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Software Highlights

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1-12 of 48

haddock3

Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a an information-driven flexible docking approach for the modeling of biomolecular complexes.

Inter-operability & linked data

Python
Fortran
C
+ 9

2840

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

2597

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

1288

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
CMake
+ 9

782

Sagecal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

Big data
GPU
High performance computing

C
C++
Cuda
+ 5

175

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

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

OMUSE

A Python environment to interface and couple oceanographic and other earth system model codes.

High performance computing
Multi-scale & multi model simulations

Fortran
Python
HTML
+ 10

HyperCanny

Finds edges in high-dimensional data using the Canny algorithm.

High performance computing

C++
C
Python
+ 3

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

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

MUSCLE3

MUSCLE3 is a coupling library for building multiscale simulations out of single-scale models.

High performance computing
Multi-scale & multi model simulations

Fortran
C++
Python
+ 2