Biological and Environmental Research Variable Ontology

The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.

Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.

A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.

End-to-end molecular dynamics engine built on PyTorch, enabling differentiable simulations with neural network potentials and GPU acceleration for machine learning-accelerated molecular dynamics (MIT License, 707+ stars)

A library for estimating thermochemical properties of molecules and adsorbates using group additivity.

A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.