Claude Skills by K-Dense-AI

Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates.

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individ...

Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experiments, cross-correlating interrogation windows, validating and replacing spurious PIV vectors, or computing vorticity, strain rate, and turbulence statistics from measured velocity fields.

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.

Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, recommendation feedback, feed export, or Atom feed URLs.

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.

Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and mol...

Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.

Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.

Run structured What-If scenario analysis with 4–6 branch possibility exploration (best, likely, worst, wild card, contrarian, second-order). Use when the user asks speculative what-if questions about uncertain futures, strategic forks, contingency planning, or stress-testing a decision before committing.

Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distinguishing capabilities are per-token bounding boxes, page raster output, and fully local processing with no cloud API.

Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.

Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.

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.

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in W...

Generate or edit images with AI models through the OpenRouter Image API (Gemini, FLUX, Seedream, Recraft, GPT-Image). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.

Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans. Use when turning observations or preliminary findings into transparent, testable research plans without treating hypotheses as facts.

Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.

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.

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.).

Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.

Convert heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data formats, batch workflows, plugins, vision OCR, Azure extraction, and the official MCP server.

Use Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests that explicitly need current web evidence, academic-source discovery, repeated entity lookups, exhaustive reports, or ongoing change tracking.

Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.

Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figure/table, and citation critique; or revision-response planning.

Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable is a PowerPoint research/conference poster and exact physical, printer, accessibility, provenance, and package-security checks are required.

Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates (.potx), layouts, speaker notes, or comments. Trigger whenever th...

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.

Compile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to gather literature, references, background evidence, competing findings, or a manuscript research packet. Uses Parallel Search by default, Parallel Extract for source verification, Parallel Research for explicitly deep/exhaustive work, optional explicit Parallel Chat, and optional Perplexity only when requested or allowed as a failure fallback.

Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.

Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.

Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash 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.

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.

Draft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission preparation when scientific accuracy and traceability matter.

Format and structurally validate local treatment-plan documentation after clinical decisions have already been supplied and verified by authorized licensed professionals. Use for source traceability, clinician-authored intervention records, goals and checkpoints, shared-decision records, reconciliation handoffs, and release gates—not for clinical decision-making.

Prepare journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Use when selecting an official template, checking current page or anonymity rules, adapting academic writing to a venue, or inspecting a submission PDF.

Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.

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.

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in W...

Generate or edit images with AI models through the OpenRouter Image API (Gemini, FLUX, Seedream, Recraft, GPT-Image). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.

Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans. Use when turning observations or preliminary findings into transparent, testable research plans without treating hypotheses as facts.

Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.

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.

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.).