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Software Highlights

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1-12 of 523

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

5938

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

1091

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
TeX
+ 9

876

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

723

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

387

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
CSS
HTML

192