BioHarbor
PYPI · BIOHARBOR
Run real bioinformatics from your AI agent. Reliable, reproducible, on your own GPUs.
Available components
Last scanned (3 hours ago)
Scores higher than 94% of PyPI servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security99
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised build step with no custom scripting around it. View diagnostics → Pass
- 4 of 36 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to danielLuo2/bioharbor). View diagnostics → Pass
- Clear OSI-approved license (Apache-2.0).Pass
- Actively maintained (last published 25 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability73
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 1623 tokens (~135/item across 12 items; 12 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management77
- Stability observed for 23 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 12 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 13 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 5 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 73 to 77. That category is still filling its 30-day observation window: 22 days of observed history at the previous scan, 23 at this one. The score rises as the window fills, whether or not the server changes.
- 2 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 63 to 67. That category is still filling its 30-day observation window: 19 days of observed history at the previous scan, 20 at this one. The score rises as the window fills, whether or not the server changes.
- 31 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 57 to 60. That category is still filling its 30-day observation window: 17 days of observed history at the previous scan, 18 at this one. The score rises as the window fills, whether or not the server changes.
- 29 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 50 to 53. That category is still filling its 30-day observation window: 15 days of observed history at the previous scan, 16 at this one. The score rises as the window fills, whether or not the server changes.
- 27 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 43 to 47. That category is still filling its 30-day observation window: 13 days of observed history at the previous scan, 14 at this one. The score rises as the window fills, whether or not the server changes.
- 25 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 37 to 40. That category is still filling its 30-day observation window: 11 days of observed history at the previous scan, 12 at this one. The score rises as the window fills, whether or not the server changes.
- 23 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 30 to 33. That category is still filling its 30-day observation window: 9 days of observed history at the previous scan, 10 at this one. The score rises as the window fills, whether or not the server changes.
- 22 Oct 26 +4
- Stability: unverified → 0.30 ▲ functional
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed pypi/bioharbor@0.1.6
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | pypi |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | danielLuo2/bioharbor |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/danielLuo2/bioharbor/.github/workflows/release.yml@refs/tags/v0.1.6 |
| Rekor log index | 3184926072 |
| Predicate type | PyPI publish attestation https://docs.pypi.org/attestations/publish/v1 |
| Subject digest | sha256:b8a86201afefe58ddf81852bd64ab5052170b329a063ace6df4364406392cc1b |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 36 packages
| Packages resolved | 36 |
|---|---|
| Stale | 3 |
| No linked repository | 1 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
cancel_job ~118
Cancel a background job that has not started running yet. Only jobs whose status is queued or waiting_gpu can be cancelled; a job that is already running is not interrupted and will still finish. Returns `cancelled: true` on success, or `cancelled: false` with a `message` if the job does not exist or has already started or finished. Use list_jobs to see job states first.
| Name | Type | Req | Description |
|---|---|---|---|
| job_id | string | yes | The `job_id` of the job to cancel (from a slow tool or list_jobs). |
Structured output declared, but exposes no named fields.
No examples provided.
describe_tool ~115
Explain how an analysis tool runs before calling it. Returns the tool's description, version, full JSON input schema (parameter types, defaults and limits), whether it needs a GPU, and whether it runs inline or as a background job. Use it when unsure about a parameter or after an invalid-parameters error. Read-only; returns a NotFound error for unknown names.
| Name | Type | Req | Description |
|---|---|---|---|
| name | string | yes | Name of an analysis tool: seq_stats, translate_sequence, find_orfs, search_homologs or predict_structure. |
Structured output declared, but exposes no named fields.
No examples provided.
find_orfs ~207
Find open reading frames (ATG to stop codon) in DNA or RNA sequences. Scans all three frames, on both strands unless both_strands is false, with the standard genetic code. Returns the top_n longest ORFs (strand, 1-based start/end on the forward strand, length_nt, length_aa, protein) and the exact input lengths; all ORFs are written to orfs.faa. If no ORF reaches min_aa, the longest shorter one is reported as longest_below_min. Protein input is rejected; use translate_sequence for a fixed frame.
| Name | Type | Req | Description |
|---|---|---|---|
| both_strands | boolean | – | Also search the reverse complement. |
| min_aa | integer | – | Minimum ORF length in amino acids (1 = any ORF). |
| sequence | string | yes | A raw sequence or FASTA text (one or more records). |
| top_n | integer | – | How many of the longest ORFs to return. |
Structured output declared, but exposes no named fields.
No examples provided.
get_job ~162
Check a background job and get its result once it has finished. Use this after a slow tool (e.g. predict_structure, search_homologs) returned a `job_id` instead of a result. Returns `status` (queued, waiting_gpu, running, succeeded, failed, cancelled), plus `result` when succeeded or `error` when failed. If it is still running, call again later, or pass wait_seconds to block briefly. Read-only: checking a job does not change it.
| Name | Type | Req | Description |
|---|---|---|---|
| job_id | string | yes | The `job_id` returned by a slow tool or listed by list_jobs. |
| wait_seconds | number | – | Seconds to wait for the job to finish before returning (0 = return the current status immediately). |
Structured output declared, but exposes no named fields.
