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mzRecal

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

mass spectrometry
proteomics

(Dockerfile)
(Go)
(Makefile)
+ 2

NPLinker

Microbial natural products data mining by integrating genomics and metabolomics data

Data processing
multi-omics integration

(Makefile)
(Mustache)
(Python)
+ 2

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)

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

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)

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

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

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

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

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)

PowerSensor3

PowerSensor is a low-cost, custom-built device that measures the instantaneous power consumption of GPUs and other devices at a high time resolution.

GPU
High performance computing

(C)
(C++)
(CMake)
+ 3

qumia-train-scripts

Scripts and files related to ML training for the QUMIA project

Machine learning
Neuromuscular
ultrasound imaging

("Jupyter Notebook")
(Python)
(Shell)

ROBIST

Robust Optimization by Iterative Scenario Sampling and Statistical Testing

optimization
python

(Python)

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

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

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)

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)

scriptcwl

Create CWL workflows by writing a simple Python script.

CWL
Workflow technologies

("Common Workflow Language")
(Python)

self-hosted runners

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

High performance computing

(Dockerfile)
(Shell)

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

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)

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)

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)

swiftmhc

SwiftMHC is a deep learning algorithm for predicting pMHC structure and binding affinity at the same time.

deep learning
Protein-Protein Interaction
Transformer

("Jupyter Notebook")
(Mask)
(Python)
+ 1

TaxoTagger

DNA barcode identification, powered by semantic searching.

Fungi
Machine learning
semantic search
+ 3

(Makefile)
(Mustache)
(Python)

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

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)

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)

Workflomics

Web platform for workflow exploration and benchmarking in bioinformatics

Inter-operability & linked data
Workflow technologies

(CSS)
(HTML)
(JavaScript)
+ 1

WRF-runner

Simple shell script to run a complete WPS/WRF experiment in one go

climate
Forecasting
workflow
+ 1

(Shell)

Angle-and-step random walk

An Python implementation of random walk in 2D space based on agent angle orientation and step distance. It defines an agent class `Walker` capable of random walk movement based on random angle and movement step distance in a continuous 2D space.

Random walk in data frames

Collection of methods for producing random walks in two-dimensional space outputting position coordinates in data frames, including alternatives for grid and non-grid space. In R, it uses tidyverse "tibble" to construct the data frames that store trajectories.

Resource exploitation procedure

This module takes an agent and lets it decide which resources to target and exploit. The agent moves to the patch to be harvested, takes the resources and returns home

Absorption Coefficient Estimator using Domain Adaptation

Code underlying the research project: Extracting absorption coefficients from a room impulse response using a convolutional neural network with domain adaptation

Absorption Coefficient
domain adaptation
Machine learning
+ 3

(Markdown)
(Matlab)
(Other)
+ 1

abstraction-mpc-integration

Code for publication: Temporal Logic Control of Nonlinear Stochastic Systems with Online Performance Optimization

Abstraction
formal methods
Hybrid Systems
+ 3

(CSS)
(HTML)
(JavaScript)
+ 4

ACDC-OpFlow

ACDC-OpFlow, Unified, Cross-Language Framework for AC/DC Optimal Power Flow Solutions

AC/DC power systems
Optimal Power Flow
power electronic converters

A demand management and frequency settings model for complying to the COVID-19 capacity limits in public transport operations

COVID-19
demand management
frequency settings
+ 3

AeoLiS v2.1.0

advection
aeolian sediment transport
coastal dunes
+ 5

Agent-based model software written for the master thesis Scaling Up, Staying Secure

Agent based modelling and simulation (ABMS)
CYBER SECURITY
Distributed energy resources (DER)
+ 2

A high spatial resolution Extended Spring Indices database over American and European regions

Citizen Science
Climate change
Cloud computing
+ 4

(Markdown)
(Other)
(Python)

AircraftDuctedFanOptimisation

The Unified Ducted Fan Code and Ducted Fan Optimisation Framework

Aircraft
Aircraft performance
Conceptual aircraft design
+ 7

(Markdown)
(Other)
(Python)

Air Traffic Control Reinforcement Learning Environment

Air Traffic Control (ATC)
Air traffic management (ATM)
Reinforcement Learning (RL)

A model for modifying the public transport service patterns to account for the imposed COVID-19 capacity

capacity
coronavirus
COVID-19
+ 7

AnisoVision

Data accompanying the publication: Characterization of the 3D-optical properties of van der Waals materials with deep learning based coherent Fourier scatterometry

anisotropic thin films
coherent Fourier scatterometry
deep learning metrology
+ 2

("Jupyter Notebook")
(Markdown)
(Other)

ANNESI: An open-source artificial neural network for estuarine salt intrusion

estuary
Neural Network
salt intrusion

Application of SDDTMPC to control a unicycle

MPC
nonlinear control
robotics
+ 2

(Markdown)
(Matlab)

ApPlyWood: a calculation tool supporting the design of plywood-based seismic retrofitting interventions on existing timber floors

Architectural conservation
Design tools
Earthquake engineering
+ 4

APS

APS: Asses Pedestrian model Speed framework

Computational Complexity
Model assessment framework
Pedestrian models
+ 1

(JSON)
(Markdown)
(Other)
+ 1