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Software Highlights

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624

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122

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1-12 of 465

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

2804

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

2568

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

1250

Chemistry Development Kit

Open Source cheminformatics library.

Cheminformatics
Chemistry
Computational Chemistry

Java
Pawn
HTML

820

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

C++
geophysics
Glacier
+ 5

C++
Python
CMake
+ 9

717

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

318

EC-Earth

A European community Earth-System Model

Climate change
Climate modeling
High performance computing

303

OpenChrom

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

chromatography
mass spectrometry

Java
CSS
HTML

178

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

141

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

GGIR

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

Big data

120

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 4

117