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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

5942

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

2689

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

1377

EC-Earth

A European community Earth-System Model

Climate change
Climate modeling
High performance computing
+ 1

1092

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
TeX
+ 9

877

Chemistry Development Kit

Open Source cheminformatics library.

Cheminformatics
Chemistry
Computational Chemistry

Java
Pawn
HTML

820

GGIR

Converts raw data from wearables into insightful reports for researchers investigating human daily physical activity and sleep.

Big data

727

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

545

DuMux

DuMux - DUNE for Multi-{Phase, Component, Scale, Physics, …} flow and transport in porous media and more. The swiss army knife of porous media research. Open-source simulator in modern C++.

Earth and Environmental Sciences
Engineering
Finite volume method
+ 9

C++
CMake
Python
+ 2

413

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

388

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

OpenChrom

OpenChrom is a vendor independent open source software for chromatography, spectrometry and spectroscopy.

chromatography
mass spectrometry

Java
HTML
CSS

192

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

Big data
GPU
High performance computing

C
C++
Cuda
+ 5

183

spec2vec

spec2vec is a novel similarity measure for comparing mass spectrometry data, which learns peak representations using Word2Vec.

Machine learning
Text analysis & natural language processing

Python
Batchfile
Makefile

181

vqls-prototype

Variational Quantum Linear Solver Library.

Numerical analysis
Quantum Computing

Python

178

ESMValCore

ESMValTool Core: core functionalities and driver for ESMValTool, a community diagnostic and performance metrics tool for routine evaluation of Earth System Models in CMIP.

Big data
Optimized data handling
Visualization
+ 1

Python
Jupyter Notebook
HTML
+ 5

127

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

NNPDF

Fitting proton substructure to observation data using neural networks

Machine learning
PDF

Python
Jupyter Notebook
C
+ 5

122

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 5

117

Kernel Tuner

Kernel Tuner greatly simplifies the development of highly-optimized and auto-tuned CUDA, OpenCL, and C code, supporting many advanced use-cases and optimization strategies that speed up the auto-tuning process.

Big data
GPU
High performance computing
+ 3

Python

116

FAIR Data Point

RESTful web service that enables data owners to expose their data sets using rich machine-readable metadata.

Big data
Inter-operability & linked data

Python
Makefile
Dockerfile

115

MS2DeepScore

Deep learning based similarity measure of mass spectrometry data.

Jupyter Notebook
Python

115

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

DeepRank GNN

DeepRank-GNN is the graph neural network of our DeepRank package. DeepRank GNN allows to train graph neural networks to classify protein-protein interface

Machine learning
Protein-Protein Interaction

Python

102

MAGMa

MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.

Big data
Visualization

Python
JavaScript
Makefile
+ 5

matchms

Python library for fuzzy comparison of mass spectrum data and other Python objects

Big data
Optimized data handling

Python
TeX
Batchfile
+ 1

splithalfr

Estimates split-half reliabilities for scoring algorithms of cognitive tasks and questionnaires.

Data Analysis
Statistics

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

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

DeepRank

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

Big data
Machine learning
Optimized data handling

Python
R
C
+ 2

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

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

Twiqs

Software behind the web server twiqs.nl, which has provided free access to statistics about Dutch tweets since 2010

Big data
Text analysis & natural language processing
Visualization

Perl
Java
HTML
+ 3

Scholia

Graphical User Interface around Wikidata that uses SPARQL to collect data

Wikidata

JavaScript
Python
HTML
+ 3

powerfit

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

cryo-electron microscopy
macromolecular structure
map fitting

Python
C
Cython
+ 1

PROTEUS

PROTEUS is a Python framework that simulates the coupled evolution of the atmospheres and interiors of rocky planets.

Exoplanets
model coupling

Python
Jupyter Notebook
Julia
+ 1

Glotaran

Glotaran: A Java-Based Graphical User Interface for the R Package TIMP

global analysis
target analysis
time-resolved spectroscopy

Java
HTML

QMflows

Construction and efficient execution of computational chemistry workflows.

Multi-scale & multi model simulations
Workflow technologies

Python
Jupyter Notebook
Shell

dtscalibration

A Python package to load raw Distributed Temperature Sensing (DTS) files, perform a calibration, and plot the result.

calibration
DTS
fiber optic
+ 1

Python
Jupyter Notebook

Vantage6

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

federated learning
healthcare
privacy preserving analysis
+ 1

Python
TypeScript
HTML
+ 6

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.

software development tools
software sustainability
template

Jinja
Python
Shell

Via Appia Visualization

A web application which visualizes the point clouds and additional data gathered in the Via Appia project with WebGL.

Visualization

JavaScript
HTML
CSS

mcfly

Helps you find a suitable neural network configuration for deep learning on time series.

auto-ml
deep learning
Machine learning
+ 1

JavaScript
Python
CSS
+ 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

hyphe

A research-driven web-crawler aimed at building, curating and categorizing a corpus of web actors and the network graph of hyperlinks connecting them.

crawling
Networks
python
+ 1

JavaScript
Python
HTML
+ 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

Ersilia Model Hub

The Ersilia Model Hub is an open source platform to serve AI/ML models for infectious disease drug discovery.

AI
Chemistry
Drug discovery
+ 1

Python
Jupyter Notebook
Dockerfile
+ 1

Research Software Directory

A content management system for research software, which promotes the visibility, reuse, and impact of research software.

FAIR
Research Software Impact
Software Citation

TypeScript
Java
PLpgSQL
+ 7