Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
EnglishRun nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data.
EnglishStrategic scientific problem selection, project ideation, and troubleshooting based on the Fischbach & Walsh framework.
EnglishDeep learning for single-cell analysis using scvi-tools and scverse ecosystem. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping, (7) RNA velocity with veloVI, or (8) QC analysis of single-cell RNA-seq data. Triggers include scVI, scANVI, totalVI, QC, quality control, batch correction, integration, multi-modal.
EnglishA conversational framework for systematic scientific problem selection, project ideation, troubleshooting, and strategic decision making.
EnglishAnalyze competitors with feature comparison matrices, positioning analysis, and strategic implications. Use when researching a competitor, comparing product capabilities, assessing competitive positioning, or preparing a competitive brief for product strategy.
EnglishMonitor competitor pricing pages and send alerts when prices change. Track discount patterns, promotional cycles, and pricing strategy shifts.
EnglishResearch customer questions by searching across documentation, knowledge bases, and connected sources, then synthesize a confidence-scored answer. Use when a customer asks a question you need to investigate, when building background on a customer situation, or when you need account context.
EnglishCombines search results from multiple sources into coherent, deduplicated answers with source attribution.
EnglishCombines search results from multiple sources into coherent, deduplicated answers with source attribution.
EnglishManages connected MCP sources for Tandem search. Detects available sources, guides users to connect new ones, handles source priority ordering, and manages rate limiting awareness.
EnglishManages connected MCP sources for enterprise search. Detects available sources and handles source priority ordering.
EnglishWrite structured product requirements documents (PRDs) with problem statements, user stories, requirements, and success metrics. Use when speccing a new feature, writing a PRD, defining acceptance criteria, prioritizing requirements, or documenting product decisions.
EnglishConvert human operational intent into a Tandem mission blueprint with phased workstreams, explicit handoffs, reusable outputs, and recurrence-aware setup.
EnglishWrite and maintain knowledge base articles from resolved support issues. Use when a ticket has been resolved and the solution should be documented, when updating existing KB articles, or when creating how-to guides, troubleshooting docs, or FAQ entries.
EnglishLegacy fallback for heavy research-plus-posting file packs. Prefer content-strategy, social-content, and seo-audit for day-to-day planning and execution. Use this only when a full research dossier and posting package is explicitly required.
EnglishDesign Tandem mission blueprints with scoped workstreams, explicit handoffs, review gates, and prompts that compile into reliable staged missions.
EnglishCreate Tandem custom modes through guided questions, then output one valid mode JSON object for preview and apply.
EnglishSynthesize qualitative and quantitative user research into structured insights and opportunity areas.
EnglishTwo-tier memory system that makes the AI a true workplace collaborator. Decodes shorthand, acronyms, nicknames, and internal language so the AI understands requests like a colleague would. Uses CONTEXT.md for working memory and a memory/ directory for the full knowledge base.
English
AGENT SKILLS ATLASIncludes Bio Instrument Data, Bio Nextflow Manager, Bio Research Strategy, and other workflows.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Bio Instrument Data
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to
Bio Nextflow Manager
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public data
Bio Research Strategy
Strategic scientific problem selection, project ideation, and troubleshooting based on the Fischbach & Walsh framework.
Bio Single Cell
Deep learning for single-cell analysis using scvi-tools and scverse ecosystem. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping, (7) RNA velocity with veloVI, or (8) QC analysis of single-cell RNA-seq data. Triggers include scVI, scANVI, totalVI, QC, quality control, batch correction, integration, multi-modal.
Bio Strategy
A conversational framework for systematic scientific problem selection, project ideation, troubleshooting, and strategic decision making.
Competitive Analysis
Analyze competitors with feature comparison matrices, positioning analysis, and strategic implications. Use when researching a competitor, comparing product capabilities, assessing competitive positioning, or preparing a competitive brief for product strategy.
Competitor Price Tracker
Monitor competitor pricing pages and send alerts when prices change. Track discount patterns, promotional cycles, and pricing strategy shifts.
Customer Research
Research customer questions by searching across documentation, knowledge bases, and connected sources, then synthesize a confidence-scored answer. Use when a customer asks a question you need to investigate, when building background on a customer situation, or when you need account context.
Data Explore Data
Profile and explore a dataset to understand its shape, quality, and patterns
Enterprise Knowledge Synthesis
Combines search results from multiple sources into coherent, deduplicated answers with source attribution.
Enterprise Search Knowledge
Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, an
Enterprise Search Source
Manages connected MCP sources for Tandem search. Detects available sources, guides users to connect new ones, handles source priority ordering, and manages rate limiting awareness.
Enterprise Search Strategy
Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific sy
Enterprise Source Management
Manages connected MCP sources for enterprise search. Detects available sources and handles source priority ordering.
Feature Spec
Write structured product requirements documents (PRDs) with problem statements, user stories, requirements, and success metrics. Use when speccing a new feature, writing a PRD, defining acceptance criteria, prioritizing requirements, or documenting product decisions.
Finance Journal Entry
Prepare journal entries with proper debits, credits, and supporting detail
Finance Sox Testing
Generate SOX sample selections, testing workpapers, and control assessments
Intent to Mission Blueprint
Convert human operational intent into a Tandem mission blueprint with phased workstreams, explicit handoffs, reusable outputs, and recurrence-aware setup.
Knowledge Management
Write and maintain knowledge base articles from resolved support issues. Use when a ticket has been resolved and the solution should be documented, when updating existing KB articles, or when creating how-to guides, troubleshooting docs, or FAQ entries.
Marketing Research Posting Plan
Legacy fallback for heavy research-plus-posting file packs. Prefer content-strategy, social-content, and seo-audit for day-to-day planning and execution. Use this only when a full research dossier and posting package is explicitly required.
Mission Blueprint Compiler
Design Tandem mission blueprints with scoped workstreams, explicit handoffs, review gates, and prompts that compile into reliable staged missions.
Mode Builder
Create Tandem custom modes through guided questions, then output one valid mode JSON object for preview and apply.
Product User Research
Synthesize qualitative and quantitative user research into structured insights and opportunity areas. Use when analyzing interview notes, survey responses, support ticket
Productivity Memory
Two-tier memory system that makes the AI a true workplace collaborator. Decodes shorthand, acronyms, nicknames, and internal language so the AI understands requests like a colleague would. Uses CONTEXT.md for working memory and a memory/ directory for the full knowledge base.
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Use the Bio Instrument Data skill to help with my task.
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