Ecosyste.ms: Awesome

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awesome

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

  • MeVisLab - a powerful, modular framework for image processing research and development with a special focus on medical imaging
  • VMTK - collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels
  • ITK - The toolkit provides leading-edge segmentation and registration algorithms in two, three, and more dimensions
  • Seg3D - Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.
  • GMSH - A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities
  • CGAL - CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library
  • TetGen - A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator
  • Cleaver - A multimaterial tetrahedral meshing library and application
  • Blender - open source modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation
  • pagmo - pagmo is a C++ scientific library for massively parallel optimization
  • pygmo - pygmo is a scientific Python library for massively parallel optimization based on pagmo.
  • pymo - Multiobjective optimization in python
  • NLopt - NLopt is a free/open-source library for nonlinear optimization,
  • Ipopt - Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization
  • Optizelle - An Open Source Software Library Designed To Solve General Purpose Nonlinear Optimization Problems
  • Moola - A set of optimisation algorithms specifically designed for PDE-constrained optimisation problems to be used with dolfin-adjoint.
  • FEniCS - Open source computing platform for solving PDEs in Python
  • OpenCMISS - Modelling and visualisation for complex bioengineering problems.
  • 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.
  • OpenFoam - Open source CFD software
  • pulse - Cardiac mechanics simulator based on FEniCS
  • pulse-adjoint - Data assimilation tool based on pulse
  • CBCBeat - an adjoint-enabled framework for computational cardiac electrophysiology
  • CARP
  • openCARP - open source version of CARP
  • SciRun - Problem solving environment for modelling, simulation and visualization
  • Chaste - Cancer Heart And Soft Tissue Environment
  • gotran - Library for declaring ODEs
  • Myokit - Python based software package designed to simplify the use of numerical models in the analysis of cardiac myocytes.
  • CellML - Cell models
  • BioModels - Repository of mathematical models of biological and biomedical systems.
  • Paraview - open-source, multi-platform data analysis and visualization application.
  • VTK - The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization
  • ImageVis3D - Volume rendering program
  • FluoRender - Interactive tool for multi-channel fluorescence microscopy data visualization and analysis
  • Map3D - 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
Programming Languages
Python 3 C++ 3
Keywords
physiology 1 mathematical-modelling 1 mathematical-biology 1 hpc-applications 1 electrophysiology 1 developmental-biology 1 computational-biology 1 cell-based 1 cancer-research 1 c-plus-plus 1 mechanics 1 fenics 1 dolfin-adjoint 1 data-assimilation 1 cardiac 1 adjoint 1 A python library for (Initial) Boundary Value Problems exploration. 1 stochastic-optimizers 1 python3 1 python 1 parallel-processing 1 parallel-computing 1 pagmo 1 optimization-tools 1 optimization-methods 1 optimization-algorithms 1 optimization 1 multi-objective-optimization 1 metaheuristics 1 genetic-algorithm 1 evolutionary-strategy 1 evolutionary-algorithms 1 artificial-intelligence 1