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Awesome list for Computational Physiology
https://github.com/ComputationalPhysiology/awesome

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Awesome list for Computational Physiology

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# Awesome list for Computational Physiology



[![Awesome](https://awesome.re/badge.svg)](https://awesome.re)



Here we would like to collect links to everything that you find awesome. If you wonder what an awesome list is you can checkout [github.com/sindresorhus/awesome](https://github.com/sindresorhus/awesome).



## Image processing



- [MeVisLab](http://www.mevislab.de/mevislab/) - a powerful, modular framework for image processing research and development with a special focus on medical imaging



- [VMTK](http://www.vmtk.org/) - collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels



- [ITK](https://itk.org) - The toolkit provides leading-edge segmentation and registration algorithms in two, three, and more dimensions



- [Seg3D](http://www.sci.utah.edu/cibc-software/seg3d.html) - Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.



## Mesh generation



- [GMSH](http://gmsh.info) - A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities



- [CGAL](http://www.cgal.org) - CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library



- [TetGen](http://wias-berlin.de/software/tetgen/) - A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator



- [Cleaver](http://sci.utah.edu/cibc-software/cleaver.html) - A multimaterial tetrahedral meshing library and application



## Gemetric modeling



- [Blender](https://www.blender.org) - open source modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation



## Optimization



- [pagmo](https://esa.github.io/pagmo2/) - pagmo is a C++ scientific library for massively parallel optimization



- [pygmo](https://esa.github.io/pygmo2/index.html) - pygmo is a scientific Python library for massively parallel optimization based on pagmo.



- [pymo](https://pymoo.org) - Multiobjective optimization in python



- [NLopt](https://nlopt.readthedocs.io/en/latest/) - NLopt is a free/open-source library for nonlinear optimization,



- [Ipopt](https://github.com/coin-or/Ipopt) - Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization



- [Optizelle](https://www.optimojoe.com/products/optizelle/)  - An Open Source Software Library Designed To Solve General Purpose Nonlinear Optimization Problems



- [Moola](https://github.com/funsim/moola) - A set of optimisation algorithms specifically designed for PDE-constrained optimisation problems to be used with dolfin-adjoint.



## Simulation software



### General



#### Finite element



- [FEniCS](https://fenicsproject.org) - Open source computing platform for solving PDEs in Python

- [OpenCMISS](http://opencmiss.org) - Modelling and visualisation for complex bioengineering problems.

- [BVPy](https://gitlab.com/oali/bvpy) - Bvpy is a python library, based on FEniCS, Gmsh & Meshio, to easily implement and study numerically Boundary Value Problems and Initial Boundary Value Problems through the Finite Element Method.



#### Finite Volume



- [OpenFoam](https://www.openfoam.com) - Open source CFD software



### Cardiac mechanics



- [pulse](https://github.com/ComputationalPhysiology) - Cardiac mechanics simulator based on FEniCS



- [pulse-adjoint](https://github.com/ComputationalPhysiology/pulse_adjoint) - Data assimilation tool based on pulse



### Electrophysiology



- [CBCBeat](https://bitbucket.org/meg/cbcbeat/src) - an adjoint-enabled framework for computational cardiac electrophysiology



- [CARP](https://carp.medunigraz.at) 



- [openCARP](https://opencarp.org/) - open source version of CARP



### Electromechanics



- [SciRun](http://www.sci.utah.edu/cibc-software/scirun.html) - Problem solving environment for modelling, simulation and visualization



- [Chaste](https://github.com/Chaste/Chaste) - Cancer Heart And Soft Tissue Environment 



### Cellular modeling



- [gotran](https://github.com/ComputationalPhysiology/gotran) - Library for declaring ODEs



- [Myokit](http://www.myokit.org) - Python based software package designed to simplify the use of numerical models in the analysis of cardiac myocytes. 



## Model repositories



- [CellML](https://models.cellml.org/cellml) - Cell models



- [BioModels](http://www.ebi.ac.uk/biomodels/) - Repository of mathematical models of biological and biomedical systems.



## Visualization



- [Paraview](https://www.paraview.org) - open-source, multi-platform data analysis and visualization application.



- [VTK](https://vtk.org) - The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization



- [ImageVis3D](http://sci.utah.edu/cibc-software/imagevis3d.html) - Volume rendering program



- [FluoRender](http://www.sci.utah.edu/software/fluorender.html) - Interactive tool for multi-channel fluorescence microscopy data visualization and analysis



- [Map3D](http://sci.utah.edu/cibc-software/map3d.html) - Scientific visualization application to display and edit complex, three-dimensional geometric models and the scalar data associated with those models. The map3d interface provides interactive display of both geometry and data assigned to elements of that geometry