SHTns is a high-performance Spherical Harmonic Transform library. It was designed for numerical simulation (fluid flows, mhd, etc.) in spherical geometries, but can be used for any kind of problem involving scalar or vector spherical harmonics. It is very fast, thanks to careful vectorization and runtime tuning. It supports multi-threaded transforms via OpenMP. It features scalar and vector transforms, synthesis and analysis, and flexible truncation and normalization. A Python interface is included.
MathGL is a library for making high-quality scientific graphics under Linux and Windows, fast data plotting and handling of large data arrays, working in window and console modes, and easily embedding into other programs. It has more than 40 general types of graphics for 1d, 2d, and 3d data arrays. It can export graphics to raster and vector (EPS or SVG) formats. It has an OpenGL interface and can be used from console programs. It has functions for data handling and MGL language scripting for simplification of data plotting. It has several types of transparency and smoothed lightning, vector fonts and TeX-like formula drawing, an arbitrary curvilinear coordinate system, and many other useful things.
DOLFIN is the C++ interface of the FEniCS project for the Automation of Computational Mathematical Modeling (ACMM), providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms through FFC; automatic and efficient assembly of linear systems; and support for general families of finite elements.
Gmsh is an automatic 3D finite element grid generator with built-in CAD and post-processing facilities. Its design goal is to provide a simple meshing tool with parametric input and advanced visualization capabilities. It is built around four modules: geometry, mesh, solver, and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface (based on FLTK and OpenGL) or in ASCII text files using Gmsh's own scripting language.
The Maximum Entropy Toolkit provides a set of tools and library for constructing maximum entropy (maxent) models in either Python or C++. It features conditional maximum entropy models, L-BFGS and GIS parameter estimation, Gaussian Prior smoothing, a C++ API, a Python extension module, a command line utility, and good documentation.
SHOGUN is a machine learning toolbox whose focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It provides a generic SVM object interfacing to several different SVM implementations, all making use of the same underlying, efficient kernel implementations. Apart from SVMs and regression, SHOGUN also features a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons, and algorithms to train hidden Markov models. SHOGUN can be used from within C++, Matlab, R, Octave, and Python.
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.