The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data. CGNS is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.
Electron Gamma Shower (EGS) is a general purpose package for the Monte Carlo simulation of the coupled transport of electrons and photons in an arbitrary geometry for particles with energies from a few keV up to several TeV. Simulations can be performed in arbitrarily complex physical geometries, and a wide range of physical processes are modeled.
MPI Parallel Environment (MPE) is a software package for MPI (Message Passing Interface) programmers. It provides users with a number of useful tools for their MPI programs such as a set of profiling libraries that collect information about the behavior of MPI programs, graphical trace file analyzers, serializers, type checkers, collective operations validators, etc.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
The National Space Science Data Center's (NSSDC) Common Data Format (CDF) is a self-describing data abstraction for the storage and manipulation of multidimensional data in a platform- and discipline-independent fashion. It consists of a scientific data management package (known as the "CDF Library") that allows programmers and application developers to manage and manipulate scalar, vector, and multi-dimensional data arrays.
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in the FITS (Flexible Image Transport System) data format. It simplifies the task of writing software that deals with FITS files by providing an easy to use set of high-level routines that insulate the programmer from the internal complexities of the FITS file format.