CodeMeta overview
This page gives a succinct overview of all software pages that export to CodeMeta.
Warning: this feature is still in development, so the generated CodeMeta data might still
change.
Implementation of all possible forms of 2x2 and 3x3 space-filling curves, and nxn curves expanded from any specific level-1 units. It also implements the H-curve and the three-dimensional Hilbert curve.
4C is a parallel multiphysics research code for simulating solid/fluid mechanics, scalar transport, and chemical reactions. It supports both single-field and coupled systems, offering ready-to-use solutions for a wide range of physical problems.
AI4HPC, part of CoE RAISE, is an open-source library to train AI models with CFD datasets on HPC systems. AI4HPC also includes a benchmarking suite to test the limits of any system with CPUs and GPUs towards Exascale and a HyperParameter Optimization (HPO) suite for scalable HPO tasks.
This AiiDA plugin provides high-throughput automation and FAIR data management for the Jülich KKR codes.
AiiDA plugin for FAIR high-throughput spin-dynamics simulations with the Spirit code (http://spirit-code.github.io/).
A Platform for Replicable Science.
Album is an open-source tool that simplifies sharing and running scientific workflows. With isolated environments, metadata for easy discovery, and cross-platform support, it ensures replicability.
Designed for collaboration, it’s adopted by leading researchers.
This tool allows for the automated generation and calibration of white-box modelica room models based on a room description in the mini-language Modelica.
The Account LInking SErvice (ALISE) is a tool to link accounts at a service. The goal is to enable federated services at sites that do not yet support federated identities.
Allpix Squared is a semiconductor detector simulation framework. The goal of the framework is to provide a complete and easy-to-use package for end-to-end simulations of semiconductor detector performance from incident ionizing radiation until the digitization of hits in the detector chip.
Alpaca (Automated Lightweight Provenance Capture) captures the provenance during the execution of Python scripts that process data and stores the information using a data model based on the the W3C PROV standard.
The alpaka library is a header-only C++17 abstraction framework designed for computing accelerator development. It enables developers to implement algorithms once and execute them across a range of platforms, including x86, ARM, and RISC-V CPUs, as well as accelerators from NVIDIA, AMD, and Intel.
AMIRIS is the open Agent-based Market model for the Investigation of Renewable and Integrated energy Systems. It aims at enabling scientists to dissect the complex questions arising with respect to future energy markets, their market design, and energy-related policy instruments.
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.
This collection provides production-ready Ansible roles used for providing services used in research and by research software engineers, but not exclusively. The collection is used to deploy popular Helmholtz Cloud services like the Helmholtz Codebase and its CI infrastructure.
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.
Arbor is a high-performance library for computational neuroscience simulations with multi-compartment, morphologically-detailed cells, from single cell models to very large networks. Arbor is written from the ground up to help neuroscientists effectively use contemporary and future HPC systems.
AROSICS is an automated and robust open-source image co-registration software for multi-sensor satellite data.
AI-enhanced differentiable Ray Tracer for Irradiation Prediction in Solar Tower Digital Twins
ASPECT is a code to simulate convection and tectonic processes in the Earth and other planetary bodies. It has grown from a mantle-convection code into a tool for many geodynamic applications, like glacial isostatic adjustment, lithospheric scale deformation, ore formation and two-phase flow.
atoMEC is a python-based average-atom code for simulations of high energy density phenomena such as in warm dense matter. It is designed as an open-source and modular python package.
AutoGaitA simplifies, accelerates, and standardises gait analyses after body posture tracking with deep learning algorithms in Python.
Automating Requirements and Documentation Comprehension (ARDoCo) is a framework to connect architecture documentation, requirements, and models while identifying missing or deviating elements (inconsistencies). An element can be any representable item of the model like a software component.
Automated point forecast-based quantile forecasts
Automated photovoltaic forecasts with limited information using an ensemble of pre-trained models.
Automated wind power forecasts with limited computing resources using an ensemble of diverse wind power curves.
Aviator is a web service facilitating easy surveillance of scientific online tools. It currently checks more than 13,000 websites twice a day for availability and saves numerous features (response time, RAM usage security certificates, analytic tools / trackers, etc.) in a FAIR data repository.
Four tools - ClimSight, pangaeaGPT, AWI_chatbot, and CMIP6 search - use LLMs to enhance research and operations. pangaeaGPT aids dataset exploration, ClimSight provides location-specific climate insights, AWI_chatbot streamlines internal tasks at AWI, and CMIP6 search improves access to CMIP6 data.
Base-repo is a generic, domain-agnostic research data repository suitable to store and manage all kinds of research data. Its content is organized as DataResources, which consist of descriptive DataCite-compliant Metadata and one or more data elements, either stored as files or linked by reference.
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.
BaSiCPy is a Python package that corrects uneven illumination and temporal drifts for microscopy images
BELUGA is a system for displaying and monitoring platforms and sensor data during operations at sea in real time. Data can be displayed on board vessels and is available in an online interface in near real time. Communication with the platforms is also possible. Try it here: https://beluga.geomar.de
Sample Java code analysing "Bending Stiffness of Actin Filaments" Experiment.
Calculation of the buckling behavior of composite shells
Bifurcation Diagrams for Discrete-Time Maps in Python
BioAutoML automatically runs an end-to-end ML pipeline that can be effectively employed by non-experts. BioAutoML does not require specialized human assistance, i.e., it only needs a training dataset of biological sequences (FASTA files) to perform an end-to-end ML experiment.
A procedural Blender pipeline for photorealistic training image generation
Software to simulate and fit neutron and x-ray reflectometry and grazing-incidence small-angle scattering. The latter is computed as usual, using the distorted-wave Born approximation, hence the name. Users can set up arbitrary multilayer samples with interface roughness and embedded nanoparticles.
Computation of effective cross-sectional properties of composite beams
Our BrainPrint tools provide shape descriptors of neuroanatomical structures and require a FreeSurfer or FastSurfer segmentation as a pre-processing step. BrainPrint is based on “ShapeDNA” a spectral shape descriptor.
CADET provides hierarchical models, efficient solvers and computational engineering tools for a range of biotechnological processes, including chromatography, filtration, crystallization, and fermentation.
calibr8 is a Python toolbox for likelihood-based calibration modeling and Bayesian inference.
It supports uni- and multivariate problems, continuous & discrete distributions and includes ready to use models for many non-linear problems.
It integrates with PyMC for advanced Bayesian inference.
Cat4KIT is an open-source framework for cataloging, managing and publishing research data according to the FAIR principles. Building on the STAC-Ecosystem, it allows for a simple and user-friendly description, integration and discovery of research data.
CATENA is a distributed automatic processing chain system developed at DLR-IMF for the processing of Earth Observation mass data. CATENA is certified under ISO9001.
An open-source Python package, offering advanced AI methods for the identification and segmentation of biomedical objects, such as cells, in image data. Includes trained models that work out-of-the-box for a wide range of use cases.
CellRank is a computational framework to study cellular fate decisions based on various types of single-cell genomics data. CellRank scales to large cell numbers, is fully compatible with the scverse ecosystem, and is easy to use.
ChASE is a modern and scalable library to solve dense Hermitian (Symmetric) algebraic eigenvalue problems based on a spectral polynomial filter. The library is fully parallelized, and is particularly effective for sequences of eigenproblems as they often arise in electronic structure theory.
Fast and differentiable particle accelerator optics simulation for reinforcement learning and optimisation applications.
Chemotion ELN is an Open Source electronic lab notebook (ELN) for scientists working in chemistry and colleagues from neighboring disciplines, developed and updated at KIT. The web-based application allows the acquisition, management, storage, processing, and sharing of research data.
