Business & Operations

--> --- name: bio-medchem description: Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-matchms description: Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within...

--> --- name: bio-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 Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix. tool_type: mixed primary_tool: Unkn...

--> --- name: bio-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. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-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 docu...

--> --- name: bio-edgartools description: Python library for accessing, analyzing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SE...

--> --- name: bio-cobrapy description: Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---

--> --- name: bio-cirq 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. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output with...

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'dmmr-crc-histopathology-agent' description: 'Predict and validate colorectal cancer dMMR signals from H&E histopathology, including non-tumor and low-magnification WSI regions.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'scientific-spectral-vqa-benchmark' description: 'Evaluate MLLMs on scientific spectral images using SpecVQA-style figure extraction, curve-aware sampling, QA design, and scoring workflows.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

Evaluate and operate released Profluent OpenCRISPR gene-editing systems, especially OpenCRISPR-1, for controlled research workflows using its published Cas9-like protein, compatible guide RNA designs, protocols, licensing, specificity testing, and experimental validation. Use when comparing OpenCRISPR-1 with SpCas9, planning nonclinical editing studies, or assessing use in nuclease, nickase, deactivated, base, prime, or epigenome-editing contexts.

--> --- name: bio-genomics-vcf-operations description: 'VCF operations: multi-allelic parsing, variant classification (SNP/MNP/INS/DEL/COMPLEX), Ti/Tv ratio, QUAL/DP filtering, INFO field parsing. Mirrors bcftools stats.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- VCF manipulation, filtering, merging, and summary statistics. Wraps bcftools and GATK Selec...

--> --- name: bio-genomics-assembly description: 'Genome assembly quality assessment: N50/N90/L50/L90 (QUAST-compatible), GC content, contig length distribution, completeness estimation. Wraps SPAdes, Megahit, Flye, Canu.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- De novo genome assembly for short and long reads. Wraps SPAdes, Megahit, Flye, and Canu.

Operate Arc Institute Evo 2 for long-context DNA sequence scoring, zero-shot variant effect analysis, genomic embeddings, sequence generation, and model deployment. Use when a task explicitly needs Evo 2, million-base genomic context, DNA likelihood comparisons, genomic foundation-model embeddings, or generated DNA candidates across species.

Use Google DeepMind AlphaGenome to predict tissue-aware regulatory effects of DNA sequence variants across expression, splicing, chromatin, and contact-map outputs. Use when prioritizing noncoding variants, comparing reference and alternate alleles, visualizing predicted regulatory changes, or designing focused AlphaGenome API analyses.

Operate CZI TranscriptFormer cross-species generative single-cell models to produce cell embeddings, contextual gene embeddings, likelihoods, zero-shot classifiers, disease-state representations, and regulatory analyses from raw-count AnnData files. Use when selecting TF-Sapiens, TF-Exemplar, or TF-Metazoa, processing in- or out-of-distribution species, or scaling embedding extraction across GPUs.

--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'stack-single-cell-icl-agent' description: 'Apply Arc Institute Stack, a single-cell foundation model that performs in-context learning at inference time without per-task fine-tuning.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---

Use when you have a written implementation plan to execute in a separate session with review checkpoints

--> --- name: 'theme-factory' description: 'Toolkit for styling artifacts with a theme. These artifacts can be slides, docs, reportings, HTML landing pages, etc. There are 10 pre-set themes with colors/fonts that you can apply to any artifact that has been creating, or can generate a new theme on-the-fly.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- This skill provides a curated collection of p...

--> --- name: 'notion-meeting-intelligence' description: 'Prepares meeting materials by gathering context from Notion, enriching with Claude research, and creating both an internal pre-read and external agenda saved to Notion. Helps you arrive prepared with comprehensive background and structured meeting docs.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Prepares you for meetings by gathering c...

--> --- name: "transcribe" description: "Transcribe audio files to text with optional diarization and known-speaker hints. Use when a user asks to transcribe speech from audio/video, extract text from recordings, or label speakers in interviews or meetings." measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Transcribe audio using OpenAI, with optional speaker diarization when requested. Prefer the bu...

Load when removing batch effects across multiple spatial samples on a multi-batch spatial AnnData via Harmony, BBKNN, or Scanorama before downstream analysis. Skip when aligning physical slice coordinates (use spatial-register) or for single-batch data (no integration needed — go straight to spatial-domains).

Load when running pathway / gene-set enrichment per cluster on a preprocessed spatial AnnData via Enrichr (over-representation), GSEA (preranked), or ssGSEA (per-cell scores). Skip when ranking spatially variable genes (use `spatial-genes`) or when comparing pathways across conditions (use `spatial-condition` for DE first, then this skill on the ranked output).

Load when deconvolving spot-level cell-type proportions on a Visium-style spatial AnnData using a labelled scRNA reference (FlashDeconv / Cell2location / RCTD / DestVI / Tangram / others). Skip when each spot is a single cell already (Xenium / MERFISH — use spatial-annotate) or for tissue-domain detection (use spatial-domains).