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Software Highlights

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405

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1-12 of 301

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

2814

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

2577

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

745

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

325

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

148

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

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

103

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

101

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

matchms

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

Big data
Optimized data handling

Python
TeX
Batchfile
+ 1