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awesome-utrecht-university

A curated list of awesome open source projects from Utrecht University.
https://github.com/utrechtuniversity/awesome-utrecht-university

Last synced: 2 days ago
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  • Projects

    • Research code

      • Aragonite_clumped - R code for processing and plotting of clumped isotope data from aragonite samples in "Temperature dependence of clumped isotopes (∆47) in aragonite"
      • ContrastiveExplanation - Contrastive Explanation (Foil Trees), developed at TNO/Utrecht University
      • DA_model - R code for simulating diffusion-advection models for leaching of trace elements into tooth enamel during burial and diagenesis of archeological and paleontological specimens in "High-resolution trace element distributions and models of trace element diffusion in enamel of Late Neolithic/Early Chalcolithic human molars from the Rioja Alavesa region (north-central Spain) help to separate biogenic from diagenetic trends"
      • GeoNewsMiner
      • PCR-GLOBWB_model - PCR-GLOBWB (PCRaster Global Water Balance) is a large-scale hydrological model intended for global to regional studies and developed at the Department of Physical Geography.
      • Aragonite_clumped - R code for processing and plotting of clumped isotope data from aragonite samples in "Temperature dependence of clumped isotopes (∆47) in aragonite"
      • ContrastiveExplanation - Contrastive Explanation (Foil Trees), developed at TNO/Utrecht University
      • DA_model - R code for simulating diffusion-advection models for leaching of trace elements into tooth enamel during burial and diagenesis of archeological and paleontological specimens in "High-resolution trace element distributions and models of trace element diffusion in enamel of Late Neolithic/Early Chalcolithic human molars from the Rioja Alavesa region (north-central Spain) help to separate biogenic from diagenetic trends"
      • GeoNewsMiner
      • PCR-GLOBWB_model - PCR-GLOBWB (PCRaster Global Water Balance) is a large-scale hydrological model intended for global to regional studies and developed at the Department of Physical Geography.
      • PuReGoMe - Notebooks of the PuReGoMe Project of the Netherlands eScience Center and Utrecht University.
      • Saliency-Tubes-Visual-Explanations-for-Spatio-Temporal-Convolutions - Implementation of Saliency Tubes for 3D Convolutions in Pytoch and Keras to localise the focus spatio-temporal regions of 3D CNNs.
      • seasonalclumped - R package for generating virtual stable isotope data to model sampling strategies for seasonality reconstructions in "Optimizing sampling strategies in high-resolution paleoclimate records"
      • SoftPool - Code for approximated exponential maximum pooling.
      • Squeeze-and-Recursion-Temporal-Gates - Code for : [Pattern Recognit. Lett. 2020] "Learn to cycle: Time-consistent feature discovery for action recognition" and [arXiv] "Right on Time: Multi-Temporal Convolutions for Human Action Recognition in Videos".
      • PuReGoMe - Notebooks of the PuReGoMe Project of the Netherlands eScience Center and Utrecht University.
      • Saliency-Tubes-Visual-Explanations-for-Spatio-Temporal-Convolutions - Implementation of Saliency Tubes for 3D Convolutions in Pytoch and Keras to localise the focus spatio-temporal regions of 3D CNNs.
      • seasonalclumped - R package for generating virtual stable isotope data to model sampling strategies for seasonality reconstructions in "Optimizing sampling strategies in high-resolution paleoclimate records"
      • SoftPool - Code for approximated exponential maximum pooling.
      • Squeeze-and-Recursion-Temporal-Gates - Code for : [Pattern Recognit. Lett. 2020] "Learn to cycle: Time-consistent feature discovery for action recognition" and [arXiv] "Right on Time: Multi-Temporal Convolutions for Human Action Recognition in Videos".
      • stdstats - Simulation and plotting code for "Optimizing the use of carbonate standards to minimize uncertainties in clumped isotope data"
      • stdstats - Simulation and plotting code for "Optimizing the use of carbonate standards to minimize uncertainties in clumped isotope data"

