Cell Annotation MCP
by haoyunLi
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| CELL_ANNOTATION_TRANSPORT | No | Transport for the MCP server. Use 'stdio' (default) or 'streamable-http' for development over HTTP. | stdio |
| CELL_ANNOTATION_SCTYPE_PANELS | No | Path to a custom ScTypeDB panels TSV file. | |
| CELL_ANNOTATION_GARNETT_PANELS | No | Path to a custom Garnett classifier panels TSV file. | |
| CELL_ANNOTATION_RUNTIME_BACKEND | No | Runtime backend for evidence storage: 'sqlite' (default) or 'tsv' for the compatibility loader. | sqlite |
| CELL_ANNOTATION_RUNTIME_DATABASE | No | Path to the runtime evidence SQLite database. | |
| CELL_ANNOTATION_CELLMATCH_MARKERS | No | Path to a custom CellMatch marker rows TSV file. | |
| CELL_ANNOTATION_GENE_NOMENCLATURE | No | Path to a custom gene nomenclature TSV file (HGNC/MGI). | |
| CELL_ANNOTATION_HRA_ASCTB_MARKERS | No | Path to a custom HRA ASCT+B marker assertions TSV file. | |
| CELL_ANNOTATION_LITERATURE_CLAIMS | No | Path to a custom literature claims TSV file. | |
| CELL_ANNOTATION_MARKER_ASSERTIONS | No | Path to a custom marker assertions TSV file. | |
| CELL_ANNOTATION_LITERATURE_RECORDS | No | Path to a custom literature records TSV file. | |
| CELL_ANNOTATION_PAN_TISSUE_MARKERS | No | Path to a custom pan-tissue marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_PENIS_MARKERS | No | Path to a custom mouse corpus cavernosum marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_CAECUM_MARKERS | No | Path to a custom mouse caecum marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_RECTUM_MARKERS | No | Path to a custom mouse rectum marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_VAGINA_MARKERS | No | Path to a custom mouse vagina marker assertions TSV file. | |
| CELL_ANNOTATION_LITERATURE_CANDIDATES | No | Path to a custom literature candidates TSV file. | |
| CELL_ANNOTATION_MOUSE_ADRENAL_MARKERS | No | Path to a custom mouse adrenal gland marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_GINGIVA_MARKERS | No | Path to a custom mouse gingiva marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_OVIDUCT_MARKERS | No | Path to a custom mouse oviduct marker assertions TSV file. | |
| CELL_ANNOTATION_SOURCE_PANEL_POLICIES | No | Path to a custom source panel policies TSV file. | |
| CELL_ANNOTATION_HPA_SINGLE_CELL_MARKERS | No | Path to a custom HPA single-cell marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_ESOPHAGUS_MARKERS | No | Path to a custom mouse esophagus marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_EYE_VANZYL_MARKERS | No | Path to a custom human eye Van Zyl marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_CELL_ATLAS_MARKERS | No | Path to a custom Mouse Cell Atlas marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_EPIDIDYMIS_MARKERS | No | Path to a custom mouse epididymis marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_NASOPHARYNX_MARKERS | No | Path to a custom human nasopharynx marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_ORAL_MUCOSA_MARKERS | No | Path to a custom human oral mucosa marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_PARATHYROID_MARKERS | No | Path to a custom human parathyroid marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_ENDOMETRIUM_MARKERS | No | Path to a custom mouse endometrium marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_GALLBLADDER_MARKERS | No | Path to a custom mouse gallbladder marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_PARATHYROID_MARKERS | No | Path to a custom mouse parathyroid marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_NASAL_CAVITY_MARKERS | No | Path to a custom human nasal cavity marker assertions TSV file. | |
| CELL_ANNOTATION_TABULA_MURIS_SENIS_MARKERS | No | Path to a custom Tabula Muris Senis marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_BRAIN_SILETTI_MARKERS | No | Path to a custom human brain Siletti marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_THYMUS_HEIMLI_MARKERS | No | Path to a custom human thymus Heimli marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_CELL_LANDSCAPE_MARKERS | No | Path to a custom Human Cell Landscape marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_PROSTATE_HENRY_MARKERS | No | Path to a custom human prostate Henry marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_SALIVARY_GLAND_MARKERS | No | Path to a custom mouse salivary gland marker assertions TSV file. | |
| CELL_ANNOTATION_HUMAN_SEMINAL_VESICLE_MARKERS | No | Path to a custom human seminal vesicle marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_ENDOCRINE_ATLAS_MARKERS | No | Path to a custom mouse endocrine atlas marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_SEMINAL_VESICLE_MARKERS | No | Path to a custom mouse seminal vesicle marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_CELL_ATLAS_TESTIS_MARKERS | No | Path to a custom Mouse Cell Atlas testis marker assertions TSV file. | |
| CELL_ANNOTATION_MOUSE_BRONCHUS_CELLCARDS_MARKERS | No | Path to a custom mouse bronchus LungMAP CellCards marker assertions TSV file. |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
No tools | |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
This server cannot be deployed
Maintenance
ActivityMaintained
ResponsivenessNo issues