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Software Highlights

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116

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1-12 of 219

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

5994

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

2697

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

1381

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
TeX
+ 9

877

DUNE (Distributed and Unified Numerics Environment)

DUNE, the Distributed and Unified Numerics Environment, is a modular toolbox for solving partial differential equations (PDEs) with grid-based methods. It supports the easy, flexible, and efficient implementation of finite element and volume methods. DUNE is C++ code and also has a Python interface.

C++
Grid-based PDE methods
High performance computing
+ 5

C++
CMake
Python
+ 2

549

ESMValTool

The Earth System Model eValuation Tool is a community diagnostics and performance metrics tool for the evaluation of Earth System Models that allows for routine comparison of models and observations.

Big data
Optimized data handling
Visualization
+ 1

NCL
Python
R
+ 7

390

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

282

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

Big data
GPU
High performance computing

C
C++
Cuda
+ 5

184

NNPDF

Fitting proton substructure to observation data using neural networks

Machine learning
PDF

Python
Jupyter Notebook
C
+ 5

127

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 5

117

Paired omics data platform

If you do metabolomics experiments with mass spectra and have sequenced the genomes of the samples, then the platform can help you link them.

Inter-operability & linked data

TypeScript
JavaScript
HTML
+ 3

105

TraP: The LOFAR Transients Pipeline

The LOFAR Transients Pipeline (or "TraP") is a Python and SQL based system for detecting and responding to transient and variable sources in a stream of astronomical images.

Image processing
radio astronomy
Source association
+ 3

Python
PLpgSQL
Mako
+ 1