These resources have been contributed and “vetted” by the community of cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators) that are participating in programs such as this one, that are supported by the ConnectCI community management platform. Additional Knowledge Base Resources are always welcome!
Numpy is a python package that leverages types and compiled C code to make many math operations in Python efficient. It is especially useful for matrix manipulation and operations.
Gaussian 16 is a computational chemistry package that is used in predicting molecular properties and understanding molecular behavior at a quantum mechanical level.
MOPAC (Molecular Orbital PACkage) is a semi-empirical quantum chemistry package used to compute molecular properties and structures by using approximations of the Schrödinger equation. This tutorial explains the process of using MOPAC for different forms of calculations.
MDAnalysis is a python based library of tools for the analysis of molecular dynamics simulations. It is able to read and write many popular simulation formats including CHARMM, LAMMPS, GROMACS, and AMBER and more. This link contains the documentation pages of all MDAnalysis functions and has links to tutorials using Jupyter Notebooks.
Weka is a collection of machine learning algorithms for data mining tasks. It contains tools for data preparation, classification, regression, clustering, association rules mining, and visualization.