All software
pdb2sql
Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.
- Big data
- Optimized data handling
- Python
- TeX
- Makefile
COVID-19 Piedmont
COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.
- Computational Epidemiology
- COVID-19
- COVID-19 Data
- + 14
- Julia
pypfilt
A Sequential Monte Carlo (SMC, or "particle filter") Python package for online model estimation and probabilistic forecasting.
- Bayesian Inference
- Forecasting
- Sequential Monte Carlo
recipy
Effortless provenance tracking in Python
- Inter-operability & linked data
- Optimized data handling
- Python
- HTML
- Jupyter Notebook
- + 2
WRFpy
WRFpy is a python application that provides an easy way to set up, run, and monitor Weather Research and Forecasting simulations
- Data Simulation
- python
- Python
Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers
Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers
- BEM
- BEMT
- Blade Element Momentum Theory
- + 2
Code supporting the paper: A Bayesian finite-element trained machine learning approach for predicting post-burn contraction
Code supporting the paper: A Bayesian finite-element trained machine learning approach for predicting post-burn contraction
- Feed-forward neural network
- Machine learning
- MATLAB
- + 5
Framework for the publication: MirrorLabs – creating similar learning environments for students all over Europe for human-robot coproduction
Framework for the publication: MirrorLabs – creating similar learning environments for students all over Europe for human-robot coproduction
- Augmented Reality
- Interactive Visualization
- robotics
- + 2
MATLAB scripts created during the work on "Multi-Δt approach for peak-locking error correction and uncertainty quantification in PIV"
MATLAB scripts created during the work on "Multi-Δt approach for peak-locking error correction and uncertainty quantification in PIV"
- PIV (Particle Image Velocimetry)
- Uncertainty Quantification
Source code of the SWAN model: Free Infragravity Waves in the North Sea
Source code of the SWAN model: Free Infragravity Waves in the North Sea
- coastal waters
- Infragravity waves
- inland waters
- + 3
SWMM_GNN_Repository_Paper_version
SWMM GNN metamodel – Code for paper: Transferable and Data Efficient Metamodeling of Storm Water System Nodal Depths Using Auto-Regressive Graph Neural Networks
- GNN
- Graph neural networks
- Machine learning
- + 5
- Other
- Python
- Jupyter Notebook
- + 2
Bacting
Bacting is an open-source platform for chemo- and bioinformatics based on Bioclipse that defines a number of common domain objects and wraps common functionality, providing a toolkit independent, scriptable solution to handle data from the life sciences.
- bioinformatics
- Cheminformatics
- Java
- TeX
ece2cmor3
Process EC-Earth output to publish for CMIP6
- Big data
- High performance computing
- Optimized data handling
- Shell
- Python
jaspProcess
A JASP implementation of the PROCESS macro for SPSS
- Data Analysis
- Statistics
- Visualization
- R
- QML
MultilayerGraphs.jl
A Julia package for the creation, manipulation and analysis of the structure, dynamics and functions of multilayer graphs.
- Graphs
- Graph Theory
- Hierarchical Graphs
- + 10
- Julia
nlppln
A flexible solution to build text mining workflows that allows you to quickly combine Natural Language Processing tools from different sources.
- Text analysis & natural language processing
- Python
- Common Workflow Language
- Dockerfile
Turing Data Safe Haven
Data Safe Haven is an open-source framework for creating Trusted Research Environments (TREs) to analyse sensitive data. It provides a set of scripts that will allow you to deploy, administer and use your own TRE on Microsoft Azure cloud.
- Cloud
- cloud storage
- Infrastructure as code
- + 3
- Python
- Shell
- Jinja
- + 3
xtas
the eXtensible Text Analysis Suite
- Text analysis & natural language processing
- Python
- Shell
- Java
[Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC
[Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC
- Deductive verification
- embedded systems
- parameterized systems
- + 2
Code and data underlying the publication: Symmetrization of 2D Polygonal Shapes Using Mixed-Integer Programming
Code and data underlying the publication: Symmetrization of 2D Polygonal Shapes Using Mixed-Integer Programming
- Design
- Digitalization
- Shape optimization
- + 1
- C
- C++
- Other
- + 3
Code complementing the paper "Feasibility Analysis of a Self-Reinforcing Electroadhesive Rotational Clutch"
Code complementing the paper "Feasibility Analysis of a Self-Reinforcing Electroadhesive Rotational Clutch"
- Clutch
- Electroadhesion
- self-reinforcement
- + 2
Code supporting the paper: Sensitivity and feasibility of a one-dimensional morphoelastic model for post-burn contraction
Code supporting the paper: Sensitivity and feasibility of a one-dimensional morphoelastic model for post-burn contraction
- Burns
- Feasibility
- MATLAB
- + 4
Data/software underlying the publication: Robust quantum-network memory based on spin qubits in isotopically engineered diamond
Data/software underlying the publication: Robust quantum-network memory based on spin qubits in isotopically engineered diamond
- distributed quantum computation
- entanglement distillation
Hanson's Model in Frequency Domain - Tonal Noise of Rotors in Uniform Inflow
Hanson's Model in Frequency Domain - Tonal Noise of Rotors in Uniform Inflow
- Hanson's model
- Propeller Aeroacoustics
- Propeller Noise
- + 1
Learning_on_SCs
Code underlying: Hodge-Aware Convolutional Learning on Simplicial Complexes
- Hodge theorem
- neural networks
- simplicial complexes
- Other
- Python
- Markdown
- + 1
Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy"
Microscopy data, code and analysis underlying the publication "Optical STEM detection for scanning electron microscopy"
- Electron Detection
- Instrumentation Development
- Scanning Electron Microscopy
- + 2
- Other
- Markdown
- Jupyter Notebook
- + 2
Software supporting the publication: Background Electromagnetic Noise Received via Ionospheric Propagation in a Remote Rural Location in Spain (set 1)
Software supporting the publication: Background Electromagnetic Noise Received via Ionospheric Propagation in a Remote Rural Location in Spain (set 1)
- ambient noise
- electromagnetic noise
- ionosphere
- + 3
Uncertainty Specification and Analysis for Thermosphere Observations
Uncertainty Specification and Analysis for Thermosphere Observations
- Accelerometer
- GNSS tracking
- Mass density
- + 2
- Other
- C
- Matlab
- + 3
eEcology Annotation Tool
Visualize and annotate GPS measurements of bird movements.
