Scipion PKPD: an Open-Source Platform for Biopharmaceutics, Pharmacokinetics and Pharmacodynamics Data Analysis

Biopharmaceutics examines the interrelationship of the drug’s physical/chemical properties, the dosage form (drug product) in which the drug is given, and the administration route on the rate and extent of sys- temic drug absorption. Pharmacokinetics is the study of the movement of drugs in the body. It uses mathematical models to evaluate the movement of absorption, distribution, metabolism, and excretion (ADME) within an organism. Finally, Pharmacodynamics is the analysis of how these drugs af- fect that organism. Pharmacokinetics data normally comes in samples over time of the drug concentration either in plasma or in some specific tissue. Similarly, pharmacodynamics data comes normally in samples over time of some quantity of interest (biophysical quantity like temperature, blood pres- sure, etc.). The data is submitted to a non-parametric analysis, in which a description of the observed data is reported (e.g., the Area Under the Curve), or to a parametric analysis by fitting a model (normally based on differential equations) so that prediction about future events can be made. This paper aims to introduce Scipion PKPD, an open-source platform for data analysis of this kind in the three domains (Biopharmaceutics, Pharmacokinetics, and Pharmacodynamics). The platform implements the most popular models and is open to new ones. The platform provides almost 100 different high-level operations that we call protocols. We have developed a Python module integrated into the work- flow engine Scipion. The plugin implements the numerical analysis and meta- data handling tools to address multiple problems (see Suppl. Material for a detailed list of the tasks solved). We illustrate the use of this package with an integrative exam- ple that involves all these areas. We show that the package successfully addresses these kinds of analyses. Scipion PKPD is freely available at https://github. com/cossorzano/scipion-pkpd .