Virtual Fly Brain
Virtual Fly Brain integrates knowledge and images from across Drosophila neurobiology: curated anatomy, registered 3D images, connectomics, single-cell transcriptomics and reagent expression, all classified with the Drosophila Anatomy Ontology and published under FAIR principles.
VirtualFlyBrain/VFB3-MCP is the canonical repository for the VFB Model Context Protocol server. The hosted service needs no installation, API key or account:
claude mcp add --transport http virtual-fly-brain https://vfb3-mcp.virtualflybrain.orgClaude Desktop, GitHub Copilot, VS Code and Gemini configurations are in the README; worked examples are in the VFB MCP tool guide.
| To do this | Go here |
|---|---|
| Browse and query the data | virtualflybrain.org |
| Use VFB from an LLM or agent | VFB3-MCP |
| Query VFB from Python | VFB_connect |
| Read the documentation | virtualflybrain.org/docs (source: VFB2) |
| Look at the web application | geppetto-vfb |
| Work with the anatomy ontology | Drosophila anatomy ontology |
| Use the standard templates and domains | DrosAdultBRAINdomains, DrosAdultVNSdomains |
Court, R., Costa, M., Pilgrim, C., et al. (2023) Virtual Fly Brain — an interactive atlas of the Drosophila nervous system. Frontiers in Physiology 14:1076533. https://doi.org/10.3389/fphys.2023.1076533
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Repositories
- vfb-pipeline-collectdata Public
- VFBquery Public
A high-performance Python library providing optimized programmatic access to the VirtualFlyBrain knowledge graph, with faster queries through intelligent caching.
- vfb-pipeline-dumps Public
Pipeline that creates dumps from the triplestore for consumption by the downstream services
- VFB_connectomics_import Public
A project to produce RDF/OWL representations of connectomics data for import to the VFB integration layer triple store.
- VFB_reporting_results Public
Repository containing the results of various data change and consistency checking.
- vfb-scRNAseq-ontology Public
An ontology of Drosophila melanogaster scRNAseq data pulled from FlyBase.
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