Lib.rs

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#bioinformatics-sequence #bioinformatics #mcp

bin+lib biors-mcp-server

Model Context Protocol server for bio-rs biological sequence processing tools

by chanmin713

30 releases (1 stable)

1.0.0 Jul 11, 2026
0.58.1 Jun 30, 2026
0.57.4 Jun 20, 2026

#368 in Biology

MIT/Apache

620KB
16K SLoC

biors-mcp-server

Model Context Protocol (MCP) server for bio-rs validation, tokenization, workflow, and package-check tools.

This crate makes bio-rs agent-callable over local stdio through deterministic JSON contracts. It is for research agents that need validation, model-ready preparation, package checks, and reproducible JSON without uploading biological data.

Usage

Run the server over stdio for local agent integration:

cargo run -p biors-mcp-server

Configure your MCP client (Claude Desktop, Cursor, etc.) to launch:

{
  "mcpServers": {
    "bio-rs": {
      "command": "cargo",
      "args": ["run", "-p", "biors-mcp-server"]
    }
  }
}

Output Policy

MCP tools return machine-readable JSON text. For long biological FASTA inputs, sequence tools protect agent context by returning summary/counts/issues by default using schema_version: "biors.mcp.compact.v0". Request full per-record payloads only when the caller actually needs them:

  • include_records: true for tokenize and validate.
  • include_payload: true for workflow.

Package tools already return validation summaries and structured issues rather than biological payloads. All tools run locally and do not upload data, telemetry, or model inputs.

The compact-output contract is summary/counts/issues by default.

Tool Catalog

Tool Purpose Default payload behavior
tokenize Tokenize FASTA text with a protein, DNA, or RNA tokenizer profile. Compact for long FASTA unless include_records=true.
validate Validate FASTA text as auto, protein, dna, or rna. Compact for long FASTA unless include_records=true.
workflow Run validation -> tokenization -> model-input preparation. Compact for long FASTA unless include_payload=true.
package_validate_fields Validate package manifest JSON fields without filesystem artifact checks. Field-only report with structured issues.
package_validate Validate a package manifest and local artifacts. Validation report with structured issues; no biological payload expansion.
package_bridge Plan package runtime bridge contract readiness from a local manifest path or manifest JSON plus base directory. Bridge report with contract_ready, artifact_checked, and execution_ready; does not execute models.
doctor Report MCP server readiness metadata. Small diagnostic payload.

Agent Sequence

  1. Validate sequence input with validate.
  2. If counts are acceptable, call workflow with a matching kind, profile, and bounded max_length.
  3. Use package_validate_fields for manifest-only checks.
  4. Use package_validate only when the local package directory is available.
  5. Use package_bridge when an agent needs package runtime compatibility planning fields without model execution.
  6. Request include_records or include_payload only when downstream work genuinely needs full per-record payloads.

Non-Goals

This server is not an autonomous research agent. It is not hosted execution and does not provide cloud model calls, telemetry, literature review, long-term memory, or remote lab automation.

License

MIT OR Apache-2.0

Dependencies

~11–16MB
~219K SLoC