The software provides a consistent and comprehensive collection of climate indices typically used to describe Earth System dynamics and serves as a new benchmark data set. It allows users to develop new machine learning methods and to compare their results to existing methods in an objective way.
CIMPredict delivers an alternative to the FRAX fracture risk calculator for osteoporosis patients based on a new Calcium isotope marker in blood.
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.
The Citation File Format (CFF) project provides a format and schema for plain text CITATION.cff files with human- and machine-readable citation information for software (and datasets). Developers/RSEs can include them in their repositories to let others know how to correctly cite their software.
The CiTYCHEM extension of the EPISODE dispersion model is designed for treating complex atmospheric chemistry in urban areas and improved representation of the near-field dispersion. Applications are urban air quality studies, environmental impact assessments and sector-specific emission studies.
ClimSight is a tool designed to make localized climate information both accessible and actionable. By integrating large language models (LLMs) with geographical and climate data, ClimSight provides users with tailored, location-specific insights essential for a variety of applications.
cnpy++ is a C++17 library that allows to read and write NumPy data files (.npy and .npz). It is designed in a way to integrate well into the modern C++ ecosystem and it provides features not available in any similar C++/npy library.
Subgroup classification is a basic task in genomic data analysis. The
cola package provides a general framework for subgroup classification by
consensus partitioning.
The Collector App is the backend of the biotic database system called CRITTERBASE. It is used for the import and administration of the underlying data.
COMANDO is a next generation modeling framework for Component-Oriented Modeling and optimizAtion for Nonlinear Design and Operation of integrated energy systems.
CoMOLA is a python tool for optimal spatial allocation of land uses. The tool creates optimal land-use maps for up to four objectives. It takes into account constraints and can be coupled with external models to evaluate different objectives (e.g. ecosystem services/biodiversity models)
Complex heatmaps are efficient in visualizing associations between different sources of data sets and revealing potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
Control and data acquisition system for small-scale experiments and experimental setup with volatile and dynamic constituents such as test beam environments or laboratory test stands
The CIPM approach keeps source code and architectural performance models consistent during software development and operation.
This project provides a Python implementation of an imputation method for energy time series. The CPI method copies data blocks with similar characteristics and pastes them into gaps of the time series while preserving the total energy of each gap.
With CorC, we implemented an IDE to create programs following the Correctness-by-Construction approach. Starting with an abstract specification, CorC supports CbC developers in refining a program by a sequence of refinement steps and in verifying the correctness of these refinements.
A Monte Carlo framework for the simulation of particle showers initiated in the Earth's atmosphere (or dense media) by high-energy particles from the cosmos.
CosmoScout VR is an open source virtual Solar System, primarily aimed at interactive visualization of huge remote sensing products in conjunction with large-scale simulation data.
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.
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.
Tango Distributed Control System - C++ library
TANGO is an object-oriented distributed control system. In TANGO all objects
are representations of devices, which can be on the same computer or
distributed over a network. Communication between devices can be synchronous,
asynchronous or event driven.
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.
CrystFEL is a suite of programs to process data from "serial crystallography" experiments.
CUAS-MPI is the MPI-parallel implementation of the confined-unconfined aquifer system model for subglacial hydrology. The model uses a single-layer equivalent porous medium approach and solves a two-dimensional Darcy-type groundwater flow equation.
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource.
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource.
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource.
Tests GPU memory for hardware errors and soft errors using NVIDIA's CUDA or AMD's HIP.
cupla is a simple user interface for the platform-independent parallel kernel acceleration library alpaka. It follows a similar concept as the NVIDIA® CUDA® API by providing a software layer to manage accelerator devices. alpaka is used as a backend for cupla.
cyCONDOR, an easy-to-use computational framework for end-to-end High-Dimensional Cytometry data analysis. cyCONDOR offers guided pre-processing, clustering, dimensionality reduction, machine learning, pseudotime analysis, and batch integration, making it ideal for clinical and research settings.
DAMNIT (Data And Metadata iNspection Interactive Thing) is a tool developed by the Data Analysis group at the European XFEL to provide users with a way to automatically create an overview of their experiment, hopefully replacing the manually-created spreadsheets that are often used.
Python RPC wrapper for the data analytics software framework DASF
The framework surrounding DataDesc, a metadata schema for software documentation with focus on interfaces, comes with a machine-actionable metadata exchange format and a software toolkit supporting the documentation, extraction and publication of software metadata.
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.
This DataLad extension package equips DataLad's run/rerun functionality with the ability to transparently execute commands in containerized computational environments. On re-run, DataLad will automatically obtain any required container at the correct version prior execution.
This DataLad extension is a staging area for add-ons, for performance upgrades, and user experience improvements. Unlike other topical extensions, the focus is on functionality with broad applicability.
DataNord - SmartReps AI Hub is a centralised platform for in-house AI-powered solutions designed to enrich PANGAEA ecosystem.
This page highlights innovative projects that leverage artificial intelligence to streamline workflows, deliver intelligent insights, and advance cutting-edge research.
DataSAIL is an open-source software tool that splits machine learning datasets while minimizing Information Leakage. It formulates the splitting of a dataset as a constrained minimization problem and optimizes the data split towards an objective function that accounts for information leakage.
A Python library for working with data in the vicinity of Git and git-annex. A focus is efficient communication with subprocesses, which read and produce data in some format.
dCache is a system for storing and retrieving huge amounts of scientific data, distributed among a large number of heterogeneous server nodes, under a single virtual filesystem tree with a variety of standard access methods including NFSv4.1 (pNFS), FTP, WebDav and xroot.
DeepLOKI is an AI-based software that uses deep learning to classify zooplankton species from high-resolution images, improving research efficiency by enabling faster and more accurate onboard image analysis in marine science.
Tree Crown Segmentation and Analysis in Remote Sensing Imagery with PyTorch
deploy2zenodo is a script to deploy your data to zenodo. You can use it in a CI pipeline as an automatic workflow. Environmental variables allow very flexible use. Depending on the flags, the data can be curated before deployment in a merge request, in the zenodo web interface or not curated at all.
Damage and Exposure Update Service
The Digital Earth Viewer is a tool for the visualisation and exploration of geospatial data in true 3D over time. It runs on Windows, MacOS and Linux and only requires a modern webbrowser to use. Common file formats such as CSV, netCDF, GeoTIFF and many more are natively supported.
A directory structure and metadata linter based on JSON Schema.
Calculation of the phase velocity of Lamb waves in plate composite structures
DL4PuDe is an AI-based framework that automatically detects pushing behavior in crowd videos, leading to a better understanding of pushing dynamics. This knowledge is crucial for better crowd management strategies and better design of public places, making public places more comfortable and safer.
easyWave-GPU computes tsunami wave propagations in a fraction of minute on GPU-powered machines. Thus , a single simulation, or several simulations with varying granularity, covering several hours of tsunami wave propagation, and tailored to the actual situation can be computed within seconds.
The enCore Community Land Model (eCLM) is based on the Community Land Model version 5, representing land surface processes including hydrology, biogeophysics, biogeochemistry and ecosystem dynamics.
A Python library and web application to select and test Ground Motion models. Online at:
https://egsim.gfz-potsdam.de
ehrapy is a modular open-source Python framework designed for exploratory end-to-end analysis of heterogeneous epidemiology and electronic health record data.
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.
Elephant (Electrophysiology Analysis Toolkit) is an open-source, community centered library for the analysis of electrophysiological data in the Python programming language.
Emipy is a Python package to access, manipulate, analyze and visualize data on various pollutants, which is collected in the European Pollutant Release Register (E-PRTR). Therefore, it enables the easy use of this data for research in different fields (e.g., public health or energy system analysis).