- Inter-operability & linked data
- Visualization
- HTML
- Python
- Mako
- + 5
IncompressibleNavierStokes
This package implements energy-conserving solvers for the incompressible Navier-Stokes equations on a staggered Cartesian grid. It is based on the Matlab package INS2D/INS3D. The simulations can be run on the single/multithreaded CPUs or Nvidia GPUs.
- HPC
- Scientific machine learning
- Julia
PSSMGen
Generates consistent PSSM and PDB files for protein-protein complexes
- Big data
- High performance computing
- Optimized data handling
- Python
- Makefile
PuReGoMe
Analyzes social media messages for polarity and stance towards governmental COVID-19 measures
- Machine learning
- Social media
- Jupyter Notebook
- Python
- Shell
rWikiPathways
Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.
- bioinformatics
- WikiPathways
- HTML
- R
- TeX
SPOT
SPOT is an interactive visualization tool for multi-dimensional data. It allows quick analysis of complex datasets and easy identification of correlations between variables.
- Big data
- Visualization
- JavaScript
- Pug
- Stylus
- + 2
TulipaEnergyModel
This package provides an optimization model for the electricity market and its coupling with other energy sectors. The objective is to determine the optimal investment and operation decisions for different types of assets.
- Energy system analysis
- Energy system modelling
- Integrated energy systems
- + 4
- Julia
- Shell
Reference evapotranspiration (FAO-56)
Calculate a daily value of reference evapotranspiration, useful for vegetation (incl. crop) models. The module code is based on FAO-56 Penman-Monteith method.
3D Slicer
3D Slicer is a free, open source software for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes; and planning and navigating image-guided procedures.
- 3D
- 3DSlicer
- Extension
- + 7
- C++
- Python
- CMake
- + 5
Code supporting the paper: Sensitivity of a two-dimensional biomorphoelastic model for post-burn contraction
Code supporting the paper: Sensitivity of a two-dimensional biomorphoelastic model for post-burn contraction
- burn
- cell proliferation
- MATLAB
- + 4
Code supporting the paper: Stability of a one-dimensional morphoelastic model for post-burn contraction
Code supporting the paper: Stability of a one-dimensional morphoelastic model for post-burn contraction
- Burns
- MATLAB
- Morphoelasticity
- + 3
Hydrodynamic Analysis of Marine Structures-Marine Renewable Energies Lab (HAMS-MREL)
Hydrodynamic Analysis of Marine Structures-Marine Renewable Energies Lab (HAMS-MREL)
- BIEM
- HAMS
- HAMS-MREL
- + 4
SBSL
Data and code underlying the publication: Overcoming Selection Bias in Synthetic Lethality Prediction
- anti-cancer therapeutics
- computational prediction
- gene dependency
- + 3
eEecology Classification
Automatic classification of accelerometer data using a supervised learning approach.
- Machine learning
- Java
- JavaScript
- HTML
- + 3
MagnumPI - Potential Integrator
A package for the calculation of scattering angles and cross sections.
- Inter-operability & linked data
- Visualization
- C++
- Mathematica
- Python
- + 2
mexca
Capture emotion expressions from video, audio, and text with a single pipeline.
- Audio processing
- Image processing
- Machine learning
- + 1
- Python
- Dockerfile
- Shell
PIQMIe
A web tool for mass spectrometry-based proteomics data analyses
- Data Analysis
- mass spectrometry
- Optimized data handling
- + 2
- HTML
- JavaScript
- Python
- + 3
sv-channels
Genome-wide detection of structural variants using deep learning
- Machine learning
- Python
- Jupyter Notebook
- R
- + 1
TIMP
TIMP is an R package for fitting superposition models that implements the partitioned variable projection algorithm. The package has been extensively applied to modeling spectroscopy and Fluorescence Lifetime Imaging Microscopy (FLIM) datasets. It serves as the backend for the Glotaran software.
- global analysis
- target analysis
- time-resolved spectroscopy
- R
- C
Get fertility rates (females, 5-year cohort)
This NetLogo code snippet provides fertility estimates of females for use in demographic simulations. The figures used are based on two different sources, and will be assigned per 5-year age cohort.