All software

QUAST

QUAST is a state-of-the-art tool for (meta)genome assembly evaluation, computing over 50 quality metrics and presenting results in plain text, static plots, and interactive HTML reports.

KeY

KeY is a deductive verification system for Java programs

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

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.

CPlantBox

CPlantBox is a functional-structural plant-soil modelling framework. It simulated the 3D architecture of a plant, coupled carbon and water flow within the plant, water flow and solute transport in a 3D dynamic soil, as well as water and nutrient uptake, and rhizodeposition.

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.

matRad

matRad is a dose calculation and inverse treatment planning toolkit for radiotherapy research and education written in Matlab.

Earth System Model Evaluation Tool (ESMValTool)

NetworKit

NetworKit is a growing open-source toolkit for large-scale network analysis. Its aim is to provide tools for the analysis of large networks in the size range from thousands to billions of edges. It implements efficient graph algorithms, many of them parallel to utilize multicore architectures.

NNPDF

Fitting proton substructure to observation data using neural networks

multiGSEA

The multiGSEA R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers. The enrichment is calculated for each omics layer separately and aggregated p-values are calculated afterwards to derive a composite multi-omics pathway enrichment.

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.