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HIFIS Software Spotlights

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1-12 of 80

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.

Data Visualization
FAIR Software
Genome assembly
+ 4

AMPL
C++
Python
+ 12

9313

circlize

Circular layout is an efficient way for the visualization of huge amounts of information. The circlize package provides an implementation of circular layout generation in R.

Data analysis
Data Science
Data Visualization
+ 3

3088

CP2K

CP2K is a quantum chemistry and solid state physics software package running on graphics processing units and thousands of processing units. It is open-source and allows simulations, spectroscopy, vibrational analysis and energy minimization on a vast variety of theory levels.

electronic structure
GPU
High performance computing
+ 5

Fortran
C
Python
+ 13

2098

anvi'o

Anvi'o is an open-source software platform for microbial 'omics research enabling analysis and visualization of 'omics data. In development since 2014, it is currently being maintained by the Ecosystem Data Science group at the Helmholtz Institute for Functional Marine Biodiversity.

Data analysis
Data Visualization
Omics
+ 1

Python
JavaScript
HTML
+ 5

1983

REMix

REMix is a powerful software for energy systems optimization. It can be used for the planning and techno-economical assessment of future multi-energy systems of any spatial, temporal and technological scope. REMix offers a wide range of methods and features that can be flexibly selected by the user.

Energy
Energy planning
ESD
+ 5

GAMS
Python
Dockerfile

1573

ETHOS.FINE - Framework for Integrated Energy System Assessment

ETHOS.FINE provides a framework for modeling, optimizing and assessing energy systems. Systems with multiple regions, commodities and time steps can be modeled. Target of the optimization is the minimization of the total annual cost while considering technical and environmental constraints.

Energy
Energy planning
ESD
+ 6

Python
Dockerfile

789

JPlag

JPlag is one of the most popular source code plagiarism detection systems worldwide.

Automated Obfuscation Attack
Collusion Detection
Data analysis
+ 9

Java
ANTLR
Rust
+ 15

531

PeTrack

PeTrack (Pedestrian Tracking) automatically extracts accurate pedestrian trajectories from video recordings (calibration, recognition, tracking). Individual codes enable personalized trajectories with static information of each participant. With a stereo camera also markerless tracking is possible.

Annotation
Calibration
Computer Vision
+ 17

C++
Python
CMake
+ 2

464

FastSurfer

FastSurfer is a fast and accurate deep-learning pipeline for the analysis of human brain MRI. FastSurfer provides a fully compatible FreeSurfer alternative for volumetric and surface-based thickness analysis, also supporting sub-mm resolutions, and sub-segmentation of neuroanatomical structures.

Data analysis
Deep Learning
Image processing
+ 3

Jupyter Notebook
Python
Shell
+ 1

259

DataLad

DataLad is a tool for the joint management of code, data, and their relationship, built on top of the version control systems Git & git-annex. It adapts principles of open-source software development & distribution to address challenges of data management, data sharing, & digital provenance capture.

DataLad
data managment
data sharing
+ 8

Python
Shell
Makefile
+ 4

230

EnrichedHeatmap

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. The EnrichedHeatmap package provides advanced solutions for normalizing genomic signals within target regions as well as offering highly customizable visualizations.

Data analysis
Data Visualization
FAIR Data
+ 2

180

simplifyEnrichment

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

Data analysis
Data Visualization
FAIR Data
+ 3

131