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Cover image for COPASI

COPASI

COPASI is an open source software for simulation and analysis of biochemical networks and their dynamics. It provides simulations using ODEs, SDEs, or Gillespie's stochastic simulation algorithm, with optional discrete events. COPASI provides several analyses, optimization, and parameter estimation.

  • Dynamics
  • optimization
  • Parameter estimation
  • + 3
  • C++
  • Java
  • Fortran
  • + 17
12
2577
Cover image for Parallel Ice Sheet Model (PISM)

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

  • C++
  • geophysics
  • Glacier
  • + 5
  • C++
  • Python
  • CMake
  • + 9
33
745
Cover image for open-DARTS

open-DARTS

Open Delft Advanced Research Terra Simulator is a simulation framework for forward and inverse modelling and uncertainty quantification of multi-physics (thermo-hydro-mechanical-chemical) processes in geo-engineering applications as geothermal, CO2 sequestration, water pumping, and hydrogen storage.

  • energy transition
  • environmental modelling
  • geothermal
  • + 3
  • Python
  • C++
  • Cuda
  • + 2
13
35
Cover image for AMBER

AMBER

A real-time pipeline to search for Fast Radio Bursts and other transient radio sources.

  • Big data
  • GPU
  • High performance computing
  • + 1
  • C++
  • CMake
3
25
Cover image for DALES

DALES

DALES is a large-eddy simulation code designed for studies of the physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers.

  • Fortran
  • C
  • TeX
  • + 8
24
11
Cover image for FastMLC

FastMLC

Detect clusters in for example large collections of DNA or protein sequences, and visualize the results in a web browser.

  • Big data
  • Machine learning
  • Visualization
  • C++
  • C
  • Makefile
  • + 5
5
11
Cover image for AMUSE

AMUSE

Combine existing numerical codes in an easy to use Python framework. With AMUSE you can simulate objects such as star clusters, proto-planetary disks and galaxies.

  • High performance computing
  • Multi-scale & multi model simulations
  • Workflow technologies
  • C
  • Fortran
  • Python
  • + 26
6
6
Cover image for 3D Slicer

3D Slicer

3D Slicer is a free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.

  • 3D
  • 3DSlicer
  • Extension
  • + 7
  • C++
  • Python
  • CMake
  • + 5
4
5
Cover image for MagnumPI - Potential Integrator

MagnumPI - Potential Integrator

A package for the calculation of scattering angles and cross sections.

  • Inter-operability & linked data
  • Visualization
  • C++
  • Mathematica
  • Python
  • + 2
6
5
Cover image for LUE

LUE

LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.

  • Agent-based modeling
  • environmental modelling
  • field based modelling
  • + 6
  • C++
  • Python
  • CMake
  • + 6
3
4
Cover image for SlicerRT

SlicerRT

SlicerRT allows users to analyze spatio-temporal accumulation of the therapeutic dosage (radiation, thermal, etc.). Tools include dose visualization, quantitative metrics computation, comparison, and import/export to DICOM format.

  • C++
  • Python
  • CMake
  • + 1
3
3
Cover image for OpenMS

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

  • C++
  • mass spectrometry
  • metabolomics
  • + 1
  • C++
  • MAXScript
  • Cython
  • + 13
27
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