Alambiq

Alambiq is software that runs computational methods for biotechnology as capabilities. A campaign lists steps, and each step runs one capability. The terms are defined in Concepts.

Version 0.1.2. Alambiq is Apache-2.0. Optional software, models and datasets keep their own licenses (LICENSING.md).

Capabilities

Capabilities belong to five families:

• Characterize: protein search and alignment, embeddings, stability change, structure prediction, genomic context and other descriptions of proteins and enzymes.
• Investigate: reactions and thermodynamics, structure preparation, binding pockets, molecular dynamics, free energies and QM/MM.
• Engineer: candidate selection, variant proposal, construct design and assembly, coding-sequence recoding.
• Measure: measurement intake and fits.
• Operate: reaction simulation from measured kinetics, uncertainty, comparison with measurements, output accounting and input costs.

alambiq capability list
alambiq capability show assay.fit

The first command prints every capability with its family. The second prints the request fields, the result, the method and the limits of assay.fit.

Reports

alambiq run --report PATH writes a report: one HTML file with the result of each step. The images show the reports of kinetics-from-measurements and lanmodulin-comparison.

Installation

Install the package from PyPI (Python 3.11 or newer). The quantitative extra adds NumPy, SciPy and scikit-learn:

pipx install "alambiq[quantitative]"

The examples are in the repository. To run one, install the core from a clone in a virtual environment:

python -m venv .venv
.venv/bin/pip install -e ".[quantitative]"
.venv/bin/alambiq run examples/kinetics-from-measurements/campaign.yaml --report report.html

The example fits a Michaelis-Menten curve to 10 initial rates and writes a report.

Capabilities that run scientific software (MMseqs2, P2Rank, ThermoMPNN, ESM, OpenMM, Boltz-2, OpenFF, OpenFE, pymbar, PySCF) use engine environments. Each is built natively from a recipe, and each except the Apple GPU environment of Boltz-2 is also a Docker image. alambiq env check shows which engine environments are ready, and alambiq resource list shows which resources are installed. The installation guide describes both routes.

Documentation

• Index: the pages by subject.
• Getting started: the core and the first run.
• Installation: extras, engine environments, resources and platforms.
• Concepts: the terms.
• Python interface: campaigns and capabilities from Python.
• Examples: worked examples.
• Methods: the capabilities of each method area.
• Reports: the contents of a report.
• Licensing: the licenses of Alambiq and of optional software.

Repository layout

• src/alambiq/core: the campaign runner.
• src/alambiq/capabilities: the capabilities by family.
• src/alambiq/engines: the code that runs inside engine environments.
• src/alambiq/report: the report writer.
• environments/: the recipes and verification files of the engine environments, and the Dockerfiles in environments/docker.
• examples/: the runnable examples.
• tests/core: the test suite (python -m pytest tests/core).