The Environmental Mapping and Analysis Program (EnMAP) is a German hyperspectral satellite mission that aims at monitoring and characterising Earth’s environment on a global scale. EnMAP measures and models key dynamic processes of Earth’s ecosystems by extracting geochemical, biochemical and biophy
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.
A generic representation of power grids, enabling open-source model conversion modules for common open and proprietary modeling tools.
ESM-Tools is a toolbox to assist you in running climate and Earth System Model simulations.
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.
ETHOS.HiSim is a Python package for simulation and analysis of household scenarios and building systems using modern components as alternative to fossil fuel based ones. This package integrates load profiles generation of electricity consumption, heating demand, electricity generation.
ETHOS.PeNALPS (Petri Net Agent based Load Profile Simulator) is a Python library for the simulation of load profiles of plants of industrial manufacturing processes. Load profiles are energy demand time series.
REFLOW is a workflow manager tool designed to streamline and automate tasks related to renewable energy potential analyses.
A spatial disaggregation workflow tool developed to disaggregate national decarbonisation pathways to LAU and other intermediate NUTS levels.
The ELIAS 2.0 software allows the identification of the footprints of rapidly ascending air streams in the atmosphere at substantially reduced computational costs compared to a conventional trajectory approach.
Eventdisplay is a reconstruction and analysis pipeline for data of Imaging Atmospheric Cherenkov Telescopes (IACT).
FAIRCORE4EOSC: Beta Release Demo (Archive, Reference, Describe, Cite)
FairMQ is designed to help implement large-scale data processing workflows needed in next-generation particle physics experiments.
FAME is the open Framework for distributed Agent-based Modelling of Energy systems. Its purpose is supporting the rapid development and fast execution of complex agent-based energy system simulations.
Fastscape is a set of open-source software components aimed at making landscape evolution models and topographic analysis algorithms readily accessible to a wide range of users.
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.
A fully automated deep learning pipeline for adipose tissue (visceral and subcutaneous) segmentation on abdominal Dixon MRI.
FESOM (Finite-Element/volumE Sea ice-Ocean Model) is a multi-resolution sea ice-ocean model that solves the equations of motion on unstructured meshes.
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).
This kit simplifies the deployment of the open-source Internet-of-Things (IoT) platform FIWARE
Use python decorators for authorising access to OIDC authenticated REST APIs
FLEUR is a feature-full, freely available FLAPW (full-potential linearized augmented-plane-wave) code, based on density-functional theory. This highly precise all-electron approach is universally applicable to all atoms of the periodic table and to systems with compact as well as open structures.
A deep-learning based multi-omics sequencing data integration suite
FlowStrider automates data flow-based threat modeling
A data management and collaboration platform based on Forgejo and extended with git-annex support. Essentially a git forge for data projects. It interoperates well with DataLad and provides a nice collaborative web hosting for datasets containing issue trackers, pull requests, CI, and more.
FormatFuzzer is a framework for high-efficiency, high-quality generation and parsing of binary inputs.
FraCSPy (Framework for Conventional microSeismic Processing) is an open-source Python library focused on providing conventional microseismic monitoring tools, particularly for the purpose of benchmarking newly proposed algorithms and workflows.
Legacy software for quasielastic neutron scattering data analysis.
This package provides quality assurance / quality control scripts for FastSurfer- or FreeSurfer-processed structural MRI data.
A framework to study the thermo-chemical evolution of rocky and icy bodies (planets, moons, and planetoids) on a global scale in the solar system and beyond.
GasNetSim is a simulation package designed for gas network steady-state simulation.
It supports the steady-state natural gas network simulations with different gas mixture
compositions, thus enabling accurate analysis of the impacts of hydrogen injection on the gas network.
GeoMultiSens provides an integrated processing pipeline to support the analysis of homogenized data from various remote sensing archives.
The unique GFZ software gfzrnx plays a central role for the processing of RINEX files from GNSS observations. The toolbox for file check and manipulation supports RINEX observation, navigation and meteorological data.
Ginkgo is a high-performance math library for the solution of sparse linear systems on GPUs (AMD, Intel, NVIDIA). Ginkgo is implemented using modern C++ and provides preconditioned Krylov solvers, multigrid, sparse direct solvers, mixed precision, and batched functionality.
A collection of software utilities that aid with initial pre-processing of recorded (seismic) data supporting users that borrow instruments from the GIPP.
git-annex allows managing large files with git, without storing the file contents in git. It can sync, backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the power and distributed nature of git to bear on your large files with git-annex.
GLAES (Geospatial Land Availability for Energy Systems) is a geospatial framework for land eligibility analyses (LEA) to incorporate various geodata into one assessment. It also allows to optimally distribute placements. The workflow is applicable to any context where land constraints are needed.
GBD is a comprehensive suite of tools for provisioning and sustainably maintaining benchmark instances and their metadata for empirical research on hard algorithmic problem classes.
GMGPolar is a geometric multigrid solver using implicit extrapolation to raise the convergence order. It is based on meshes in tensor- or product-format. GMGPolar's focus applications are geometries that can be described by polar or curvilinear coordinates for which suited smoothing is available.
Global Optimization of Atomistic Configurations by Coulomb
GOLEM is a modelling platform for thermal-hydraulic-mechanical and non-reactive chemical processes in fractured and faulted porous media, based on the MOOSE framework
The go-oidfed library is an implementation of OpenID Federation in the go language with the goal to enable go applications to make use of OpenID federation.
GravIS visualizes and describes Level-3 products based on the most recent GRACE and GRACE-FO data release from GFZ and the Combination Service for Time-Variable Gravity Fields (COST-G) of the International Gravity Field Service (IGFS).
A collection of tools for (quantum) gravimeter data processing.
Process raw gravity data including all necessary corrections in a well documented and reproducible way to obtain final absolute gravity measurement values, create measurement PDF reports or live-monitor your ongoing measurement.
GR is a framework for cross-platform visualization applications
for interactive plots or live displays of instruments. GR can easily be embedded in Qt applications or Jupyter notebooks. It can produce publication quality plots and provides interfaces for C, Julia, Python, Rust and JS.
GSTools is a Python-based software suite for solving a wide range of geostatistical problems. GSTools provides methods for generating different classes of correlated random fields; it can perform kriging, variogram estimation and much more.
A C++ framework for collaborative engineering
Habitat Sampler (HaSa, Community Version), an innovative tool that autonomously generates representative reference samples for predictive modelling of surface class probabilities.
hCoCena is an R-package that allows you to comprehensively and easily analyse your transcriptomics data. It also provides the option to integrate several datasets using a network-based integration approach and analyse them jointly. Tutorials and a Docker image exist to help you get to know the tool.
Heat is a flexible and seamless open-source software for high performance data analytics and machine learning. It provides highly optimized algorithms and data structures for tensor computations using CPUs, GPUs and distributed cluster systems on top of MPI.
HeatNetSim is a simulation package designed for the simulation of unidirectional and bidirectional networks such as fifth generation thermal networks. It can be used for both steady-state simulations and additionally enables a dynamic temperature calculation.
HELDA (Helmholtz MCDA Tool) is a generic MCDA software with features tailored for sustainability assessment.
The guidance system HELIPORT aims to make the entire life cycle of a scientific project according to the FAIR principles. In particular, our data management solution deals with the areas from the generation of the data to the publication of primary research data, the workflows and results.
The Helmholtz Research Software Directory is a place to discover and promote research software. Designed for Research Software Engineers and Scientists, it aims to foster FAIR and reuseability of software.
Implementation of the HERMES workflow to automate software publication with rich metadata.
Model Training and Evaluation for Higgs Dataset
Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.
