All software

Items

1-48 of 1281

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

(BitBake)
(C)
(C++)
+ 11

6916

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

(Batchfile)
(C)
(C#)
+ 17

2887

TOTEM_M

Code underlying: Topology Optimization of Thermo-Electro-Mechanical elements (TOTEM)

Non-convexity
Power constraint
SIMP
+ 3

(HTML)
(large-text-file)
(Markdown)
+ 2

2772

Chemistry Development Kit

Open Source cheminformatics library.

Cheminformatics
Chemistry
Computational Chemistry

(HTML)
(Java)
(Pawn)

1833

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

(Batchfile)
(C)
(C++)
+ 8

1603

EC-Earth

A European community Earth-System Model

Climate change
Climate modeling
High performance computing
+ 1

1398

GGIR

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

Big data

984

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

(C)
(C++)
(CMake)
+ 9

934

UseGalaxy Canada

The main Canadian public Galaxy server

AI
astronomy
climate
+ 10

(HCL)
(HTML)
(Jinja)
+ 3

779

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)
(Hack)
+ 2

588

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)
(C++)
(CMake)
+ 2

465

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

(Dockerfile)
("Emacs Lisp")
(Jinja)
+ 7

110

463

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

(Assembly)
(C)
(C++)
+ 23

326

Code for Appscanner: Automatic fingerprinting of smartphone apps from encrypted network traffic

Mobile Traffic
Security

(Markdown)
(Other)
(Python)

299

Code for FlowPrint: Semi-Supervised Mobile-App Fingerprinting on Encrypted Network Traffic

Mobile Traffic
Security

(Markdown)
(Other)
(Python)

299

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

(Batchfile)
(Makefile)
(Python)

249

snvec

snvec: Pre-computed Precession-Tilt solutions and C code.

astronomical solution
Astrophysics
obliquity
+ 3

242

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)

242

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

(Batchfile)
(CSS)
(HTML)
+ 5

236

OpenChrom

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

chromatography
mass spectrometry

(CSS)
(HTML)
(Java)

219

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

Big data
GPU
High performance computing

(C)
(C++)
(CMake)
+ 5

215

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++)
(Makefile)
+ 2

190

MS2DeepScore

Deep learning based similarity measure of mass spectrometry data.

("Jupyter Notebook")
(Python)

187

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)

186

NNPDF

Fitting proton substructure to observation data using neural networks

Machine learning
PDF

(C)
(CSS)
(HTML)
+ 5

186

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

(Dockerfile)
(HTML)
(JavaScript)
+ 4

160

HEAST

Hybrid Electric Aircraft Sizing Tool (HEAST)

Conceptual aircraft design
Distributed propulsion
Hybrid electric propulsion
+ 1

(Markdown)
(Matlab)
(Other)

155

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

(Cuda)
(Python)

150

ArrayAnalysis

ArrayAnalysis provides a user-friendly solution for transcriptomic data analysis. It allows researchers, regardless of their bioinformatics expertise, to efficiently analyse, explore, and interpret RNA sequencing and microarray datasets.

Data Analysis
data visualization
microarray
+ 2

(Batchfile)
(HTML)
("Inno Setup")
+ 2

146

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

(Dockerfile)
(Makefile)
(Python)

146

matchms

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

Big data
Optimized data handling

(Batchfile)
(Makefile)
(Python)
+ 1

145

Scholia

Graphical User Interface around Wikidata that uses SPARQL to collect data

Wikidata

(CSS)
(Dockerfile)
(HTML)
+ 3

136

splithalfr

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

Cognitive tasks
Confounding effects
Non-linear scoring algorithms
+ 1

128

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

(CSS)
(Dockerfile)
(HTML)
+ 3

126

Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds

Building
Point Cloud
Surface-reconstruction
+ 1

(Automake)
(C)
(C++)
+ 8

124

DeepRank

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

Big data
Machine learning
Optimized data handling

(C)
(Makefile)
(Python)
+ 2

123

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)

123

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")
(PureBasic)
(Python)
+ 1

112

MAGMa

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

Big data
Visualization

(CSS)
(Cython)
(Dockerfile)
+ 5

110

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

(Mako)
(PLpgSQL)
(Python)
+ 1

110

Matlab codes for Probabilistic Field Approach for Motorway Driving Risk Assessment

automated driving
Collision probability
Reachability analysis
+ 1

109

R package for WALRUS (Wageningen Lowland Runoff Simulator)

discharge simulation
hydrological model
hydrology
+ 4

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

(C++)
(Cuda)
(Makefile)
+ 1

PROTEUS

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

Exoplanets
model coupling

(Dockerfile)
(Julia)
("Jupyter Notebook")
+ 2

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

CHI2023_DKE

User Interaction Dataset for CHI 2023 paper "Knowing About Knowing: An Illusion of Human Competence Can Hinder Appropriate Reliance on AI Systems."

Appropriate Reliance
DunningKruger Effect
Human-AI Decision Making
+ 1

(large-text-file)
(Markdown)
(Other)
+ 2

grlc

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

garlic
Inter-operability & linked data

(CSS)
(Dockerfile)
(HTML)
+ 4

Code for Tiresias: Predicting Security Events Through Deep Learning

Event Analysis
Security

(Markdown)
(Other)
(Python)