Skip to main content
Ctrl K

All software

1289 software items. Page 10 of 27. 48 items per page.
433-480 of 1289

BIRCH

BIRCH is a powerful framework for organizing and using bioinformatics. BIRCH comes with hundreds of commonly-used tools, and allows you to customize your BIRCH site by adding new ones.

  • bioinformatics
  • BLAST
  • genomics
  • + 3
1
1

BrainBrowser

BrainBrowser is an open source JavaScript library exposing a set of web-based 3D visualization tools primarily targetting neuroimaging

  • 3D
  • brainbrowser
  • neurology
  • + 2
  • (CSS)
  • (HTML)
  • (JavaScript)
  • + 1
5
1

byteparsing

Parser library for reading custom binary files from Python.

  • Big data
  • Multi-scale & multi model simulations
  • Optimized data handling
  • (Batchfile)
  • (C++)
  • (CSS)
  • + 5
2
1

CBRAIN

CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.

  • CBRAIN
  • cluster
  • Data Analysis
  • + 6
  • (CSS)
  • (HTML)
  • (JavaScript)
  • + 3
14
1

ChemTools

ChemTools is a free and open source Python library for interpreting the results of quantum chemistry calculations.

  • atoms in molecules
  • conceptual dft
  • density matrices kinetic energy density
  • + 2
  • (Python)
1
1

dCacheFS

Python file-system interface for dCache storages.

  • Data
  • Inter-operability & linked data
  • Optimized data handling
  • + 1
  • ("Jupyter Notebook")
  • (Python)
1
1

Emo-spectre

Interactive visualization and exploration of multi modal time-series data and video

  • Visualization
  • Workflow technologies
  • ("Common Workflow Language")
  • (Dockerfile)
  • (JavaScript)
  • + 5
5
1

emvoice

A Python package for computing emotion expression-related features from speech signals.

  • Emotion expressions
  • python
  • Speech processing
  • (Python)
  • (Shell)
1
1

Lysander

Find people on Twitter given a small initial set of interesting people.

  • Text analysis & natural language processing
  • (Python)
1
1

GameBus FHIR Layer

Enable FHIR service for GameBus and beyond

  • Data Harmonization
  • FHIR
  • healthcare
  • + 1
  • (Dockerfile)
  • (Java)
  • (Shell)
5
1

Geodisy

Geodisy is a research data discovery tool that harvests information from existing research data repositories and displays applicable records onto a map-based search interface.

  • geospatial
  • metadata
  • research data
  • (CSS)
  • (HTML)
  • (Java)
  • + 6
1
1

IRIDA

Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, distributed, open source bioinformatics and analytical web platform that was developed to support real-time infectious disease outbreak investigations using whole genome sequencing data.

  • genomics
  • infectious disease
  • (CSS)
  • (Dockerfile)
  • (HTML)
  • + 6
3
1

ISAAC Chrome extension

Chrome Web Extension for support of the NWO ISAAC platform. This extension is not endorsed or developed by the NWO.

  • BibTeX
  • CITATION.cff
  • DataCite
  • + 1
  • (CSS)
  • (HTML)
  • (JavaScript)
  • + 1
2
1

i-VRESSE workflow-builder

Need to write a complex config file then the i-VRESSE workflow builder might be the tool for you.

  • Workflow technologies
  • (CSS)
  • (HTML)
  • (JavaScript)
  • + 3
5
1

Kernel Launcher

Dynamically compile GPU kernels and launch them easily and safely using C++ magic. Tight integration with Kernel Tuner results in blazing fast CUDA code that is maintainable and performance portable.

  • auto-tuning
  • CUDA
  • GPU
  • + 2
  • (C)
  • (C++)
  • (CMake)
  • + 3
2
1

LORIS

Longitudinal Online Research and Imaging System (LORIS) is a web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework for storing and processing behavioural, clinical, neuroimaging and genetic data.

  • Computational Neuroscience
  • database
  • neuroimaging
  • + 3
  • (CSS)
  • (GLSL)
  • ("Go Template")
  • + 10
8
1

Mahiru

A prototype for a federated, distributed data sharing and processing system.

