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HIFIS Software Spotlights

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1-12 of 19

PDAF

PDAF - the Parallel Data Assimilation Framework is a software framework for interdisciplinary data assimilation. PDAF provides support for ensemble modeling and fully implemented data assimilation methods to merge models and observational data which let models learn from observations.

Atmospheric science
data assimilation
Earth & Environment
+ 9

Fortran
Shell
Makefile
+ 4

372

CADET

CADET provides hierarchical models, efficient solvers and computational engineering tools for a range of biotechnological processes, including chromatography, filtration, crystallization, and fermentation.

adsorption
chromatography
compartment modelling
+ 4

C++
CMake
C
+ 1

284

CryoGrid

The CryoGrid Model Suite provides a set of numerical tools for simulating the thermal soil regime and the ice-water balance for permafrost and glaciers. Depending on the application needs different model tools are offered, characterized by different levels complexity and modularity.

Climate
Earth & Environment
Modeling
+ 1

MATLAB
HTML
Mercury
+ 2

257

matRad

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

Health
Medical Physics
Particle Therapy
+ 2

MATLAB
TeX
C++

241

JEMRIS

JEMRIS is a versatile, open-source, multi-purpose MRI simulator. It is well-suited for research and education.

MRI
Simulation

C++
Python
MATLAB
+ 5

SUMO

Eclipse SUMO is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.

Aeronautics, Space and Transport
Modelling
open source
+ 2

Python
C++
C
+ 13

TomoBEAR

TomoBEAR is an open-source configurable and customizable modular pipeline for streamlined and parallelized processing of large-scale cryo-electron tomography data for subtomogram averaging.

Alignment
automated reasoning
cluster
+ 16

MATLAB
M
Python
+ 1

ELECTRODE

ELECTRODE extends the atomistic simulation tool LAMMPS to model different types of electrochemical situations. Simulations are performed at constant potential or constant charge using different approaches to control potential or charge at the electrodes.

Constant Potential Method
Electrochemistry
Molecular Dynamics

C++
Tcl
Cuda
+ 24

BaSiC

BaSiC is a specialized MATLAB tool designed for the background and shading correction of optical microscopy images. BaSiC addresses critical challenges in image processing, thereby enhancing the quality and reliability of microscopy data.

MATLAB

ePowCoRe

A generic representation of power grids, enabling open-source model conversion modules for common open and proprietary modeling tools.

Energy
ESD
python

Python
MATLAB

FishInspector

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

Earth & Environment
image feature detection
pattern recognition
+ 1

MATLAB
HTML

InteractiveVis

The InteractiveVis software framework provides a blueprint for evaluating 3D datasets with convolutional neural networks (CNNs), and for deriving and visualizing CNN relevance maps. This tool was developed and tested for disease detection in MRI scans. We plan to extend it to other domains.

Data Visualization
MRI
open source
+ 1

Jupyter Notebook
HTML
MATLAB
+ 5