Software Highlights

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1-12 of 73
Logo for haddock3

haddock3

Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a modular software for for the integrative modeling and refinement of biomolecular complexes.

  • biomolecular complexes
  • docking
  • energetics
  • + 4
  • Python
  • Fortran
  • C++
  • + 10
12
6027
Logo 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
2704
Logo for ASTRA Toolbox

ASTRA Toolbox

The ASTRA Toolbox is a Python and MATLAB library of flexible, high-performance GPU-accelerated primitives for 2D and 3D tomography.

  • CT
  • GPU
  • Image reconstruction
  • + 4
  • C++
  • Cuda
  • MATLAB
  • + 8
2
1389
Logo 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
  • TeX
  • + 9
33
878
Logo for DuMux

DuMux

DuMux - DUNE for Multi-{Phase, Component, Scale, Physics, …} flow and transport in porous media and more. The swiss army knife of porous media research. Open-source simulator in modern C++.

  • Earth and Environmental Sciences
  • Engineering
  • Finite volume method
  • + 9
  • C++
  • CMake
  • Hack
  • + 2
21
417
Logo 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
282
Logo for SAGECal

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

  • Big data
  • GPU
  • High performance computing
  • C
  • C++
  • Cuda
  • + 5
4
184
Logo for NNPDF

NNPDF

Fitting proton substructure to observation data using neural networks

  • Machine learning
  • PDF
  • Python
  • Jupyter Notebook
  • C
  • + 5
7
131
Logo for Parcels

Parcels

Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as plastic and fish.

  • lagrangian-ocean-modelling
  • ocean-circulation-models
  • particles
  • Python
  • C
25
123
Logo for DeepRank

DeepRank

Deep learning framework for data mining protein-protein interactions using CNN

  • Big data
  • Machine learning
  • Optimized data handling
  • Python
  • R
  • C
  • + 2
8
91
Logo for Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds

Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds

Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds

  • Building
  • Point Cloud
  • Surface-reconstruction
  • + 1
  • C
  • C++
  • Other
  • + 8
4
72

powerfit

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

  • cryo-electron microscopy
  • macromolecular structure
  • map fitting
  • Python
  • C
  • Cython
  • + 1
5
59