biors-0.6.0 is not a library.

bio-rs

Open source Rust/WASM tools for biological AI models.

Python is where many bio-AI models are born. bio-rs is where the tooling around them becomes portable, inspectable, and easier to use from CLIs, browsers, servers, and agents.

bio-rs is starting with small, production-quality building blocks for biological AI model migration. The current release provides a protein FASTA seed module and a portable package manifest that can describe model artifacts, preprocessing, postprocessing, runtime targets, fixtures, and expected outputs.

1.0.0 Goal

bio-rs reaches 1.0.0 when a Python-born biological AI model can be packaged, inspected, verified against its Python baseline, and executed through portable runtime surfaces:

CLI tools
browser-ready WASM/WebGPU
server-side Rust usage
agent-friendly machine-readable interfaces

The long-term goal is not only model format conversion. bio-rs should also make the surrounding bio/chem tooling portable: the practical pieces currently often handled by Python libraries such as BioPython and RDKit.

Performance and cost improvements are benchmark targets, not current claims.

Current Modules

Protein FASTA

The protein FASTA seed module validates protein FASTA input and tokenizes FASTA records into stable protein-20 token ids.

Package Manifest

The package manifest module describes a portable biological AI model package:

model artifact format and path
preprocessing and postprocessing steps
runtime backend and target
parity fixtures and expected outputs

biors package inspect emits a compact manifest summary. biors package validate emits a machine-readable validation report and exits non-zero when the manifest is incomplete.

Current Features

FASTA parsing for one or more protein sequences
protein-20 residue validation
lowercase sequence normalization
ambiguous residue reporting for X, B, Z, J, U, and O
invalid residue reporting
JSON array output from the CLI
portable model package manifest structs in biors-core
package manifest inspection and validation from the CLI

Release Path

0.6.0: Portable package manifest inspect/validate.
0.7.0: Runtime bridge planning for ONNX/WebGPU package targets.
0.8.0: Verification harness for Python-baseline parity fixtures.

Not Yet

bio-rs does not yet provide a full model migration engine, a browser AlphaFold runtime, or a Rust replacement for all BioPython/RDKit functionality. Those are the milestones this repository is moving toward.

Quickstart

Inspect FASTA records:

cargo run -p biors -- inspect examples/protein.fasta

Tokenize FASTA records:

cargo run -p biors -- tokenize examples/protein.fasta

Tokenize FASTA records from stdin:

cat examples/protein.fasta | cargo run -p biors -- tokenize -

Tokenize a multi-record FASTA file:

cargo run -p biors -- tokenize examples/multi.fasta

Inspect a portable model package manifest:

cargo run -p biors -- package inspect examples/protein-package/manifest.json

Validate a portable model package manifest:

cargo run -p biors -- package validate examples/protein-package/manifest.json

Use the Rust library:

cargo add biors-core

use biors_core::{summarize_tokenized_proteins, tokenize_fasta_records};

let tokenized = tokenize_fasta_records(">seq1\nACDE\n")?;
let summary = summarize_tokenized_proteins(&tokenized);

assert_eq!(summary.records, 1);
assert_eq!(tokenized[0].tokens, vec![0, 1, 2, 3]);
# Ok::<(), Box<dyn std::error::Error>>(())

JSON Contracts

tokenize always emits an array of records:

[
  {
    "id": "seq1",
    "length": 4,
    "alphabet": "protein-20",
    "valid": true,
    "tokens": [0, 1, 2, 3],
    "warnings": [],
    "errors": []
  }
]

inspect always emits a summary object:

{
  "records": 1,
  "total_length": 4,
  "valid_records": 1,
  "warning_count": 0,
  "error_count": 0
}

package inspect always emits a manifest summary object:

{
  "schema_version": "biors.package.v0",
  "name": "protein-seed",
  "model_format": "onnx",
  "runtime_backend": "onnx-webgpu",
  "runtime_target": "browser-wasm-webgpu",
  "preprocessing_steps": 1,
  "postprocessing_steps": 1,
  "fixtures": 1
}

package validate always emits a validation report:

{
  "valid": true,
  "issues": []
}

Checks

scripts/check.sh

The check suite runs cargo fmt, native Rust checks, a biors-core wasm32-unknown-unknown build check, tests, and cargo clippy with warnings denied.

Run the Rust library example:

cargo run -p biors-core --example tokenize

Workspace

packages/
  rust/
    biors/       CLI
    biors-core/  FASTA parsing, tokenization, and package contracts
examples/
  multi.fasta
  protein-package/
  protein.fasta

Protein-20

A C D E F G H I K L M N P Q R S T V W Y

Token ids follow that order, starting at 0.

License

Dual licensed under MIT OR Apache-2.0.

biors 0.6.0