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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
2
8
Logo for COVID-19 Piedmont

COVID-19 Piedmont

COVID-19 Surveillance Data Modelling and Management Pipeline in Piedmont.

  • Computational Epidemiology
  • COVID-19
  • COVID-19 Data
  • + 14
  • Julia
2
8
Logo for pypfilt

pypfilt

A Sequential Monte Carlo (SMC, or "particle filter") Python package for online model estimation and probabilistic forecasting.

  • Bayesian Inference
  • Forecasting
  • Sequential Monte Carlo
    1
    8

    recipy

    Effortless provenance tracking in Python

    • Inter-operability & linked data
    • Optimized data handling
    • Python
    • HTML
    • Jupyter Notebook
    • + 2
    2
    8

    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
    4
    8
    Logo for Blade Element Momentum Theory Code for Positive and Negative Thrust Propellers

    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
      1
      7
      Logo for 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

      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
        3
        7
        Logo for 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

        Framework for the publication: MirrorLabs – creating similar learning environments for students all over Europe for human-robot coproduction

        • Augmented Reality
        • Interactive Visualization
        • robotics
        • + 2
          2
          7
          Logo for 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"

          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
            3
            7
            Logo for 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

            Source code of the SWAN model: Free Infragravity Waves in the North Sea

            • coastal waters
            • Infragravity waves
            • inland waters
            • + 3
              3
              7
              Logo for SWMM_GNN_Repository_Paper_version

              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
              4
              7

              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
              1
              7

              ece2cmor3

              Process EC-Earth output to publish for CMIP6

              • Big data
              • High performance computing
              • Optimized data handling
              • Shell
              • Python
              2
              7
              Logo for jaspProcess

              jaspProcess

              A JASP implementation of the PROCESS macro for SPSS

              • Data Analysis
              • Statistics
              • Visualization
              • R
              • QML
              2
              7
              Logo for MultilayerGraphs.jl

              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
              2
              7

              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
              2
              7
              Logo for Turing Data Safe Haven

              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
              29
              7

              xtas

              the eXtensible Text Analysis Suite

              • Text analysis & natural language processing
              • Python
              • Shell
              • Java
              2
              7
              Logo for [Artifact] Deductive Verification of Parameterized Embedded Systems modeled in SystemC

              [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
                6
                6
                Logo for  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

                Code and data underlying the publication: Symmetrization of 2D Polygonal Shapes Using Mixed-Integer Programming

                • Design
                • Digitalization
                • Shape optimization
                • + 1
                • C
                • C++
                • Other
                • + 3
                3
                6
                Logo for 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"

                Code complementing the paper "Feasibility Analysis of a Self-Reinforcing Electroadhesive Rotational Clutch"

                • Clutch
                • Electroadhesion
                • self-reinforcement
                • + 2
                  3
                  6
                  Logo for 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

                  Code supporting the paper: Sensitivity and feasibility of a one-dimensional morphoelastic model for post-burn contraction

                  • Burns
                  • Feasibility
                  • MATLAB
                  • + 4
                    3
                    6
                    Logo for 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

                    Data/software underlying the publication: Robust quantum-network memory based on spin qubits in isotopically engineered diamond

                    • distributed quantum computation
                    • entanglement distillation
                      12
                      6
                      Logo for 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 in Frequency Domain - Tonal Noise of Rotors in Uniform Inflow

                      • Hanson's model
                      • Propeller Aeroacoustics
                      • Propeller Noise
                      • + 1
                        1
                        6
                        Logo for Learning_on_SCs

                        Learning_on_SCs

                        Code underlying: Hodge-Aware Convolutional Learning on Simplicial Complexes

                        • Hodge theorem
                        • neural networks
                        • simplicial complexes
                        • Other
                        • Python
                        • Markdown
                        • + 1
                        1
                        6
                        Logo for 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"

                        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
                        6
                        6
                        Logo for 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)

                        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
                          4
                          6
                          Logo for Uncertainty Specification and Analysis for Thermosphere Observations

                          Uncertainty Specification and Analysis for Thermosphere Observations

                          Uncertainty Specification and Analysis for Thermosphere Observations

                          • Accelerometer
                          • GNSS tracking
                          • Mass density
                          • + 2
                          • Other
                          • C
                          • Matlab
                          • + 3
                          1
                          6

                          eEcology Annotation Tool

                          Visualize and annotate GPS measurements of bird movements.

                          • Inter-operability & linked data
                          • Visualization
                          • HTML
                          • Python
                          • Mako
                          • + 5
                          1
                          6
                          Logo for IncompressibleNavierStokes

                          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
                          5
                          6

                          PSSMGen

                          Generates consistent PSSM and PDB files for protein-protein complexes

                          • Big data
                          • High performance computing
                          • Optimized data handling
                          • Python
                          • Makefile
                          2
                          6

                          PuReGoMe

                          Analyzes social media messages for polarity and stance towards governmental COVID-19 measures

                          • Machine learning
                          • Social media
                          • Jupyter Notebook
                          • Python
                          • Shell
                          3
                          6

                          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
                          2
                          6

                          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
                          7
                          6
                          Logo for TulipaEnergyModel

                          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
                          9
                          6

                          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.

                            1
                            5
                            Logo for 3D Slicer

                            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
                            4
                            5
                            Logo for 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

                            Code supporting the paper: Sensitivity of a two-dimensional biomorphoelastic model for post-burn contraction

                            • burn
                            • cell proliferation
                            • MATLAB
                            • + 4
                              4
                              5
                              Logo for 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

                              Code supporting the paper: Stability of a one-dimensional morphoelastic model for post-burn contraction

                              • Burns
                              • MATLAB
                              • Morphoelasticity
                              • + 3
                                3
                                5
                                Logo for Hydrodynamic Analysis of Marine Structures-Marine Renewable Energies Lab (HAMS-MREL)

                                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
                                  5
                                  5
                                  Logo for SBSL

                                  SBSL

                                  Data and code underlying the publication: Overcoming Selection Bias in Synthetic Lethality Prediction

                                  • anti-cancer therapeutics
                                  • computational prediction
                                  • gene dependency
                                  • + 3
                                    3
                                    5

                                    eEecology Classification

                                    Automatic classification of accelerometer data using a supervised learning approach.

                                    • Machine learning
                                    • Java
                                    • JavaScript
                                    • HTML
                                    • + 3
                                    1
                                    5

                                    MagnumPI - Potential Integrator

                                    A package for the calculation of scattering angles and cross sections.

                                    • Inter-operability & linked data
                                    • Visualization
                                    • C++
                                    • Mathematica
                                    • Python
                                    • + 2
                                    6
                                    5
                                    Logo for mexca

                                    mexca

                                    Capture emotion expressions from video, audio, and text with a single pipeline.

                                    • Audio processing
                                    • Image processing
                                    • Machine learning
                                    • + 1
                                    • Python
                                    • Dockerfile
                                    • Shell
                                    5
                                    5

                                    PIQMIe

                                    A web tool for mass spectrometry-based proteomics data analyses

                                    • Data Analysis
                                    • mass spectrometry
                                    • Optimized data handling
                                    • + 2
                                    • HTML
                                    • JavaScript
                                    • Python
                                    • + 3
                                    1
                                    5

                                    sv-channels

                                    Genome-wide detection of structural variants using deep learning

                                    • Machine learning
                                    • Python
                                    • Jupyter Notebook
                                    • R
                                    • + 1
                                    4
                                    5

                                    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
                                    2
                                    5

                                    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.

                                      1
                                      4