Clean description fields

.claude-plugin/marketplace.json

@@ -6,7 +6,7 @@
   },
   "metadata": {
     "description": "Claude scientific skills from K-Dense Inc",
-    "version": "2.14.0"
+    "version": "2.15.0"
   },
   "plugins": [
     {

scientific-skills/alphafold-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+description: Access AlphaFold 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.

scientific-skills/benchling-integration/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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
 compatibility: Requires a Benchling account and API key
 metadata:

scientific-skills/brenda-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/chembl-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+description: Query ChEMBL 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.

scientific-skills/cirq/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: cirq
-description: Google's quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
+description: Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
 license: Apache-2.0 license
 metadata:
     skill-author: K-Dense Inc.

scientific-skills/clinical-decision-support/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/clinical-reports/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/clinicaltrials-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/clinpgx-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/clinvar-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/cobrapy/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: cobrapy
-description: "Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis."
+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.

scientific-skills/cosmic-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/datamol/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+description: Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including 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.

scientific-skills/deeptools/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/diffdock/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/dnanexus-integration/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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
 compatibility: Requires a DNAnexus account
 metadata:

scientific-skills/document-skills/docx/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: docx
-description: "Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing."
+description: Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
 license: Proprietary. LICENSE.txt has complete terms
 ---
 

scientific-skills/document-skills/pdf/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: pdf
-description: "PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis."
+description: PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
 license: Proprietary. LICENSE.txt has complete terms
 ---
 

scientific-skills/document-skills/pptx/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: pptx
-description: "Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification."
+description: Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
 license: Proprietary. LICENSE.txt has complete terms
 ---
 

scientific-skills/document-skills/xlsx/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: xlsx
-description: "Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis."
+description: Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
 license: Proprietary. LICENSE.txt has complete terms
 ---
 

scientific-skills/ena-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/ensembl-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/etetoolkit/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: etetoolkit
-description: "Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics."
+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.

scientific-skills/fda-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/flowio/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/gene-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/generate-image/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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.
+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 is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
 license: MIT license
 compatibility: Requires an OpenRouter API key
 metadata:

scientific-skills/geo-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/gwas-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/hmdb-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/kegg-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/labarchive-integration/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/latchbio-integration/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/latex-posters/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/market-research-reports/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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 Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
 allowed-tools: [Read, Write, Edit, Bash]
 license: MIT license
 metadata:

scientific-skills/markitdown/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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
 metadata:

scientific-skills/medchem/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: medchem
-description: "Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering."
+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.

scientific-skills/metabolomics-workbench-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/molfeat/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: molfeat
-description: "Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML."
+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.

scientific-skills/neuropixels-analysis/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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
 metadata:
     skill-author: K-Dense Inc.

scientific-skills/omero-integration/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/opentargets-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pdb-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/perplexity-search/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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.
+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 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
 compatibility: An OpenRouter API key is required to use Perplexity search
 metadata:

scientific-skills/pptx-posters/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/pubchem-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pubmed-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pydeseq2/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pymatgen/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: pymatgen
-description: "Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science."
+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.

scientific-skills/pymc/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pymoo/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pysam/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pytdc/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/pytorch-lightning/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/qiskit/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: qiskit
-description: IBM's quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM's optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
+description: IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
 license: Apache-2.0 license
 metadata:
     skill-author: K-Dense Inc.

scientific-skills/rdkit/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/reactome-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/research-grants/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: research-grants
-description: "Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements."
+description: Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. 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:

scientific-skills/research-lookup/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+description: Look up current research information using Perplexity 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:

scientific-skills/scientific-brainstorming/SKILL.md

@@ -1,6 +1,6 @@
 ---
 name: scientific-brainstorming
-description: Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you don't have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
+description: Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
 license: MIT license
 metadata:
     skill-author: K-Dense Inc.

scientific-skills/scientific-schematics/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/scientific-slides/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/scientific-writing/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (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:

scientific-skills/scikit-bio/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/string-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/torch_geometric/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/treatment-plans/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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:

scientific-skills/umap-learn/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/uniprot-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/uspto-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/vaex/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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.
+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 do not fit in memory.
 license: MIT license
 metadata:
     skill-author: K-Dense Inc.

scientific-skills/zarr-python/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.

scientific-skills/zinc-database/SKILL.md

@@ -1,6 +1,6 @@
 ---
 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."
+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.