No examples provided.
gpu_status ~94
Show live GPU memory and utilisation on this machine. Returns, per NVIDIA GPU, its index, name, total and free memory (GB) and utilisation (%), counting other users' processes too. Use it to explain why a GPU job is in waiting_gpu, or to check capacity before a large predict_structure run. You do not need it to schedule jobs: BioHarbor picks a GPU itself. Read-only.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
list_databases ~102
List the sequence databases that search_homologs can search. Call this before search_homologs to pick a `database` value. Returns `installed` (name, source and sequence count of each ready database) and `available_to_install` (known databases such as swissprot, pdb and uniref50 that are not installed yet). Agents cannot install databases; ask the user to run `bioharbor setup-db <name>`. Read-only.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
list_jobs ~115
List recent background jobs, newest first. Use this to find a `job_id` you no longer have, or to see what is queued or running. Each entry has job_id, tool, status, gpu and duration_s; results are omitted, so call get_job for a job's result. Read-only.
| Name | Type | Req | Description |
|---|---|---|---|
| limit | integer | – | Maximum number of jobs to return. |
| status | – | – | Only return jobs in this state: queued, waiting_gpu, running, succeeded, failed or cancelled. Omit for all states. |
Structured output declared, but exposes no named fields.
No examples provided.
predict_structure ~113
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.
| Name | Type | Req | Description |
|---|---|---|---|
| num_recycles | integer | – | Recycling iterations; more can help hard targets. |
| sequence | string | yes | Protein sequence(s), raw or FASTA (≤20 records). |
Structured output declared, but exposes no named fields.
No examples provided.
read_file ~141
Read a text output file written by a BioHarbor tool. Tool results are compact summaries; use this only when you need the full output, e.g. all ORFs in orfs.faa or all hits of a homology search. Returns `content`, the file's `size_bytes`, and `truncated: true` if the file is longer than max_bytes. Only files inside the BioHarbor workspace can be read. Read-only.
| Name | Type | Req | Description |
|---|---|---|---|
| max_bytes | integer | – | Return at most this many bytes from the start of the file. |
| path | string | yes | A path exactly as listed in a tool result's `files` list. |
Structured output declared, but exposes no named fields.
No examples provided.
search_homologs ~207
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.
| Name | Type | Req | Description |
|---|---|---|---|
| database | string | – | Installed database name (see list_databases). |
| evalue | number | – | E-value cutoff. |
| max_hits | integer | – | Max hits per query kept in the output file. |
| min_coverage | number | – | Minimum alignment coverage of query and target. |
| sensitivity | number | – | MMseqs2 -s: 1 fast … 7.5 most sensitive. |
| sequence | string | yes | Protein (or DNA, searched translated) sequence(s), raw or FASTA. |
| top_n | integer | – | Hits per query shown inline. |
Structured output declared, but exposes no named fields.
No examples provided.
seq_stats ~76
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.
| Name | Type | Req | Description |
|---|---|---|---|
| sequence | string | yes | A raw sequence or FASTA text (one or more records). |
Structured output declared, but exposes no named fields.
No examples provided.
translate_sequence ~88
Translate DNA/RNA to protein, in one frame or all six. Uses the standard genetic code; stop codons appear as '*'.
| Name | Type | Req | Description |
|---|---|---|---|
| frame | – | – | Reading frame; negative = reverse complement; 'all' = six frames. |
| sequence | string | yes | A raw sequence or FASTA text (one or more records). |
| to_stop | boolean | – | Stop at the first stop codon. |
Structured output declared, but exposes no named fields.
No examples provided.
How do I install the BioHarbor MCP server?
BioHarbor runs locally as a PyPI package, launched with uvx bioharbor. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · bioharbor
claude mcp add danielluo2-bioharbor -- uvx bioharbor
What is the BioHarbor MCP server?
BioHarbor is an MCP server listed in the public MCP registry as io.github.danielLuo2/bioharbor. Run real bioinformatics from your AI agent. Reliable, reproducible, on your own GPUs. This page covers its PyPI package (bioharbor).
Is the BioHarbor MCP server safe to use?
BioHarbor scores 91 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the BioHarbor MCP server expose?
BioHarbor exposes 12 tools: seq_stats, translate_sequence, find_orfs, search_homologs, predict_structure, and 7 more. Their descriptions and schemas cost roughly 1,538 tokens of context every time the server is loaded.
Is the BioHarbor MCP server still maintained?
BioHarbor is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.
What licence is the BioHarbor MCP server under?
BioHarbor declares the Apache-2.0 licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.