The HIPpocampal Shape and Thickness Analysis Toolbox (HIPSTA) present a geometry-based method for the analysis of local hippocampal thickness and curvature and constructs an intrinsic coordinate system (unrolling/flattening) for statistical analysis across multiple participants.
HoloWizard is a software to reconstruct near-field holograms form x-ray microscopy experiments and other sources.
The hybridMT is MATLAB/shell environment software package for the seismic moment tensor inversion in time domain. The package allows to estimate fault plane parameters and the balance between volumetric and non-volumetric strain in the seismic source using different decomposition schemes.
A Python package to model radiative response to various aircraft emissions at different altitudes and latitudes. The model combines empirical emission sensitivities with linear interpolation to estimate total radiative effects.
ICGEM is archiving all global Earth gravity field models in citable form (DOIs). ICGEM provides visualization of the archived models incl. their differences and time variation. ICGEM is coordinated by the International Gravity Field Service (IGFS) of the International Association of Geodesy (IAG).
The Python script OMR_model.py allows to simulate oxygen membrane reactors with continuous gas flow rates.
IGMAS+ (Interactive Gravity and Magnetic Application System) is a software combining 3-D forward and inverse modeling, interactive visualization and interdisciplinary interpretation of potential fields and their applications under geophysical and geological data constrains.
ILTpy is a python library for performing regularized inversion of one-dimensional or multi-dimensional data without non-negativity constraint. Primary applications include magnetic resonance (NMR, EPR), and electrochemical impedance spectroscopy (distribution of relaxation times; DRT).
IPPL is a C++ library to develop performance portable code for fully Eulerian, Lagrangian or hybrid Eulerian-Lagrangian methods. IPPL supports simulations in one to six dimensions, mixed precision, and asynchronous execution in different execution spaces (e.g. CPUs and GPUs).
Inst.dlr is an instrument metadata database which follows the PIDINST schema. The application is a python package which handles transactions with a MongoDB database. Also, it uses FastAPI to create end-points for the user to introduce data or retrieve entries from the database.
InteractiveComplexHeatmap is an R package that converts static heatmaps produced from ComplexHeatmap package into an interactive Shiny app only with one extra line of code.
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.
ioProc is a light-weight workflow manager for Python ensuring robust, scalable and reproducible data pipelines. The tool is developed at the German Aerospace Center (DLR) for and in the scientific context of energy systems analysis, however, it is widely applicable in other scientific fields.
Collection of code for working with offline complex valued time series data in Python.
In Situ Animation of Accelerated Computations
The Joint Application, Review, and Dispatch Service (JARDS) is a software for the management of allocation processes for High Performance Computing (HPC) resources. It is a web application based on PHP and JavaScript using open source libraries like Symfony, , jQuery, Bootstrap and DataTables.
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource.
JEMRIS is a versatile, open-source, multi-purpose MRI simulator. It is well-suited for research and education.
JPlag is one of the most popular source code plagiarism detection systems worldwide.
JTrack is a software(s) and mobile application ecosystem for digital biomarkers collection and remote assessment. JTrack is designed to collect health-related information from participants' smartphones. It also has a clinicians and administration dashboard for study, user, and data management.
JUBE is a generic, lightweight, configurable environment to run, monitor and analyse application execution in a systematic way. This software is commonly used to execute benchmarks and complex workflows on High Performance Computers, but is not limited to these systems.
The Korringa-Kohn-Rostoker (KKR) Greens function method is a highly accurate all-electron method to perform density functional theory calculations for the prediction of materials properties based on quantum mechanical simulations.
Julearn aims to provide an easy-to-use but flexible interface to build predictive models with cross-validation (CV) consistent performance estimates. It poses as a solution accessible to domain experts without extensive ML training, enabling them to quickly fit and evaluate ML algorithms.
The python package `JumpDiff` offers methods to generate and analyze stochastic processes that are described by a jump-diffusion process.
JuMPER (Jülich open access Modelling Platform for Electrochemistry Research) is a collaborative platform designed for modelling and analyzing electrochemical processes. It supports open access research on electrochemical devices, including fuel cells, electrolyzers and batteries.
JuPedSim is a framework designed to support students and researchers in investigating pedestrian dynamics and conducting research related to the development and validation of new models or model features. It enables the analysis of experiments and facilitates the proper visualization of results.
JupyterHub Outpost can be used as an additional, external source to start and manage single-user servers. Like in JupyterHub itself, different Spawners can be configured at the Outpost. It's best used together with the jupyterhub-outpostspawner configured at JupyterHub.
The OutpostSpawner in combination with the JupyterHub Outpost service enables JupyterHub to spawn single-user notebook servers on heterogenous remote resources.
The Juelich Rapid Spectral Simulation Code (JURASSIC) is a fast infrared radiative transfer model for the analysis of atmospheric remote sensing measurements.
JURI (Jülich Reporting Interface) provides a template-driven fully client-based web framework to visualise data lists and associated data graphs.
Kaapana is an open source toolkit for state of the art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging.
Kadi4Mat is a generic and open source virtual research environment.
Network generators help to provide synthethic instances with controllable parameters by algorithm developers and researchers. KaGen provides generators for a large variety of network models, which are communication-free by making use of pseudorandomization and divide-and-conquer schemes.
KaHyPar is a fast, high-quality, and scalable algorithm for partitioning graphs and hypergraphs with billions of edges. It finds applications in minimizing communication costs for distributed (hyper)graph computations, quantum circuit simulations, storage sharding in databases, and VLSI design.
Shared-Memory and Distributed-Memory Graph Partitioning
KaMPIng is a flexible and (near) zero-overhead C++ wrapper for MPI, covering the whole range of abstraction levels from low-level MPI calls to convenient STL-style bindings. This allows for both rapid prototyping and highly engineered distributed algorithms.
KaRRi is a state-of-the-art dispatcher for the dynamic taxi sharing problem with meeting points. KaRRi utilizes highly engineered many-to-many shortest path queries to compute optimal assignments of riders to vehicles and according meeting points within milliseconds.
KD-Tree Implementation in Python
KeY is a deductive verification system for Java programs
An aXiomatic Tactical Theorem Prover for Hybrid Systems
KinFit can be used for kinematic fitting in particle and hadron physics experiments. The iterative procedure is based on the Langrange multiplier technique. Constraints such as mass, vertex and momentum conservation are included.
The Python package `kramersmoyal` provides functions to analyze stochastic drift-diffusion and discontinuous stochastic processes in observational and experimental data.
Library to compute the Fourier-Laplace transform of the stretched exponential function.
LaPy is an open-source Python package for differential geometry on triangle and tetrahedra meshes. It includes an FEM solver to estimate the Laplace, Poisson or Heat equations, also the computations of gradients, divergence, mean-curvature flow, conformal mappings, geodesics, ShapeDNA and more.
Complex error function library
LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets and live data streams using a stream-based programming model. The current focus is pixelated scanning transmission electron microscopy (4DSTEM) and scanning electron beam diffraction data.
LightHouse helps to navigate the wild and complex sea of OpenID Federation.
LightHouse is a flexible and configurable OpenID Federation Entity, and can be used as a Trust Anchor / Intermediate Authority / Resolver / Trust Mark Issuer or everything at the same time.
The lightning-uq-box is a PyTorch library that provides various Uncertainty Quantification (UQ) techniques for modern neural network architectures.
LinMOG is a collection of tools for the generation of linear models for
univariate and multivariate functions. Furthermore, the linear model can be
automatically transformed into a MILP optimization formulation.
LiSSA: A Framework for Generic Traceability Link Recovery
In software development and maintenance, numerous artifacts such as requirements and code are produced. LiSSA aims to provide a generic solution for Traceability Link Recovery (TLR) by utilizing LLMs in combination with RAG techniques.
