All software
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
- Jupyter Notebook
- + 11
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
TOTEM_M
Code underlying: Topology Optimization of Thermo-Electro-Mechanical elements (TOTEM)
- Non-convexity
- Power constraint
- SIMP
- + 3
- Other
- Matlab
- HTML
- + 2
Chemistry Development Kit
Open Source cheminformatics library.
- Cheminformatics
- Chemistry
- Computational Chemistry
- Java
- Pawn
- HTML
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
EC-Earth
A European community Earth-System Model
- Climate change
- Climate modeling
- High performance computing
- + 1
Parallel Ice Sheet Model (PISM)
An open-source modelling framework for ice sheets and glaciers
- C++
- geophysics
- Glacier
- + 5
- C++
- Python
- TeX
- + 9
GGIR
Converts raw data from wearables into insightful reports for researchers investigating human daily physical activity and sleep.
- Big data
- R
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
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
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
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
- + 23
BridgeDb Java
Java library for identifier mapping
- Data
- persistent identifiers
- Java
- Perl
- Shell
- + 5
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
OpenChrom
OpenChrom is a vendor independent open source software for chromatography, spectrometry and spectroscopy.
- chromatography
- mass spectrometry
- Java
- HTML
- CSS
SAGECal
Fast, memory efficient and GPU accelerated radio interferometric calibration program
- Big data
- GPU
- High performance computing
- C
- C++
- Cuda
- + 5
Code for Appscanner: Automatic fingerprinting of smartphone apps from encrypted network traffic
Code for Appscanner: Automatic fingerprinting of smartphone apps from encrypted network traffic
- Mobile Traffic
- Security
- Python
- Markdown
- Other
Code for FlowPrint: Semi-Supervised Mobile-App Fingerprinting on Encrypted Network Traffic
Code for FlowPrint: Semi-Supervised Mobile-App Fingerprinting on Encrypted Network Traffic
- Mobile Traffic
- Security
- Python
- Other
- Markdown
OpenLB
OpenLB is a C++ package for the implementation of lattice Boltzmann methods (LBM) to address a vast range of transport problems, e.g. in computational fluid dynamics. The modular open source code enables fast implementation of academic test problems and advanced engineering applications.
- Computational Fluid Dynamics
- High Performance Computation
- Lattice Boltzmann Methods
- + 4
- C++
- C
- Python
- + 2
NNPDF
Fitting proton substructure to observation data using neural networks
- Machine learning
- Python
- Jupyter Notebook
- C
- + 5
MS2DeepScore
Deep learning based similarity measure of mass spectrometry data.
- Jupyter Notebook
- Python
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
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
HEAST
Hybrid Electric Aircraft Sizing Tool (HEAST)
- Conceptual aircraft design
- Distributed propulsion
- Hybrid electric propulsion
- + 1
- Matlab
- Markdown
- Other
Scholia
Graphical User Interface around Wikidata that uses SPARQL to collect data
- Wikidata
- JavaScript
- Python
- HTML
- + 3
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
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
- Cuda
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
matchms
Python library for fuzzy comparison of mass spectrum data and other Python objects
- Big data
- Optimized data handling
- Python
- TeX
- Batchfile
- + 1
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
splithalfr
Estimates split-half reliabilities for scoring algorithms of cognitive tasks and questionnaires.
- Data Analysis
- Statistics
- R
MAGMa
MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.
- Big data
- Visualization
- Python
- JavaScript
- Makefile
- + 5
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
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
Matlab codes for Probabilistic Field Approach for Motorway Driving Risk Assessment
Matlab codes for Probabilistic Field Approach for Motorway Driving Risk Assessment
- automated driving
- Collision probability
- Reachability analysis
- + 1
R package for WALRUS (Wageningen Lowland Runoff Simulator)
R package for WALRUS (Wageningen Lowland Runoff Simulator)
- discharge simulation
- hydrological model
- hydrology
- + 4
snvec
snvec: Pre-computed Precession-Tilt solutions and C code.
- astronomical solution
- Astrophysics
- obliquity
- + 3
- C
svnecR
Easily calculate precession and obliquity from an astronomical solution and assumed or reconstructed values for dynamical ellipticity (Ed) and tidal dissipation (Td). This is a translation and adaptation of the C-code in Zeebe and Lourens (2022), with further details in Zeebe (2022).
- astronomical solution
- cyclostratigraphy
- dynamical ellipticity
- + 12
- R
- Rez
Tillage-controlled Runoff Pattern model (TCRP) v1.1; a GIS model to adjust runoff patterns for tillage induced roughness in agricultural catchments
Tillage-controlled Runoff Pattern model (TCRP) v1.1; a GIS model to adjust runoff patterns for tillage induced roughness in agricultural catchments
- DEM
- erosion pattern
- modelling
- + 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
Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds
Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds
- Building
- Point Cloud
- Surface-reconstruction
- + 1
- C
- C++
- Other
- + 8
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
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
powerfit
Rigid body fitting of atomic strucures in cryo-electron microscopy density maps
- cryo-electron microscopy
- macromolecular structure
- map fitting
- Python
- C
- Cython
- + 1
openAVEM (Open Aviation Emissions)
openAVEM (Open Aviation Emissions)
- aircraft emissions
- air pollution
- aviation
- + 1
QMflows
Construction and efficient execution of computational chemistry workflows.
- Multi-scale & multi model simulations
- Workflow technologies
- Python
- Jupyter Notebook
- Shell