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Inflam

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Inflam is a data management system written in Python that manages trial data used in clinical inflammation studies.

Main features

Here are some key features of Inflam:

  • Provide basic statistical analyses over clinical trial data
  • Ability to work on trial data in Comma-Separated Value (CSV) format
  • Generate plots of trial data
  • Analytical functions and views can be easily extended based on its Model-View-Controller architecture

Prerequisites

Inflam requires the following Python packages:

  • NumPy - makes use of NumPy's statistical functions
  • Matplotlib - uses Matplotlib to generate statistical plots

The following optional packages are required to run Inflam's unit tests:

  • pytest - Inflam's unit tests are written using pytest
  • pytest-cov - Adds test coverage stats to unit testing

Installation/deployment

After cloning the repository (download) the attached requirements file can be used to install dependencies with:

$ pip3 install -r requirements.txt

Basic usage

To view data in a csv file, call the inflamation-analysis python file with --view record option, for the patient you would like view, and with a pointer to the csv file containing the data.

python3 inflammation-analysis.py --view record --patient 1 --infile data/inflammation-01.csv --file_type csv

You can also view a json file by changing the --file_type to json.

python3 inflammation-analysis.py --view record --patient 1 --infile tests/patients.json --file_type json

Credits/Acknowledgements

This software was created via the Carpentries Incubator project: Intermediate Research Software Development in Python.

Licence

The software is available under a MIT licence.

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