Strain Authentication and Identification Methods - saim

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saim (Strain Authentication and Identification Methods) is a Python toolkit for reproducible identification, authentication, and metadata handling of microbial strains. It provides utilities for validating strain metadata, harmonizing identifiers, running identification workflows, and exporting results for downstream analysis.

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Installation - Development

Prerequisites

• GNU/Linux
• Docker (optional)
• Docker Compose (optional)
• Dev Container CLI (optional)

Steps

1. Clone the repository:

   git clone https://github.com/LeibnizDSMZ/saim.git
   cd saim

Docker

2. If using Docker, start the development container manually or use VSCode:

   devcontainer up --workspace-folder .
   devcontainer exec --workspace-folder . bash

3. Create and activate a virtual environment (inside docker the container):

   make dev
   make runAct

Local

2. Create and activate a virtual environment:

   python -m venv .venv
   source .venv/bin/activate

3. Install the dependencies:

   pip install .
   pip install -r configs/dev/requirements.dev.txt
   pip install -r configs/dev/requirements.test.txt
   pip install -r configs/dev/requirements.docs.txt

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Contributors

• Artur Lissin
• Julius Witte