Image processing tools for the validation of CryoEM maps.

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.

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

PURPOSE: 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. METHODS: 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). RESULTS: We illustrate the use of this package with an integrative exam- ple that involves all these areas. CONCLUSIONS: We show that the package successfully addresses these kinds of analyses. Scipion PKPD is freely available at https://github. com/cossorzano/scipion-pkpd .