ASCEND is a mathematical modelling program that lets you write object-oriented models and solve them with a number of different solvers, including NLA, NLP, DAE and ODE solvers. It is research code from Art Westerberg's group at Carnegie Mellon University. We have recently been adding support for IDA; this work is ongoing but currently IDADense is working well. We want to build in a sparse direct solver too.
CANTERA is an open-source, object-oriented software package for problems involving chemically-reacting flows.
Delphin 5 is a simulation program for the calculation of the coupled heat, moisture, air, pollutant and salt transport in porous building materials, assemblies of such materials and building envelopes in general.
EMSO stands for Environment for Modeling, Simulation, and Optimization. It is a graphical environment where the user can model complex dynamic or steady-state processes by simply selecting and connecting model blocks. In addition, the user can develop new models using the EMSO modeling language or use those already made from the EMSO Modeling Library - EML.
magpar is a finite element micromagnetics package which combines several unique features:
- Applicability to a variety of static and dynamic micromagnetic problems including uniaxial anisotropy, exchange, magnetostatic interactions and external fields
- Flexibility of the finite element method concerning the geometry and accuracy by using unstructured graded meshes
- Availability due to its design based on free, open source software packages
- Portability to different hardware platforms, which range from simple PCs to massively parallel supercomputers
- Scalability due to its highly optimized design and efficient libraries
- Versatility by including static energy minimization and dynamic time integration methods
From simple calculator operations to large-scale programming and interactive-document preparation, Mathematica is the tool of choice at the frontiers of scientific research, in engineering analysis and modeling, in technical education from high school to graduate school, and wherever quantitative methods are used.
The NDSolve function uses IDA for the solution of differential-algebraic equations.
MOSILAB from the Fraunhofer-Gesellschaft is a newly developed Modelica simulator for complex technical systems. One innovative feature of MOSILAB is the mapping of state-dependent changes of the model structure during the simulation experiment. This enables, for example, simulation experiments with models of variable modeling depth or varying model physics.
NablaX is a software package for solving strongly nonlinear Maxwell’s equations in the 3D-space. It is primarily intended for applications involving high-temperature superconductors (HTS). NablaX was developed by R. Pecher at the Department of Engineering Science, University of Oxford.
NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient.
NEWCON is an advanced control framework. It features a Newton-type nonlinear constrained model predictive controller that runs under the GNU/Linux operating system. It is being developed as an open-source package that will be released soon.
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.
The Systems Biology Toolbox 2 for MATLAB offers systems biologists a powerful, open, and user extensible environment, in which to build models of biological systems. Experiments can be performed on models, just like in real lab life but in silico. The representation of models, experiments, and measurement data is intuitive and easy to use. The toolbox features a wide variety of specialized analysis tools and MATLAB adds to that by a large number of inbuilt functions and a high level scripting language, allowing the user to quickly and efficiently add new functionality.
The SBPD extension package for the Systems Biology Toolbox 2 adds high-speed simulations (through SUNDIALS CVODES), combination of models, experiments, and measurement data in so called projects. Functions are available that support the complete model building process. The projects are a powerful construct that allows to keep a perfect overview over your modeling task at any time. Graphical user interfaces support the workflow.
The SBML ODE Solver Library (SOSlib) is both a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI/ISO C and distributed under the terms of the GNU Lesser General Public License (LGPL). The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. SUNDIALS' version of CVODE is incorporated for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems.
Simtk.org is the home of the software framework initiated and developed by Simbios, the National NIH Center for Biomedical Computing focusing on Physics-based Simulation of Biological Structures. Simtk.org represents a centralized organization, a place, where like-minded people can gather to collectively pursue their interests in research areas, related to physics-based simulation of biological structures. One important goal is for Simtk.org to serve as a repository for models that are published (as well as the associated code) to create a "living" archive of simulation scholarship. Hence, anyone interested in physics-based simulation in biomedicine can come to the site and find the right project.
Virtual Cell is a web-based software environment for modeling and simulation of reaction-diffusion systems in cell biology. The multi-view user interface allows experimentalists and modelers to create mathematical models, define cellular geometry, specify simulations and analyze, visualize, or export simulation results. For each model, Virtual Cell generates a nonlinear coupled system of ordinary differential equations (non-spatial models) or partial differential equations (spatial models), and solves the equations numerically. Typically, spatial models include multiple spatially resolved volume and membrane variables in multiple compartments, with nonlinear reaction kinetics and flux interface conditions. The numerical solvers are designed as a black box, so minimal user input is required.
add your project here