The Interactive Spectral Interpretation System (ISIS) is designed to facilitate the interpretation and analysis of high resolution X-ray spectra. It is being developed as a programmable, interactive tool for studying the physics of X-ray spectrum formation, supporting measurement and identification of spectral features and interaction with a database of atomic structure parameters and plasma emission models.

ESMF is software for building and coupling weather, climate, and related models. The premise is that complicated applications should be broken up into smaller pieces, or components. A component is a unit of software composition that has a coherent function, and a standard calling interface and behavior. Components can be assembled to create multiple applications, and different implementations of a component may be available.

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.

MBDyn features the integrated multidisciplinary analysis of multi-body, multi-physics systems, including nonlinear mechanics of rigid and flexible constrained bodies, smart materials, electric networks, active control, hydraulic networks, and essential fixed-wing and rotorcraft aerodynamics. It allows you to simulate the behavior of heterogeneous mechanical, aero-servo-elastic systems based on first principles equations. It is being actively developed and used in the aerospace and automotive fields for dynamics analysis and simulation of complex systems. The extension of available analysis domains to new models, and new analysis domains, is planned and problem-driven.

Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems. It supports distributed-memory parallel simulations, nonlinear, anisotropic, and dispersive media, PML absorbing boundaries, and 1D/2D/3D and cylindrical problems. It is completely scriptable from either C++ or a Scheme (GNU Guile) interface.

Animath is a 2D/3D Finite Element Method library entirely implemented in C++. It is suited for fluid-structure interaction simulation, and it is mathematically based on higher-order tetrahedral/triangular elements. It provides front-ends to matrix solvers and mesh generators.