BioHarbor
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
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
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| seq_statsA | Validate sequences: type, length, GC%, molecular weight. Reports dna/rna/protein type, length, GC content (nucleotides) or molecular weight (proteins) and composition. A cheap first step before heavier tools. |
| translate_sequenceA | Translate DNA/RNA to protein, in one frame or all six. Uses the standard genetic code; stop codons appear as '*'. |
| find_orfsB | Find open reading frames (ATG to stop) on both strands. Returns the longest ORFs in DNA/RNA with coordinates (1-based, on the forward strand) and writes all ORFs to a FASTA file. |
| search_homologsA | Find homologous proteins with MMseqs2 (Swiss-Prot, PDB, ...). Searches a local database (default Swiss-Prot). Returns the best hits per query with identity, E-value, coverage, organism and description; the full hit table is written to a TSV file. Runs as a background job; may return a job_id to poll with get_job. |
| predict_structureA | Predict 3D protein structure with ESMFold on a GPU. Returns per-protein mean pLDDT, confidence bands, low-confidence regions and pTM; PDB files are written to disk (B-factor column = pLDDT). Runs as a background job; may return a job_id to poll with get_job. |
| get_jobB | Status and (when finished) result of a background job. |
| list_jobsA | Recent jobs, newest first (results omitted; use get_job for details). |
| cancel_jobB | Cancel a job that is still queued or waiting for a GPU. |
| describe_toolC | Full input schema, version and resource needs of a BioHarbor tool. |
| list_databasesB | Sequence databases installed for search_homologs, and ones that can be added. |
| gpu_statusA | Live GPU memory and utilisation (includes other users' processes). |
| read_fileB | Read (the start of) a text output file produced by a BioHarbor tool. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 12 tools
Each tool targets a distinct operation: sequence statistics, translation, ORF finding, homology search, structure prediction, and job management are clearly separated. No overlapping purposes; get_job, list_jobs, and cancel_job are distinct job operations.
Names uniformly use snake_case and mostly follow a verb_noun pattern (e.g., translate_sequence, find_orfs, get_job). Minor deviation: seq_stats and gpu_status are noun phrases, but overall consistent and readable.
12 tools is well within the ideal 3-15 range, each tool serves a clear purpose in the bioinformatics workflow without redundancy. The set is well-scoped for the domain.
Covers a sequence analysis pipeline from validation to structure prediction, with job management and resource introspection. Minor gap: no explicit tool for retrieving or loading input sequences (e.g., from files or databases), though read_file exists for outputs.