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Software Highlights

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1-12 of 43

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++
+ 8

2814

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

2577

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

1257

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
CMake
+ 9

745

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

123

DeepRank

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

Big data
Machine learning
Optimized data handling

Python
R
C
+ 2

HyperCanny

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

High performance computing

C++
C
Python
+ 3

compareMS2

compareMS2 is a tool for direct comparison of tandem mass spectrometry datasets, typically from liquid chromatography-tandem mass spectrometry (LC-MS/MS), defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics and food science.

Forensics
mass spectrometry
phylogenetics
+ 1

JavaScript
C
HTML
+ 2

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

ExploreASL

ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators.

ASL
Image processing
MRI

MATLAB
C
Python

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

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