| COPASI |
software application
for simulation and analysis of biochemical
networks and their dynamics |
C, SMBL |
open
source |
GUI + code-based |
http://copasi.org/ |
| VCell |
VCell, (Virtual Cell) is a comprehensive
platform for modeling
cell biological systems that is built on a central database and disseminated
as a web application. |
VCell Math description language,
SBML |
open source |
GUI + code-based |
https://vcell.org/ |
| COMPUCELL3D |
COMPUCELL3D is a software
framework for three-dimensional (3D)
simulation of morphogenesis in different organisms that uses a stochastic
cellular potts model (CPM) and PDE solvers. |
C++ |
open source |
GUI-based |
http://www.compucell3d.org/ |
| FLAME |
FLAME is a generic
agent-based modeling system |
XML |
open source |
GUI-based |
http://flame.ac.uk/ |
| FreeFEM |
FreeFEM is a partial
differential equation solver for nonlinear
multiphysics systems in 2D and 3D |
C++ |
open source |
code-based; many algorithms implemented |
https://freefem.org/ |
| FEBIO |
FEBio software suite
is a set of software tools for nonlinear
finite element analysis in biomechanics and biophysics |
C++ |
open source |
GUI-based |
https://febio.org/ |
| Comsol Multiphysics |
a cross-platform finite
element analysis, solver, and multiphysics
simulation software. |
Comsol language |
closed
source |
GUI-based |
https://www.comsol.com/ |
| MATLAB |
is a multiparadigm numerical
computing environment and proprietary
programming language developed by MathWorks. |
MATLAB;
can interface with programs written in C++, Java, R,
and Python |
closed source |
code-based; many
inbuilt algorithms |
https://nl.mathworks.com/?s_tid=gn_logo |
| GNU Octave (alternative for MATLAB) |
GNU Octave is a high-level language, primarily intended for
numerical computations |
Octave |
open source |
code-based |
https://www.gnu.org/software/octave/ |
