Python库 | vivarium-chemotaxis-0.0.2.tar.gz

# Vivarium-chemotaxis [Vivarium-chemotaxis](https://github.com/vivarium-collective/vivarium-chemotaxis) is a library for the multi-scale model of chemotaxis described in: [Agmon, E.; Spangler, R.K. A Multi-Scale Approach to Modeling E. coli Chemotaxis. Entropy 2020, 22, 1101.](https://www.mdpi.com/1099-4300/22/10/1101) Supplementary materials can be found [here](doc/AgmonSpangler2020_supplementary.pdf). Visit [the Vivarium Core documentation](https://vivarium-core.readthedocs.io/) to learn how to use the core Vivarium engine to create multi-scale computational biology models.  The [**Chemotaxis Master Composite**](chemotaxis/composites/chemotaxis_master.py), with processes for metabolism (MTB), transport (TXP), transcription (TSC), translation (TRL), complexation (CXN), degradation (DEG), proton motive force (PMF), flagella activity (FLG), and chemoreceptor activity (CHE). This repository includes the processes for CHE, FLG, and PMF; the other processes are imported from [vivarium-cell](https://github.com/vivarium-collective/vivarium-cell). ## Setup Please refer to the Vivarium Core documentation for more complete instructions. Make a python environment with Python 3 (pyenv is recommended) and install dependencies. First install numpy: ``` $ pip install numpy ``` Then the remaining requirements: ``` $ pip install -r requirements.txt ``` ## Run individual processes and composites Each process file under `chemotaxis/processes` can run on its own. Some of these have their own command line options. For example, call the `chemoreptor_cluster` process with: ``` $ python chemotaxis/processes/chemoreptor_cluster.py ``` Composites with multiple integrated processes can also be executed on their own: ``` $ python chemotaxis/composites/chemotaxis_flagella.py ``` ## Experiments All experiments from the paper are available in the file `chemotaxis/experiments/paper_experiments.py`. Run them from the command line by specifying the corresponding figure number. ``` $ python chemotaxis/experiments/paper_experiments.py 7b ``` ## Tests Tests are performed with pytest. Simply call the following to ensure everything is working properly: ``` $ pytest ``` To run only the fast tests: ``` $ pytest -m 'not slow' ``` ## Logging To print out logging information, run a simulation with: ``` $ LOGLEVEL=INFO python chemotaxis/.. ```