LLAMA is a cross-platform C++17/C++20 header-only template library for the abstraction of data layout and memory access. It separates the view of the algorithm on the memory and the real data layout in the background.
LLview is a set of software components to monitor clusters that are controlled by a resource manager and a scheduler system.
LYNX (Lithosphere dYnamics Numerical toolboX) is a novel numerical simulator for modelling thermo-poromechanical coupled processes driving the deformation dynamics of the lithosphere.
maftools is a comprehensive toolkit for processing somatic variants from cohort-based cancer genomic studies
Mainzelliste is an extensible web-based pseudonymisation tool used for generating and managing the pseudonyms from identifying data which supports multiple ways of secure, error-tolerant record linkage.
Automated Reasoning in HPC and Cloud Environments: Scheduling, Solving, Proving
This project provides a framework for fast memory managers on many core accelerators. It is based on alpaka to run on many different accelerators and implements the ScatterAlloc algorithm.
MapMan visualises data from gene expression analyses. Genes or proteins with a common function are visualised and evaluated together. Mercator assigns the annotations for this. Changes in processes and pathways can be revealed, visualised and evaluated quantitatively.
MassBank is an open source mass spectral library for the identification of small chemical molecules of metabolomics, exposomics and environmental relevance.
MALA (Materials Learning Algorithms) is a data-driven framework to accelerate electronic structure calculations based on machine learning. Its purpose is to construct neural-network surrogate models for bypassing computationally expensive steps in state-of-the-art density functional simulations.
matRad is a dose calculation and inverse treatment planning toolkit for radiotherapy research and education written in Matlab.
Calculation of pristine and damaged composite structures
me-compute: a Python software to download events and data from FDSN web services and compute their energy magnitude (Me)
A free and open-source software for the development of interactive medical image processing applications. MITK provides a powerful and free application called the MITK Workbench, which allows users to view, process, and segment medical images.
MemBrain v2 aims to facilitate the analysis of membranes in cryo-electron tomography data.
It consists of the components membrain-seg for membrane segmentation, membrain-pick for membrane protein localization, and membrain-stats for the extraction of membrane-based metrics.
MemRBC is an R package for spectral modeling of red blood cell shapes in R. It is the result of open science research, demonstrating the idea of hi-level apps with metadata creation in a lightweight obejct oriented approach.
The marine mercury cycling model MERCY v2.0 is a chemistry transport and bio-accumulation model for mercury (Hg). It implements all known processes for marine (pelagic and benthic) Hg cycling into a biogeochemical 3D ocean-ecosystem model.
https://gmd.copernicus.org/preprints/gmd-2021-427/
Merkle-Directed Acyclic Graph (DAG) in MATLAB
The tool MeshIT generates quality tetrahedral meshes based on structural geological information. It has been developed at the GFZ Potsdam and some extensions were later added by PERFACCT. All procedures are fully automatized and require at least scattered data points as input.
MESSy is a software framework for the assembly of Earth System Models with components, which are numerical representations of processes in the Earth system. The unique feature of MESSy is its modular structure that facilitates continuous development and flexible model configurations.
Analysis of Microcalorimetric Metabolic Data Using Monod's Equation.
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing.
The mission of Metrics Reloaded toolkit is to guide researchers in the selection of appropriate performance metrics for biomedical image analysis problems and to provide a comprehensive online resource for metric-related information and pitfalls.
The Python package `MFDFA` provides the tools to perform a multifractal detrended fluctuation analysis that enables the investigation of stochastic processes where long-range memory and persistence are necessary to consider.
The mesoscale Hydrologic Model (mHM) is a well established hydrological model used by the scientific community. It is under active development with dozens of contributors and has an open community always interested in discussions.
Mibianto is an easy to use web service for efficient compositional analysis of metagenomic sequencing data.
By using FracMinHash on client side the uploaded sequence data is anonymized and drastically reduced in size.
MiCoFaM (Micromechanical Composite Fatigue Modeler) is a model generator for creating representative volume elements (RVEs) consisting of fibre, interface and matrix phases for a given fiber volume content with randomized fiber placements. The application is provided as an ABAQUS plug-in.
Graphical User Interface (GUI) software for analyzing nanoindentation experimental data
Millepede II has been developed to solve the linear least squares problem with a simultaneous fit of all global and local parameters, irrespectively of the number of local parameters.
Minion is an optimization library designed for solving complex optimization problems where gradients are unavailable or unreliable. It implements state-of-the-art evolutionary algorithms which are often missing in standard optimization libraries.
Minterpy is an open-source Python package for multivariate polynomial interpolation as well as related tasks, like nonlinear polynomial regression, numerical integration, global optimization, level-set methods, and much more.
MIRP is a python package for quantitative analysis of medical images. It focuses on processing images for integration with radiomics workflows. These workflows either use quantitative features computed using MIRP, or directly use MIRP to process images as input for deep learning models.
MLAir (Machine Learning on Air data) is an environment that simplifies and accelerates the creation of new machine learning (ML) models for the analysis and forecasting of meteorological and air quality time series.
Raytracing code for x-ray spectrometers with (not only) mossaic crystals
Helps with design and analysis of x-ray spectrometers. Useful tool for (rather) experienced physicist.
mDIS is a database management application for capturing and curating meta data on geological samples, drilling progress, and related datasets such as images or geophysical well logs. It is easily adaptable and ensures that all data is compiled and quality controlled in one place.
MO|DE.behave is a Python-based software package for the estimation and simulation of
discrete choice models and shall enable rapid quantitative analyses based on survey data on choice behavior, utilizing advanced discrete choice methods. Please refer to 'doi.org/10.21105/joss.05265'.
MooViE is an easy-to-use tool to display multidimensional data with input-output semantics from all research domains. It supports researcher in studying the mapping of several inputs to several outputs in large multivariate data sets.
enable SSH with federated identities
Massive-Parallel Trajectory Calculations (MPTRAC) is a Lagrangian particle dispersion model for the analysis of atmospheric transport processes in the free troposphere and stratosphere.
For discussion of the possibilites of research flights, the Mission Support System (MSS) was developed. This software helps to review a big amount of metereological and model data by viewing the forecasted parameters of interest along possible regions of a proposed flight path.
MTRESS (Model Template for Renewable Energy Supply Systems) facilitates the creation of energy system optimisation models for individual residential and commercial buildings as well as for neighbourhoods and entire industrial properties.
This software publication is released by Helmholtz-Zentrum Dresden-Rossendorf according to FAIR principles. It contains experimental research work for the numerical simulation of multiphase flows. The development is based on the open-source software released by the OpenFOAM Foundation.
Mytoken is a web service to obtain OpenID Connect Access Tokens in an easy but secure way for extended periods of time and across multiple devices. In particular, mytoken was developed to provide OIDC Access Tokens to long-running compute jobs.
NEST is a simulator for spiking neuronal networks. A well tested and efficient tool, NEST works on your laptop and also on the world’s largest supercomputers to study behaviour of large networks of neurons.
NESTML is a domain-specific language for neuron and synapse models. It combines an easy to understand, yet powerful syntax with good simulation performance by means of code generation.
The Nuclear Elastic X-ray scattering Universal Software (Nexus) is a Python package for simulating and fitting of Mossbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities, and polarization dependent electronic scattering.
Automatic configuration and training of U-Net-based segmentation pipelines. Works out-of-the-box for a broad range of datasets from all imaging domain! Supports 2D and 3D (multi-channel) images.
