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Software Highlights

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307

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109

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1-12 of 192

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

2811

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

2573

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

733

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
+ 6

323

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 4

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

GrainLearning

Unsure about the parameters of your grains in a computer simulation? Use Iterative Bayesian Filtering to learn parameter distributions from limited data. Is your model running slowly? Speed up your simulations with machine-learning surrogates. All these features are integrated within GrainLearning.

Bayesian Inference
Data assimilation
Machine learning
+ 2

Jupyter Notebook
Python
PureBasic
+ 1

grlc

Builds a web API from SPARQL queries hosted on GitHub to accessing triple store data.

garlic
Inter-operability & linked data

Python
HTML
TeX
+ 4

DeepRank

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

Big data
Machine learning
Optimized data handling

Python
R
C
+ 2

Netherlands eScience Center Python Template

Generic template for Python packages, so you can spend less time setting up and configuring, and comply with the Netherlands eScience Center Software Development Guide from the start.

Jinja
Python
Shell

Vantage6

An open-source platform for supporting the development of federated learning projects

federated learning
healthcare
privacy preserving analysis
+ 1

Python
TypeScript
HTML
+ 6