Gwyddion is a modular SPM (Scanning Probe Microsope) data visualization and analysis tool. It can be used for all most frequently used data processing operations including: leveling, false color plotting, shading, filtering, denoising, data editing, integral transforms, grain analysis, profile extraction, fractal analysis, and many more. The program is primarily focused on SPM data analysis (e.g. data obtained from AFM, STM, NSOM, and similar microscopes). However, it can also be used for analyzing SEM (scaning electron microscopy) data or any other 2D data.
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.
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.
Madagascar is a software package for multidimensional data analysis and reproducible computational experiments. Its mission is to provide a convenient and powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.
Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results (populations and reaction counts) in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. Solvers are implemented as command line executables, which makes it easy to launch batch jobs and simplifies the process of adding new solvers. Solvers include Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, and Hybrid direct/tau-leaping.
Yet Another Dynamic Engine (YADE) is an extensible framework that is designed with dynamic libraries in a way that it is easy to add new numerical models and objects. There are four different models: Discrete Element Method based on spheres, a second method based on tetrahedra, modelling with lattice elements, and Finite Element Method.