TCP Communication with Node.js
TLS Communication with Node.js
Web-based interactive editor for creating, editing and visualizing research object crates.
novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data. An existing reference database of marker genes is not required, but significantly enhances performance if available.
The O3as service provides tools to extract essential information on ozone trends from large climate prediction model data and allows the production of scientifically valuable figures coherently.
A tool to migrate sensor metadata from the observation data model to the Helmholtz Sensor Management System via API.
Ocean Data View (ODV) - Interactive exploration, analysis and visualization of oceanographic and other environmental data.
oemof.solph is a model generator for energy system modelling and optimisation. It facilitates the formulation of (mixed-integer) linear programs from a generic graph-based structure, allowing to create multi-sector models on different levels of detail with user-defined time-resolution.
OFFA offers easy to use OpenID Federation Authentication and Authorisation for existing services. OFFA can be deployed along existing services and handle all OpenID Federation communication for your services.
oidc-agent is an OpenID Connect tool suite designed to simplify authentication processes for command-line applications and workflows that require access to resources protected by OIDC. It provides a secure, but user-friendly way to manage tokens on the command-line.
openCARP is a multiscale cardiac electrophysiology simulator for in silico experiments ranging from single heart cells and cardiac tissue to organ models up to the body surface ECG.
openFuelCell2 is a computational fluid dynamics (CFD) toolbox for simulating electrochemical devices such as fuel cells and electrolysis. The solver is based on the open-source library, OpenFOAM®.
OpenGeoSys (OGS) is a scientific open source project for the development of numerical methods for the simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fractured media.
openPMD is an open meta-data schema that provides meaning and self-description for datasets in science and engineering.
This library provides a reference API for openPMD data handling, supporting established I/O backends such as HDF5, ADIOS2, JSON and TOML from serial to MPI-parallel workflows.
Open-source Python toolbox called OSADCP for scientists to convert, clean, calibrate and organize binary raw vessel-mounted Acoustic Doppler Current Profiler (ADCP) data for scientific use. The toolbox is designed to process ADCP measurements in deep water by Teledyne RDI Ocean Surveyor ADCPs.
The otter Framework combines community network analysis using Co-Occurrence networks, Louvain Clustering and Convergent Cross Mapping networks.
Funding through the Helmholtz DataHub Initiative; project iLOVE.
Palladio is a software architecture simulation approach which analyses software at the model level for performance bottlenecks, scalability issues, reliability threats, and allows for subsequent optimisation.
The PaN Training Catalogue is a fork from the TeSS Training Catalogue (ELIXIR) and was initially developed in our Photon and Neutron (PaN) projects ExPaNDS and PaNOSC.
ParFlow is a parallel, integrated hydrology model that simulates spatially distributed surface and subsurface flow.
This header-only library contains a highly tuned (uncompressed) bit vector implementation with multiple space efficient rank and select support data structures. Our fastest rank and select support has a space overhead of only ~3.51% and makes use of data level parallelism via SIMD instructions.
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.
PeakPerformance is a Python toolbox for estimating peak areas from mass-spectrometry or HPLC datasets under uncertainty. It applies Bayesian inference using the PyMC library to parametric models of peak curves.
PeCon.py is a Python-Software, that enables the calculation of the ionic and electronic conductivities of Perovskite-type ceramic materials, i.e. the conductivities within oxygen-transport ceramic membranes.
PedPy is a Python library for the analysis of pedestrian movement data.
The PEPC project (Pretty Efficient Parallel Coulomb Solver) is a public tree code that has been developed at Jülich Supercomputing Centre since the early 2000s. Our code is a non-recursive version of the Barnes-Hut algorithm, using a level-by-level approach to both tree construction and traversals.
PeriHub is a platform that provides a numerical implementation of the peridynamic theory. It is an extension of the open source Peridigm software. Peridynamics is a non-local theory that overcomes discontinuity problems of the classical theory of continuum mechanics.
PeriLab is a Software to solve Peridynamic problems. It is written in Julia to overcome many issues related to the Software Peridigm.
perun is a Python package that calculates the energy consumption of Python scripts by sampling usage statistics from hardware interfaces. It can handle MPI applications, gather data from hundreds of nodes, and accumulate it efficiently.
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.
Codemeta conversions tool
The PIA Software is a Python analysis software to derive time series data (Level 1) and temperature spectra (Level 2) of INP concentrations from measurements with the PINE (Portable Ice Nucleation Experiment) instrument.
PIConGPU is a relativistic Particle-in-Cell code running on graphic processing units as well as regular multi-core processors. It is Open Source und is freely available for download. It can be used to study plasmas with relativistic dynamics, solving the Maxwell-Vlasov system of equations.
PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.
A new metric named 'dependency heaviness' is proposed that measures the number
of additional dependency packages that a parent package brings to its child package
and are unique to the dependency packages imported by all other parents.
PointNeighbors.jl is a package for neighborhood search with fixed search radius in 1D, 2D and 3D point clouds.
PostWRF is a bunch of interactive tools, written in NCL and Bash scripts, to visualize and post-process the WRF and ERA5 model outputs.
PORT is a software package dedicated to the analysis of modern and historical Very Long Baseline Interferometry (VLBI) observations. It is utilized to perform the GFZ VLBI Analysis Center responsibilities, as well as state-of-the-art research in space geodesy, geophysics, and astrometry.
PROFASI (PROtein Folding and Aggregation SImulator) is a C++
package for HPC Monte Carlo simulations of protein folding and aggregation. It
provides an all atom, implicit solvent force field, and a set of tools to
perform Monte Carlo simulations. A plugin mechanism allows for user extensions.
An asynchronous evolutionary optimization algorithm and software package for global optimization and hyperparameter search on high-performance computers.
PIA is a free open-source eResearch System for monitoring of incident events and provides a digital infrastructure for conducting population-based studies in any research field - at a study centre or at home. PIA focuses on repeated surveys.
#DigitalEpidemiology #LongitudinalDataCollection #FOSS
A cross-platform, open-source inverse modeling toolbox for conventional and Fourier ptychography
A Python library to read and manipulate RSCAD® draft files, used for power system modeling and simulation on RTDS simulators.
A python toolbox for deriving rainfall information from commercial microwave link (CML) data.
py-cordex is a Python library for managing CORDEX grids, handling rotated/projection-based domains, and supporting CMORization of regional climate data. It enables compliant metadata, grid generation, and integration with xarray for climate workflows.
Pydidas (Python diffraction data analysis suite) is a toolkit for the analysis of X-ray diffraction datasets. It is designed to be accessible also for domain scientists with little experience in diffraction data analysis.
Pydidas includes a graphical user interface and a command line interface.
pyGMS: lithosphere-scale rheological analyses of GMS models with Python
PyPlaque is an open-source Python package for automated analysis of virus plaque assays. It quantifies plaque morphology, size, and intensity from plate images, integrates with Python data tools, and enables reproducible, customizable workflows for high-throughput infection biology studies.
A slim python library to link maps and sampling data with prediction methods. Needs scipy, numpy, matplotlib, pykrige, osgeo, rasterio.
pySDC is a Python implementation of the spectral deferred correction approach and its flavors, esp. the parallel-in-time extension PFASST. It is intended for rapid prototyping and educational purposes. New ideas can be tested and first toy problems can be easily implemented.
PyTango is a python module that exposes to Python the complete Tango C++ API. This means that you can write not only Tango applications (scripts, CLIs, GUIs) that access Tango device servers but also Tango device servers themselves, all of this in pure python.
Python interface to ICAT and IDS
Harmonized interfaces and workflows to selected software development tools
is a software package containing a collection of exemplary application implementations based on quark.
is a software package to support the mapping of combinatorial optimization problems to quantum computing interfaces via QUBO and Ising problems.
