILL.md +++ b/scientific-skills/scientific-writing/SKILL.md @@ -2,6 +2,7 @@ name: scientific-writing description: "Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scikit-bio/SKILL.md b/scientific-skills/scikit-bio/SKILL.md index 16fd933..42e40dd 100644 --- a/scientific-skills/scikit-bio/SKILL.md +++ b/scientific-skills/scikit-bio/SKILL.md @@ -1,6 +1,7 @@ --- name: scikit-bio description: "Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scikit-learn/SKILL.md b/scientific-skills/scikit-learn/SKILL.md index 4fbb10f..cef95d4 100644 --- a/scientific-skills/scikit-learn/SKILL.md +++ b/scientific-skills/scikit-learn/SKILL.md @@ -1,6 +1,7 @@ --- name: scikit-learn description: Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scikit-survival/SKILL.md b/scientific-skills/scikit-survival/SKILL.md index 95d1a43..641c04a 100644 --- a/scientific-skills/scikit-survival/SKILL.md +++ b/scientific-skills/scikit-survival/SKILL.md @@ -1,6 +1,7 @@ --- name: scikit-survival description: Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library. +license: GPL-3.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/scvi-tools/SKILL.md b/scientific-skills/scvi-tools/SKILL.md index f1f9a04..e966c7f 100644 --- a/scientific-skills/scvi-tools/SKILL.md +++ b/scientific-skills/scvi-tools/SKILL.md @@ -1,6 +1,7 @@ --- name: scvi-tools description: This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks. +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/seaborn/SKILL.md b/scientific-skills/seaborn/SKILL.md index 0fe360e..35ee5c6 100644 --- a/scientific-skills/seaborn/SKILL.md +++ b/scientific-skills/seaborn/SKILL.md @@ -1,6 +1,7 @@ --- name: seaborn description: "Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/shap/SKILL.md b/scientific-skills/shap/SKILL.md index f25e71d..28c89af 100644 --- a/scientific-skills/shap/SKILL.md +++ b/scientific-skills/shap/SKILL.md @@ -1,6 +1,7 @@ --- name: shap description: Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/simpy/SKILL.md b/scientific-skills/simpy/SKILL.md index 30c5c72..d460a20 100644 --- a/scientific-skills/simpy/SKILL.md +++ b/scientific-skills/simpy/SKILL.md @@ -1,6 +1,7 @@ --- name: simpy description: Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/stable-baselines3/SKILL.md b/scientific-skills/stable-baselines3/SKILL.md index 4d09184..2c76397 100644 --- a/scientific-skills/stable-baselines3/SKILL.md +++ b/scientific-skills/stable-baselines3/SKILL.md @@ -1,6 +1,7 @@ --- name: stable-baselines3 description: Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), creating custom Gym environments, implementing callbacks for monitoring and control, using vectorized environments for parallel training, and integrating with deep RL workflows. This skill should be used when users request RL algorithm implementation, agent training, environment design, or RL experimentation. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/statistical-analysis/SKILL.md b/scientific-skills/statistical-analysis/SKILL.md index 55f9523..a7682cb 100644 --- a/scientific-skills/statistical-analysis/SKILL.md +++ b/scientific-skills/statistical-analysis/SKILL.md @@ -1,6 +1,7 @@ --- name: statistical-analysis description: "Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/statsmodels/SKILL.md b/scientific-skills/statsmodels/SKILL.md index 98930cd..2e1ba88 100644 --- a/scientific-skills/statsmodels/SKILL.md +++ b/scientific-skills/statsmodels/SKILL.md @@ -1,6 +1,7 @@ --- name: statsmodels description: "Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/string-database/SKILL.md b/scientific-skills/string-database/SKILL.md index e91b912..5ab5072 100644 --- a/scientific-skills/string-database/SKILL.md +++ b/scientific-skills/string-database/SKILL.md @@ -1,6 +1,7 @@ --- name: string-database description: "Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/sympy/SKILL.md b/scientific-skills/sympy/SKILL.md index 14a33f8..b943707 100644 --- a/scientific-skills/sympy/SKILL.md +++ b/scientific-skills/sympy/SKILL.md @@ -1,6 +1,7 @@ --- name: sympy description: Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters. +license: https://github.com/sympy/sympy/blob/master/LICENSE metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/torch_geometric/SKILL.md b/scientific-skills/torch_geometric/SKILL.md index fc2ca99..5d7375e 100644 --- a/scientific-skills/torch_geometric/SKILL.md +++ b/scientific-skills/torch_geometric/SKILL.md @@ -1,6 +1,7 @@ --- name: torch-geometric description: "Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/torchdrug/SKILL.md b/scientific-skills/torchdrug/SKILL.md index e84847a..77c4cfd 100644 --- a/scientific-skills/torchdrug/SKILL.md +++ b/scientific-skills/torchdrug/SKILL.md @@ -1,6 +1,7 @@ --- name: torchdrug description: "Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs." +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/transformers/SKILL.md b/scientific-skills/transformers/SKILL.md index 60d3380..3c4a656 100644 --- a/scientific-skills/transformers/SKILL.md +++ b/scientific-skills/transformers/SKILL.md @@ -1,6 +1,7 @@ --- name: transformers description: This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets. +license: Apache-2.0 license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/treatment-plans/SKILL.md b/scientific-skills/treatment-plans/SKILL.md index ff82689..476b4f4 100644 --- a/scientific-skills/treatment-plans/SKILL.md +++ b/scientific-skills/treatment-plans/SKILL.md @@ -2,6 +2,7 @@ name: treatment-plans description: "Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability." allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/umap-learn/SKILL.md b/scientific-skills/umap-learn/SKILL.md index 0151579..91c1b66 100644 --- a/scientific-skills/umap-learn/SKILL.md +++ b/scientific-skills/umap-learn/SKILL.md @@ -1,6 +1,7 @@ --- name: umap-learn description: "UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data." +license: BSD-3-Clause license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/uniprot-database/SKILL.md b/scientific-skills/uniprot-database/SKILL.md index 92d2b41..5649429 100644 --- a/scientific-skills/uniprot-database/SKILL.md +++ b/scientific-skills/uniprot-database/SKILL.md @@ -1,6 +1,7 @@ --- name: uniprot-database description: "Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/uspto-database/SKILL.md b/scientific-skills/uspto-database/SKILL.md index 123fdce..4c1e339 100644 --- a/scientific-skills/uspto-database/SKILL.md +++ b/scientific-skills/uspto-database/SKILL.md @@ -1,6 +1,7 @@ --- name: uspto-database description: "Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches." +license: Unknown metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/vaex/SKILL.md b/scientific-skills/vaex/SKILL.md index ace1caa..774da8c 100644 --- a/scientific-skills/vaex/SKILL.md +++ b/scientific-skills/vaex/SKILL.md @@ -1,6 +1,7 @@ --- name: vaex description: Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that don't fit in memory. +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/venue-templates/SKILL.md b/scientific-skills/venue-templates/SKILL.md index bdbc2f1..11f6911 100644 --- a/scientific-skills/venue-templates/SKILL.md +++ b/scientific-skills/venue-templates/SKILL.md @@ -2,6 +2,7 @@ name: venue-templates description: Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates. allowed-tools: [Read, Write, Edit, Bash] +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/zarr-python/SKILL.md b/scientific-skills/zarr-python/SKILL.md index 61a7af0..ecb94f0 100644 --- a/scientific-skills/zarr-python/SKILL.md +++ b/scientific-skills/zarr-python/SKILL.md @@ -1,6 +1,7 @@ --- name: zarr-python description: "Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines." +license: MIT license metadata: skill-author: K-Dense Inc. --- diff --git a/scientific-skills/zinc-database/SKILL.md b/scientific-skills/zinc-database/SKILL.md index c6abc1f..33bf4d3 100644 --- a/scientific-skills/zinc-database/SKILL.md +++ b/scientific-skills/zinc-database/SKILL.md @@ -1,6 +1,7 @@ --- name: zinc-database description: "Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery." +license: Unknown metadata: skill-author: K-Dense Inc. ---