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Software Highlights

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1-12 of 51

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++
+ 9

5888

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

2681

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

1367

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
TeX
+ 9

876

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

280

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

Big data
GPU
High performance computing

C
C++
Cuda
+ 5

183

iScore

A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.

Big data
Machine learning
Protein-Protein Interaction

Python
Cuda
Makefile
+ 1

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

HyperCanny

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

Data Analysis
edge detection
High performance computing

C++
C
Python
+ 3

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

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
+ 4