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.
The software quantifies climate impact of hypersonic aircraft trajectories as a number and within seconds instead of very long numerical simulations that produce Petabytes of data. The input requires water vapor, hydrogen and nitrogen oxide emission data along flight trajectories.
RadiationDosePlan- Image/Biomarker-Outcome-platform (RPB) is a collection of open source software systems integrated via portal to deliver a core software infrastructure necessary to support the operation of non-commercial trials unit.
RAFCON uses hierarchical state machines, featuring concurrent state execution, to represent robot programs. It ships with a graphical user interface supporting the creation of state machines and contains IDE like debugging mechanisms.
A simple tool to generate points on the (n−1)-dimensional simplex.
Rankings Reloaded is an open-source toolkit for robust and accurate benchmark visualization and ranking. It is an out-of-the-box and open-source framework for analyzing and visualizing algorithm results in an accurate way. It uses challengeR and brings advantages of it with user-friendly interface.
Optical Simulation Software for Synchrotron Radiation
RCE is a distributed integration environment for scientists and engineers to analyze, optimize, and design complex systems like aircraft, ships, or satellites.
All-in-one component for rendering an elastic search UI for searching anything. Built-in support for visualizing related items in a graph and resolving unique identifiers. Initially built for searching Fair-DOs.
Reflectorch is a Python package for the analysis of X-ray and neutron reflectivity data using Pytorch-based neural networks. It provides fast simulation of reflectometry curves by GPU, parameterization via YAML configuration files, and prior-aware training.
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.
ReStore for MPI programs enables scalable in-memory recovery of data after process failures via an appropriate data distribution and replication. It supports shrinking and replacing recovery-schemes and is substantially faster than parallel file system based approaches.
GREAT is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm, also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application.
RiboDetector is designed to rapidly and accurately detect rRNA sequences from metagenomic, metatranscriptomic, and ncRNA sequencing data. It has been optimized for use with both CPUs and GPUs. It outperforms existing software by delivering 10-50x faster runtime and ~10x fewer false classifications.
A Java library to create and modify RO-Crates. The aim of this implementation is to not require too deep knowledge of the specification, and avoiding crates which do not fully comply to the specification, at the same time.
A frontend to parse and analyze RTLola specifications
An interpreter for RTLola specifications
The S2Downloader allows to download Sentinel-2 L2A data from the cost-free element84 AWS Amazon server. It specifically serves the purpose to download data for user-defined area of interests (AOI). It offers several parameters for filtering the data, can stack the results, mosaic and crop to AOI.
SampleDB is a web-based electronic lab notebook with a focus on sample and measurement metadata. With SampleDB, you can track each step in the sample lifecycle and its schema system allows you to define exactly what metadata should be stored for each process, from a simple check box to time series.
A consistent, extensible, easy-to-use tool/framework for reproducible quality control of time series data.
Open-source InSAR time series analysis software developed within the project SAR4Infra. SARvey aims to analyze InSAR displacement time series for engineering applications.
The Scalasca Trace Tools support performance optimization of parallel programs with a collection of highly scalable trace-based tools for in-depth analyses of concurrent behavior, in particular with respect to communication and synchronization, and offers guidance in exploring their causes.
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
A tool to benchmark Time-series on different databases.
Score-P provides insight into massively parallel HPC applications, their communication, synchronization, I/O, and scaling behaviour to pinpoint performance bottlenecks and their causes.
scPower is a statistical framework for design and power analysis of multi-sample single cell transcriptomics experiments. It enables users to identify the optimal experimental parameters for cell type specific inter-individual DE and eQTL analysis using single cell RNA-seq data given a fixed budget.
Simple machine learning tool in Python computing an anomaly score of seismic waveform amplitudes. By using a pre-trained Isolation forest model, the program can be used for identification of outliers in semismic data, assign robustness weights, or check instruments and metadata errors
SeisBench is an open-source Python toolbox for machine learning in seismology. It brings together the whole machine learning model lifecycle: datasets and benchmarks, models and training pipelines, and efficient implementations for deploying the models in production.
SeisComP is a widely distributed seismological software package for real-time monitoring of earthquakes and other seismic events and provides for data acquisition, processing, distribution and interactive analysis. It has been developed within the GEOFON Program by GFZ and gempa GmbH.
The Sensor Management System (SMS) allows the comprehensive acquisition, administration and export of meta data of platforms, sensors and measurement configurations by stations and campaigns operated in the Helmholtz research field Earth & Environment.
The Simulation EnviRonment for Geomorphology, Hydrodynamics and Ecohydrology in Integrated form (SERGHEI) is a multi-dimensional, multi-domain, and multi-physics model framework for environmental and landscape simulation, intended to simulate water flow and transport across landscape scales.
sfctools is a modeling suite for agent-based, macroeconomic and stock-flow consistent (ABM-SFC) modeling written in Python. It concentrates on agents in economics and provides a graphical model design interface.
shepard is a multi-database storage system for highly heterogenous experimental research data. Simple connection options via standardized interfaces enable the automated recording of data including an annotation with meta information.
A perfect hash function is a function that has no collisions on a given set. ShockHash constructs very compact perfect hash functions significantly faster than previous approaches.
A perfect hash function is a function that has no collisions on a given set. SicHash places objects in a cuckoo hash table and then stores the final hash function choice of each object in a retrieval data structure. Using irregular cuckoo hashing, each object has a different number of hash functions
Signal Processor in Python
Simulation of CSDs for Automated Tuning Solutions (SimCATS) is a python framework for simulating charge stability diagrams (CSDs) typically measured during the tuning process of qubits.
This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.
SIMPA facilitates realistic simulations for optical and acoustic imaging modalities by providing a communication layer between various forward and inverse models. Non-experts can easily create sensible simulations from default parameters and domain experts can set up a highly customisable pipeline.
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.
simtools is a toolkit for simulations of ground-based imaging Cherenkov observatories like the Cherenkov Telescope Array Observatory (CTAO). It allows to set, derive, and manage simulation model parameters describing the observatory and to configure and execute large-scale simulation productions.
SMASH is a relativistic hadronic transport approach for the dynamical description of heavy-ion reactions. It is a microscopic non-equilibrium approach and incorporates all well known hadronic states and their interactions.
SMG2S (Sparse Matrix Generator with Given Spectrum) is able to generate large-scale non-Hermitian and non-Symmetric matrices in parallel with the spectral distribution functions or eigenvalues given by users, and the spectrum of generated matrix is the same as the one specified by the users.
Somesy (software metadata sync) is a CLI tool to avoid messy software project metadata by keeping it in sync.
SpatialData is an open and interoperable data framework for ingesting, representing, processing and visualizing spatial omics datasets.
An integrated cloud-ready geospatial data management system.
SpecHomo is a Python package for spectral homogenization of multispectral satellite data, i.e., for the transformation of the spectral information of one sensor into the spectral domain of another one.
Spex is a computer code based on many-body perturbation theory and is part of the FLEUR code family. It uses the full-potential linearized augmented plane-wave method (FLAPW), which provides an accurate basis set for all kinds of materials including transition metals, oxides, and f-electron systems.
It visualizes data along an Archimedean spiral, makes so-called spiral graph or spiral chart.
It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high
resolution. 2. It is efficient for time series data to reveal periodic patterns.
Spirit is a platform-independent framework for atomistic spin-dynamics. It combines the traditional cluster workflow through a C-API with python bindings with modern visualisation capabilities in order to maximise scientists' productivity.
Stable Baselines3 (SB3) is a set of reliable implementations of reinforcement learning algorithms in PyTorch.