  • Data processing
  • Data Sharing
  • Policies
  • + 1
  • (C)
  • (Dockerfile)
  • (Makefile)
  • + 2
2
1

Massive PotreeConverter

Use parallel processing to quickly convert large point cloud data sets to the format used by the Potree viewer.

  • Big data
  • Optimized data handling
  • (Python)
3
1

Mass Spec Studio

A user-friendly, fully extensible framework for mass spectrometry analysis.

  • mass spectrometry
  • proteins
1
1

MMSODA Toolbox for MATLAB

MATLAB toolbox for global optimization and state estimation of dynamic models using distributed computing.

  • (Batchfile)
  • (C)
  • (CSS)
  • + 5
3
1

Motus Wildlife Tracking System

The Motus Wildlife Tracking System (Motus) is an international collaborative research network that uses coordinated automated radio telemetry to facilitate research and education on the ecology and conservation of migratory animals.

  • conservation science
  • movement ecology
  • wildlife tracking
  • (R)
2
1

mzRecal

mzRecal recalibrates mass spectrometry (MS1) data in mzML format, using peptide identifications in mzIdentML.

  • mass spectrometry
  • proteomics
  • (Dockerfile)
  • (Go)
  • (Makefile)
  • + 2
2
1

NPLinker

Microbial natural products data mining by integrating genomics and metabolomics data

  • Data processing
  • multi-omics integration
  • (Makefile)
  • (Mustache)
  • (Python)
  • + 2
5
1

Open Computational Multiphysics

OpenCMP is a computational multiphysics software package based on the finite element method

  • Computational Fluid Dynamics (CFD)
  • computational Multiphysics
  • diffuse interface method
  • + 3
  • (Python)
  • (TeX)
1
1

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

  • C++
  • mass spectrometry
  • metabolomics
  • + 1
  • (Batchfile)
  • (C)
  • (C++)
  • + 15
27
1

OpenPNM

OpenPNM is an open source project aiming to provide porous media researchers with a ready-made framework for performing a wide range of pore network simulations.

  • Pore network modeling
  • (Makefile)
  • (Python)
5
1

openPSTD

openPSTD is a Python-based research software that allows efficient and detailed calculation of sound propagation in a 2D built environment. It is especially useful as a reference tool for other developed software on acoustic sound propagation.

  • Acoustics
  • GPU
  • python
  • (C)
  • (C++)
  • (CMake)
  • + 3
3
1

PAVICS

PAVICS is a virtual laboratory facilitating the analysis of climate data. It provides access to several data collections ranging from observations, climate projections and reanalyses. It also provides a Python programming environment to analyze this data without the need to download it.

  • analysis
  • climate
  • Climate change
  • + 5
  • (CSS)
  • (HTML)
  • (JavaScript)
  • + 3
25
1

PhenoTips

PhenoTips is a software tool that makes it easy for clinicians and researchers to draw pedigrees and collect structured phenotype data for patients with genetic disorders.

  • API
  • deep phenotyping
  • genogram
  • + 6
  • (Batchfile)
  • (CSS)
  • (HTML)
  • + 4
2
1

Plus Toolkit

Toolkit for data acquisition, pre-processing, calibration, and real-time streaming of imaging, position tracking, and other sensor data for medical applications.

  • 3D Slicer
  • electromagnetic tracking
  • image capture
  • + 7
  • (Batchfile)
  • (C)
  • (C++)
  • + 2
4
1

PoreSpy

PoreSpy is a collection of image analysis tools used to extract information from 3D images of porous materials (typically obtained from X-ray tomography).

  • image analysis
  • porous media
  • tomography
  • (Batchfile)
  • (Python)
  • (Shell)
2
1

qumia-train-scripts

Scripts and files related to ML training for the QUMIA project

  • Machine learning
  • Neuromuscular
  • ultrasound imaging
  • ("Jupyter Notebook")
  • (Python)
  • (Shell)
3
1

ROBIST

Robust Optimization by Iterative Scenario Sampling and Statistical Testing

  • optimization
  • python
  • (Python)
2
1

Rocket

Rocket is a framework for efficient execution of all-pair applications on heterogeneous platforms.