    • Research software

      • ShellChron - R package for constructing age models based on stable oxygen isotope records from accretionary carbonate archives
      • Stitch - A program for de novo sequencing of antibodies/proteins based on massspectrometry data.
      • StratPal - R package to build modeling pipelines for paleontology
      • text_explainability - A generic explainability architecture for explaining text machine learning models.
      • text_sensitivity - Extension of text_explainability for sensitivity testing (robustness, fairness).
      • admtools - R package to transform data using age-depth models
      • asreview - Active learning for systematic reviews
      • bain - Bayes Factors for Informative Hypotheses
      • iBridges - Python API and commandline interface to easily interact with Yoda and iRODS servers
      • iBridges-GUI - A graphical user interface for iBridges
      • LUE - Modelling framework for simulating large geographical systems of agents and fields
      • mice - Multivariate Imputation by Chained Equations
      • ggmice - Visualize incomplete and imputed data with the R package `ggmice`
      • oceanexplorer - An R interface to the [NOAA World Ocean Atlas](https://www.ncei.noaa.gov/products/world-ocean-atlas)
      • osmenrich - Enrich sf data with geographic features from OpenStreetMaps.
      • parcels - Main code for Parcels (Probably A Really Computationally Efficient Lagrangian Simulator)
      • pdb-tools - A dependency-free cross-platform swiss army knife for PDB files.
      • recordlinkage - A toolkit for record linkage and duplicate detection in Python
      • Ricgraph - With Ricgraph, you can create a graph from research information that is stored in various source systems. You can explore this graph and discover relations you were not aware of. For code, extensive documentation and videos follow the link.
      • text_sensitivity - Extension of text_explainability for sensitivity testing (robustness, fairness).
      • admtools - R package to transform data using age-depth models
      • asreview - Active learning for systematic reviews
      • bain - Bayes Factors for Informative Hypotheses
      • iBridges - Python API and commandline interface to easily interact with Yoda and iRODS servers
      • iBridges-GUI - A graphical user interface for iBridges
      • LUE - Modelling framework for simulating large geographical systems of agents and fields
      • mice - Multivariate Imputation by Chained Equations
      • ggmice - Visualize incomplete and imputed data with the R package `ggmice`
      • oceanexplorer - An R interface to the [NOAA World Ocean Atlas](https://www.ncei.noaa.gov/products/world-ocean-atlas)
      • osmenrich - Enrich sf data with geographic features from OpenStreetMaps.
      • parcels - Main code for Parcels (Probably A Really Computationally Efficient Lagrangian Simulator)
      • PCRaster - Environmental modeling software
      • pdb-tools - A dependency-free cross-platform swiss army knife for PDB files.
      • recordlinkage - A toolkit for record linkage and duplicate detection in Python
      • Ricgraph - With Ricgraph, you can create a graph from research information that is stored in various source systems. You can explore this graph and discover relations you were not aware of. For code, extensive documentation and videos follow the link.
      • ShellChron - R package for constructing age models based on stable oxygen isotope records from accretionary carbonate archives
      • Stitch - A program for de novo sequencing of antibodies/proteins based on massspectrometry data.
      • StratPal - R package to build modeling pipelines for paleontology
      • text_explainability - A generic explainability architecture for explaining text machine learning models.
      • PCRaster - Environmental modeling software

    • Research data

      • childdevdata - R package with *Child Development Data* from ten studies, containing 1,116,061 assessments made on 10,831 unique children during 28,465 visits, covering 21 different instruments.
      • CoronaWatchNL - Numbers concerning COVID-19 disease cases in The Netherlands by RIVM, LCPS, NICE, ECML, and Rijksoverheid.
      • childdevdata - R package with *Child Development Data* from ten studies, containing 1,116,061 assessments made on 10,831 unique children during 28,465 visits, covering 21 different instruments.
      • CoronaWatchNL - Numbers concerning COVID-19 disease cases in The Netherlands by RIVM, LCPS, NICE, ECML, and Rijksoverheid.

    • Research project management

      • labphew - a minimalist functioning code module and folder structure, built to teach and exercise with computer-controlled measurements using Python.
      • UU-dissertation-template - a Utrecht University dissertation template for LaTeX.
      • worcs - Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)
      • labphew - a minimalist functioning code module and folder structure, built to teach and exercise with computer-controlled measurements using Python.
      • UU-dissertation-template - a Utrecht University dissertation template for LaTeX.
      • worcs - Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)

    • Education and workshops

    • Collaboration groups

      • CLARIAH - CLARIAH offers humanities scholars a Common Lab providing access to large collections of digital resources and innovative tools for research
      • stan - Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation. Thousands of users rely on Stan for statistical modeling, data analysis, and prediction in the social, biological, and physical sciences, engineering, and business.
      • CLARIAH - CLARIAH offers humanities scholars a Common Lab providing access to large collections of digital resources and innovative tools for research
      • stan - Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation. Thousands of users rely on Stan for statistical modeling, data analysis, and prediction in the social, biological, and physical sciences, engineering, and business.

  • Add project to this list

  • Background

  • Contact

Programming Languages
R 28 Python 26 HTML 4 TeX 4 C++ 4 Jupyter Notebook 4 CSS 2 C# 2
Categories
Projects 86 Contact 8 Add project to this list 2 Background 2
Sub Categories
Research software 40 Research code 22 Education and workshops 10 Implementing Awesome lists for your university 8 Research project management 6 Collaboration groups 6 Research data 4 What is an Awesome list? 2
Keywords
utrecht-university 18 python 8 r 8 palaeontology 6 palaeobiology 6 sedimentology 6 shiny 6 paleontology 6 stratigraphy 6 datascience 4 r-package 4 rstats 4 visualization 4 paleobiology 4 spatio-temporal-modeling 4 dataset 4 earth-science 4 irods-client 4 pytorch 4 stratigraphic-paleobiology 4 geology 4 3d-cnn 4 mice 4 machine-learning 4 Machine Learning 4 Transparency 4 natural-language-processing 2 neural-network 2 research 2 llm 2 literature 2 learning-algorithms 2 language-model 2 deep-learning 2 asreview 2 active-learning 2 geochronology 2 age-depth-model 2 systematic-literature-reviews 2 systematic-reviews 2 data-analysis 2 data-engineering 2 data-science 2 data-visualization 2 graphical-user-interface 2 amt 2 asynchronous-tasks 2 cartographic-modelling 2 computational-geography 2 distributed-computing 2