Proof-of-concept Implementation of Cytotoxic Power Calculation in Python
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cytpower
docs
example-workflow
.travis.yml
DESCRIPTION.rst
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README.rst
requirements.txt
setup.cfg
setup.py

README.rst

cytpower

https://travis-ci.org/maximtrp/cytpower.svg?branch=master

Cytotoxicity is an ability of chemical compounds to destroy cells either directly or indirectly. Cytotoxicity assays are used in drug discovery to screen potentially toxic compounds. The results are routinely presented as percentages of affected cells vs concentrations used. These data are usually discrete or even disjoint, and do not even rely on the concept of drug dose (concentration per number of cells). Unfortunately, there are no suitable measure indices to estimate cytotoxic potential of a compound within a dose range.

example-workflow/A1_plot.png example-workflow/A2_plot.png

We have recently introduced a concept of cytotoxic power, a parameter that is based on numerical integration and drug doses instead of concentrations (Goncharov et al., 2018). Previously, we endorsed two other indices that may be used to highlight drug specifics (e.g. apoptosis prevalence over necrosis): apoptotic and necrotic difference (AND) and apoptotic and necrotic areas under curves (ANAUCs) (Smetanin et al., 2016, Galenko et al., 2017).

https://latex.codecogs.com/png.latex?CP=\frac{\int_{a}^{b}&space;f(x)&space;dx}{\Delta&space;t}

where x is a compound dose, f(x) is a dose-response function, Δt is incubation duration, a is minimal dose, and b is maximum dose.

This Python package is a proof-of-concept implementation of cytotoxic power calculation algorithm to assist researchers in processing cell assay results and presenting data.

Features

  • Integration with NumPy, Scipy, and Pandas: import, computations, etc.
  • Estimation of complex indices related to cytotoxic power of compounds.
  • Manual curve fitting based on SciPy and lmfit.
  • Bootstrap statistics routines.
  • Plotting functionality (matplotlib and seaborn).

Dependencies

Compatibility

Package is compatible with both Python 2 and 3 versions.

Install

You can install the package with:

$ pip install cytpower

Usage

Extended example is provided in example-workflow folder in this repository as a Jupyter Notebook.