OpenAI

Look up Gene Ontology terms, which classify gene functions, and their links to gene products through QuickGO. Get concise summaries, explore broader or narrower terms, and save full responses when needed.

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• Looking up GO term details
• Checking GO annotations for a gene product
• Exploring broader and narrower GO terms

Plan DNA variant detection workflows by identifying the assay and sample model, then routing to germline, cancer somatic, or molecular-barcode panel skills. It also supports focused local BAM/CRAM checks with variant files, depth summaries, and optional filters.

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• Choosing a workflow for WGS, WES, or DNA panels
• Routing inherited, cancer, and molecular-barcode analyses
• Checking reference genomes and required input files

Analyze marker-gene sequencing data to study microbial communities. Supports FASTQ quality checks and, with primers, metadata, and taxonomy resources, workflows that produce sequence variant tables, taxonomic assignments, diversity measurements, and plots.

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• Check amplicon FASTQ quality and analysis readiness
• Generate sequence variant and taxonomy tables
• Visualize microbial diversity and taxon composition

Build or review quality control workflows for single-cell and single-nucleus RNA sequencing data. Select filters from observed data, detect doublets, assign cell types, and create UMAP plots that summarize cell relationships, while recording analysis decisions and outputs.

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• Choosing quality filters from dataset distributions
• Detecting doublets and checking ambient RNA
• Assigning cell types using references or marker genes

Manage Mixpanel Headless login and connection settings, check credentials, and switch accounts, projects, or workspaces. Save named combinations of these settings as targets so an agent can select the intended connection together.

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• Check the active account and project
• Set up login and test credentials
• Switch projects or workspaces

Find and inspect UI components in MagicPath, add them to an app, and adapt their behavior and styling. Apply themes or create and edit canvas components from code, including work based on an existing repository interface.

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• Find UI components and add them to an app
• Apply a MagicPath theme to an interface
• Create or edit a component on the canvas

Look up one genetic variant in UKB-TOPMed and summarize its associations with traits. Accept rsID identifiers or GRCh37 and GRCh38 coordinates, resolve the required query format, and report association totals and any result truncation.

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• Look up trait associations for a variant identified by rsID
• Query UKB-TOPMed using GRCh37 coordinates
• Review a limited set of associations and the total count

Query STRING for protein interaction networks, interaction partners, and enrichment results showing functions common in a gene set. Receive concise summaries with limited result counts, with options for machine-readable JSON or saved full results.

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• Checking a protein’s interaction network
• Finding interaction partners for a protein
• Reviewing functions enriched in a gene set

Retrieve focused information from PubChem, including molecular formulas, molecular weights, compound descriptions, assay summaries, and substance metadata. Get concise Markdown summaries, with the option to save the full response for further use.

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• Looking up a compound's molecular formula and weight
• Getting a short description from a compound ID
• Checking an assay summary

Plan or run quality checks and peak calling, which identifies enriched genomic regions, for ChIP-seq, CUT&RUN, and CUT&Tag. The workflow accounts for controls and replicates and prepares signal tracks, quality reports, and differential binding designs.

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• Check data quality and enrichment signals
• Choose narrow or broad peaks for the biological target
• Create bigWig tracks and quality dashboards

Plan or run ATAC-seq analysis to identify accessible DNA regions. Check sequencing quality, align reads, detect peaks, combine evidence across replicate samples, and prepare comparisons between conditions with quality summaries and visualization tracks.

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• Check the quality of ATAC-seq samples
• Detect accessible DNA regions from FASTQ or BAM files
• Build consensus peaks across replicate samples

Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.

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• Check sequencing quality before downstream analysis
• Summarize quality reports across multiple samples
• Assess whether adapter or quality trimming is needed

Retrieve genes, genetic variants, clinical annotations, and dosing guidelines from the PharmGKB API, then turn the results into concise summaries. Save the full response when you need the underlying data.

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• Look up a gene or genetic variant by ID
• Find clinical annotations related to a drug
• Retrieve and summarize dosing guidelines

Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.

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• Choose an analysis workflow for an epigenomics assay
• Check FASTQ inputs and sample-sheet readiness
• Organize control and biological replicate information

Find proteomics projects, which study proteins on a broad scale, in PRIDE Archive and summarize their metadata. Search by keyword or use a PXD accession to inspect a specific project's registered information.

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• Find proteomics projects by keyword
• Look up a project by its PXD accession
• Review concise summaries of project metadata

Prepare a Python environment for Mixpanel analysis by installing required libraries and checking credentials and connectivity. Use it for first-time setup, missing dependencies, or guidance on service account and OAuth sign-in options.

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• Set up a new environment for Mixpanel analysis
• Install missing Python analysis libraries
• Configure service account or OAuth credentials

Look up TPMI associations for a single genetic variant using an rsID or genome coordinates. Get a concise summary showing the queried variant, the total number of associations, and whether the displayed results are incomplete.

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• Check TPMI associations for a variant identified by rsID
• Look up a variant using GRCh37 genome coordinates
• Save the full association response to a file

Guide the use of NVIDIA cuOpt for route planning and mathematical optimization, choosing values to minimize cost or maximize profit under constraints. Covers requirements, environment checks, installation guidance, and verification of solver results.

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• Clarify vehicle routing requirements and constraints
• Plan how to use cuOpt through Python, REST, C, or CLI
• Review installation and server setup options

Look up RNA entries in RNAcentral by identifier or targeted search, retrieve cross-references to related database records, and receive concise summaries. Raw JSON output is also available when requested for further processing.

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• Look up an RNA entry by its identifier
• Search for RNA entries using a specific term
• Retrieve cross-references to related database records

Search Rhea, a biochemical reaction database, using reaction IDs, compound names, enzyme classification numbers, or reaction terms. Get concise summaries of focused search results, with raw JSON available when you need machine-readable output.

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• Looking up a reaction by its Rhea ID
• Finding reactions associated with a compound
• Searching reactions by enzyme classification number

Analyze Mixpanel data with Python to explore usage trends, conversion steps, returning users, and differences between user groups. Also manage business context documents that explain an organization's structure and goals to AI assistants.

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• Find where users drop out before purchasing
• Compare retention across user groups
• Explore feature usage and revenue trends

Prepare meeting agendas and reading materials using relevant Notion pages and supplemental research. Tailor the content to attendees and required decisions, with source links, discussion owners, time allocations, and follow-up actions.

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• Preparing an agenda for a project decision
• Gathering context for sprint planning
• Organizing discussion topics for a one-on-one

Retrieve focused target, disease, drug, variant, and study data from Open Targets Platform. Produce concise summaries or disease-by-source evidence matrices to compare available evidence while keeping queries and returned results compact.

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• Summarize information about a target or disease
• Look up drug, variant, or study data
• Compare disease evidence scores across data sources

Start shotgun metagenomics workflows for mixed-community DNA reads in FASTQ files. Check read quality, remove host sequences, and profile organisms and biological functions using supported tools and databases, producing tables and visual summaries when results are available.

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• Checking FASTQ quality and analysis readiness
• Removing host-derived sequences before profiling
• Summarizing microbial composition across samples