# METABOLATOR: Analysis of Microcalorimetric Metabolic Data Using Monod's Equation Curve fitting automation for metabolic load of bacteria in solutions. The service is deployed at HZDR and available at . See also our software presentation [in the Helmholtz Research Software Directory](https://helmholtz.software/software/metabolator).  ## Installation To install METABOLATOR with pipx, run: ```bash pipx install git+https://codebase.helmholtz.cloud/metabolator/metabolator.git ``` ## Usage Start the METABOLATOR web app by running the following command: ```bash metabolator-web ``` This is roughly equivalent to `voila metabolator/METABOLATOR.ipynb`. However, `metabolator-web` loads the notebook file from the package resources. Thus, it can be run without checking out the git repository. Voilà's command line options may be passed to `metabolator-web` as well. ## CLI Tool A first iteration of a basic command line tool is provided with METABOLATOR. You can run it as `metabolator` which is equivalent to `python -m metabolator.cli`. To perform analysis on an example dataset, run: ```bash metabolator 10.14278/rodare.3175 Schizophyllum_example.xls 0 ``` ## Development For development, check out the repository, then install METABOLATOR including its dev dependencies in editiable mode: ```bash python -m venv venv source venv/bin/activate python -m pip install -e .[dev] ``` Use Ruff to format your code contributions: ```bash ruff format . ``` Run the linter and apply potential fixes: ```bash ruff check --fix . ``` If the environment variable `METABOLATOR_DEVELOPMENT` is set, the app presents itself as a development instance (e.g. via the header text). ## Deployment The `conf` directory contains an [example service file for systemd](conf/metabolator.service.example) as well as an [example nginx configuration](conf/metabolator.example.com). We suggest running the application service as a dedicated user (not root). This can be achieved by enabling lingering for the user with `loginctl`. For more information see the [Voilà documentation](https://voila.readthedocs.io/en/stable/deploy.html#running-voila-on-a-private-server). ## Providing (Example) Datasets Example dataset files (common spreadsheet formats) can be placed inside the `metabolator/static/datasets` directory. Please make sure to place a license file next to the dataset. This can be done with `reuse annotate` The app also shows search links for Rodare and Zenodo. These searches will find publications of type dataset on the respective platform that have been tagged with the keyword `metabolator`.