Data reduction software for materials diffraction
Simplify complex composite calculations. Launch and runtime environment for software projects developed by the Department of Structural Mechanics at the Institute of Lightweight Structures (DLR).
A Python library and command line application to download, process and visualize event-based seismic waveform segments, specifically designed to manage big volumes of data
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.
A Python package to model ozone column changes and radiative effects in response to various aircraft emissions at different altitudes over specific regions. The model combines empirical emission sensitivities to estimate effects of supersonic transport on ozone and radiation.
supervillain does Markov-Chain Monte Carlo for modified Villain constructions of quantum field theory.
Software Heritage API Client
t8code (spoken as "tetcode") is a C/C++ library to manage parallel adaptive meshes with various element types. t8code uses a collection (a forest) of multiple connected adaptive space-trees in parallel and scales to at least one million MPI ranks and over 1 trillion mesh elements.
The Tamarin Prover is a state-of-the-art tool for the analysis of security protocols, which underpin the security of modern distributed computing.
Our tool uses Temporal Behavior Trees (TBT), a novel formalism for monitoring specifications, to segment traces provided as CSVs. Developers input a trace, and the tool analyzes it using a TBT to identify which parts of the software worked and which didn’t, aiding in system analysis and debugging.
A web-based application for creating, publishing, and managing digital object identifiers (DOIs) especially for publications within the TERENO initiative.
TetraX is a package for finite-element-method (FEM) micromagnetic modeling with the aim of providing user-friendly and versatile micromagnetic workflows. Among other features, it allows to efficiently calculate spin-wave spectra in different magnetic systems of general geometries.
TiGL is a parametric aircraft geometry modeler. Using the CPACS file format and TiGL, you can model a wide range of aircraft, spacecraft and rotorcraft.
Tigramite is a python package for causal inference with a focus on time series data. It allows to efficiently estimate causal graphs from high-dimensional time series datasets (causal discovery) and to use graphs for the estimation and prediction of direct, total, and mediated effects.
A fully integrated and comprehensive timeseries management system
The Timeseries Management allows to store, visualise, organise and share timeseries data and provides access to a (broad) selection of data from different long-term projects and campaigns (e.g. TERENO, MOSES).
TiXI is a fast and simple XML interface library and could be used from applications written in C, C++, Fortran, JAVA and Python.
The Tomato Tools are a collection of graphical user interface applications related to the Acquisition, Curation and Management Workflow of marine image data.
The tools can be used as standalone applications or, using the Tomato Launcher, in conjunction to form whole workflows.
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.
TREAMS is an open-source program to perform T-matrix-based scattering calculations for nanophotonic systems. It focuses on efficiently solving the interaction in 1D, 2D, and 3D lattices of complex unit cells using quickly convergent lattice sums. It also solves the interaction in finite clusters.
TRIDEC Cloud serves functionality to handle and share threat specific information. It integrates services for obtaining event related geo-data, e.g. of earthquakes, for automated computations, e.g. of tsunami propagations, for mapping, summarizing, and communicating hazard specific data.
Trimmomatic is a command line tool that performs a variety of functions for Illumina paired-end and single-end sequencing data, including sequence trimming and adapter removal. It is a flexible and efficient NGS preprocessing tool, which greatly improves downstream applications.
Trixi.jl is a numerical simulation framework for conservation laws written in Julia with an extensible design with a fast implementation, Trixi.jl is focused on being easy to use for new or inexperienced users, including the installation and postprocessing procedures.
Particle-based multiphysics simulations in Julia
The Terrestrial Systems Modelling Platform (TSMP) is an open source framework implementing a scale-consistent, highly modular, massively parallel regional Earth system model. It represents transport and feedback processes of mass, energy and momentum across geo-ecosystem compartments and scales.
The Terrestrial Systems Modelling Platform (TSMP) is an open source framework implementing a scale-consistent, highly modular, massively parallel regional Earth system model. It represents transport and feedback processes of mass, energy and momentum across geo-ecosystem compartments and scales.
The Typed PID Maker enables the creation, maintenance, and validation of PIDs. It ensures the PID contains typed, machine-actionable information using validation. This is especially helpful in the context of FAIR Digital Objects (FAIR DOs / FDOs).
UKIS Cloud Shadow MASK (ukis-csmask) package masks clouds and cloud shadows in Sentinel-2, Landsat-9, Landsat-8, Landsat-7 and Landsat-5 images. Masking is performed with a pre-trained convolution neural network. It is fast and works directly on Level-1C data (no atmospheric correction required).
A universal transport distribution model written in Python.
Natural organic matter is the most complex chemical mixture on our planet. UME is an open access, browser-based tool that allows efficient, interactive, transparent, and reproducible exploration and evaluation of ultrahigh resolution mass spectra of complex organic matter.
UNICORE (UNiform Interface to COmputing REsources) provides tools and services for building federated systems, making high-performance computing and data resources accessible in a seamless and secure way for a wide variety of applications in intranets and the internet.
A Python3 library of uncertainty quantification (UQ) test functions
UrbEm enables in a modular manner downscaling of gridded regional emissions with specific spatial proxies based on a variety of open access, robust, sustainable and frequently updated sources. UrbEm can be applied to any urban area in Europe and provides methodological homogeneity between cities.
UrMoAC is a tool for computing accessibility measures, supporting aggregation, variable limits, and intermodality.
Automated workflow using deep learning for the analysis of videos containing oxygen bubbles in PEM electrolyzers: 1. preparing annotated dataset and training models to conduct semantic seg- mentation of bubbles and 2. automating the extraction of bubble properties for further distribution analysis.
VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples.
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The VAriable Source Cluster Analysis (VASCA) is an astronomy pipeline
for time-variable sources.
A command line utility to convert seismic P- and S-wave velocities in the lithospheric mantle to temperature and density, based on Goes et al. (2000).
A tool to derive battery electric vehicle energy demands from given trip data. venco.py provides normalized, aggregated electric vehicle fleet demand profiles for two cases: Uncontrolled charging and a technical (mobility-constrained) potential for controlled charging including vehicle-to-grid.
A Social-Ecological Systems (SES) model focussing on the adaptive behaviour of fishers facing regulatory, economic, and resource changes.
Vitess is an open source software package for the simulation of neutron scattering experiments that comprises all established instrument hardware such as neutron optics, wavelength selectors and a growing variety of samples.
View-based System Development on Consistent Models
VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is also capable of analyzing multiple types of spatially-aware data modalities.
WaTTS allows using any legacy service with federated identities, such as eduGain or google.
An implementation of the Workflow Execution Service API of the Global Alliance for Genomic Health (GA4GH), with the aim to be reliable for production purposes and robust and scalable.
Wavefront optic measurement and beam analysis tool: A modular software for analyzing laser beams profiles and the measurement of laser beam wavefronts using the Shack-Hartmann principle.
A wrapper framework around the WPS 4.0 server by 52° North to allow easy integration of command line scripts into WPS services.
WRaINfo is a software for real-time weather radar data processing. It is specifically designed for X-band weather radars of FURUNO. The software was developed by Helmholtz Innovation Lab FERN.Lab (GFZ Potsdam) and is distributed under Apache 2.0 license.
XCASCADE (3D) software models electron cascades in solids induced by X-ray impact or by an impact of high-energy electron in non-relativistic energy regime. The code can provide temporal and spatial characteristics of the excited electrons, such as their transient density and energy.
An extensible data flow diagram constraint analysis framework for information security
XDibias is a modular image analysis software system for processing and analyzing earth oberservation imagery. XDibias is developed at the DLR-IMF (Remote Sensing Technologies Institute) and the former Institute for Optoelectronics since the 1980s and a main software-knowledge repository of IMF.
A software package for modeling x-ray-induced dynamics of matter