Contributed by cyberinfrastructure professionals (researchers, research computing facilitators, research software engineers and HPC system administrators), these resources are shared through the ConnectCI community platform. Add resources you find helpful!
Gaussian 16 is a computational chemistry package that is used in predicting molecular properties and understanding molecular behavior at a quantum mechanical level.
Bioinformatics Toolbox provides algorithms and apps for Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. Using toolbox functions, you can read genomic and proteomic data from standard file formats such as SAM, FASTA, CEL, and CDF, as well as from online databases such as the NCBI Gene Expression Omnibus and GenBank.
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.
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.
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.
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.