  • Big data
  • GPU
  • High performance computing
  • + 1
  • (C++)
  • (Cuda)
  • (Java)
  • + 2
1
1

rocrate-action-recorder

Python package to record calls of Python CLI commands into a Research Object Crate (RO-Crate). Supports RO-Crate 1.1 specification. Specifically the Process Run Crate profile.

  • Inter-operability & linked data
  • Workflow technologies
  • (Python)
1
1

Rucio deployment for KM3NeT

This repository contains the Rucio deployment for KM3NeT. It can be used as an example of how to deploy Rucio.

  • Big data
  • High performance computing
3
1

SalientDescriptor-matlab

If you need to automate your image matching tasks for the purposes of object detection or photo-identification in an easy way, the SalientDescriptor-matlab is right for you

  • Image processing
  • (HTML)
  • (MATLAB)
1
1

SARXarray

An Xarray extension to process coregistered Single Look Complex (SLC) image stacks acquired by Synthetic Aperture Radar (SAR).

  • Dask
  • InSAR
  • Interferometry
  • + 6
  • (Python)
  • (ReScript)
  • (TeX)
4
1

scriptcwl

Create CWL workflows by writing a simple Python script.

  • CWL
  • Workflow technologies
  • ("Common Workflow Language")
  • (Python)
8
1

self-hosted runners

Collection of resources to set up GitHub runners on self-hosted infrastructure

  • High performance computing
  • (Dockerfile)
  • (Shell)
5
1

SimVascular

The only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.

  • Cardiovascular
  • Fluid mechanics
  • Medical image computing
  • + 1
  • (Batchfile)
  • (C)
  • (C++)
  • + 9
4
1

sirup

Sirup is an open-source Python package that makes it easy to connect to, and rotate across, VPN servers provided by services such as ProtonVPN and Surfshark.

  • ip-rotation
  • openvpn
  • python
  • + 1
  • (Python)
  • (Shell)
1
1

SlicerIGT

Software toolkit for rapid development of image-guided therapy systems - for minimally invasive medical procedures, where operators rely on computer-generated images rather than direct sight of the target organs.

  • 3D Slicer
  • deep learning
  • Medical image computing
  • + 2
  • (C++)
  • (CMake)
  • (Python)
2
1

snakemake-wrf

A snakemake workflow to run WRF, including pre- and postprocessing. See our blog post for a detailed description.

  • geospatial
  • High performance computing
  • python
  • + 1
  • ("Jupyter Notebook")
  • (Python)
  • (Shell)
2
1

TaxoTagger

DNA barcode identification, powered by semantic searching.

  • Fungi
  • Machine learning
  • semantic search
  • + 3
  • (Makefile)
  • (Mustache)
  • (Python)
1
1

Umple

Umple allows generation of code in Java, PHP and other languages from a textual representation of UML state machines, associations and other modeling constructs, thus saving coding effort

  • Code Generation
  • Software Modeling
  • State Machines
  • + 1
  • (Batchfile)
  • (C++)
  • (CSS)
  • + 19
14
1

ValidSense

The ValidSense toolbox aims to assess the agreement between two quantitative methods using the Limits of Agreement analysis, aka the Bland-Altman analysis. Four existing variants are available. Moreover, a Longitudinal analysis is developed to assess agreement over time.

  • Agreement Analysis
  • Bland-Altman
  • Limits of Agreement
  • + 1
  • (Python)
4
1

WAM2layers

WAM2layers is an atmospheric moisture-tracking model that can be used to determine where precipitation originally evaporated (backtracking), or where evaporated moisture eventually ends up (forward tracking).

  • atmospheric rivers
  • ERA5
  • hydrological cycle
  • + 4
  • ("Jupyter Notebook")
  • (Python)
  • (Shell)
4
1