PyVista
PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK) - Published in JOSS (2019)
PVGeo
PVGeo: an open-source Python package for geoscientific visualization in VTK and ParaView - Published in JOSS (2019)
osfr
osfr: An R Interface to the Open Science Framework - Published in JOSS (2020)
stanscofi and benchscofi
stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering - Published in JOSS (2024)
covidregionaldata
covidregionaldata: Subnational data for COVID-19 epidemiology - Published in JOSS (2021)
Git-RDM
Git-RDM: A research data management plugin for the Git version control system - Published in JOSS (2016)
simpeg
Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
citations
Citation manager support for GAP. This helps with citations for reports, papers, data, and presentations!
itk
Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
avogadro
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
itk-wasm
High performance spatial analysis in a web browser and across programming languages and hardware architectures
stars-simpy-example-docs
STARS Project: Example `simpy` model documentation using JupyterBook, GitHub Pages, and STRESS
stars-reproduce-wood-2021
Assessing the computational reproducibility of Wood et al. 2021 as part of STARS.
fr.inria.gforge.spirals
Open-science code of the program repair tool described in "Dynamic Patch Generation for Null Pointer Exceptions Using Metaprogramming" (SANER'17)
manuscript
This repository implements an automated system to write our collaborative manuscript, while tracking changes and contributions.
awesome-open-geoscience
Curated from repositories that make our lives as geoscientists, hackers and data wranglers easier or just more awesome
stars-reproduce-allen-2020
Test-run of our reproducibility protocol on Allen et al. 2020: "A simulation modelling toolkit for organising outpatient dialysis services during the COVID-19 pandemic"
biodt-fair
Documentation, resources, and other materials related to FAIR and open science from the BioDT project.
afiksasi-verba-bahasa-indonesia
Repositori bahan pendukung (data, grafik, dan kode pemrograman R) untuk naskah berjudul "Afiksasi verba dalam bahasa Indonesia", yang menjadi bagian dari buku Tatabahasa Bahasa Indonesia Kontemporer (TBIK) berbasis korpus.
itkwidgets
An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
chromatographr
Toolset for the reproducible analysis of chromatography data in R (HPLC-DAD/UV, GC-FID).
reproducibility_in_plant_pathology
A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.
moltemplate
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
nestarchorg
Research Compendium for the preprint DOI: https://doi.org/10.1101/2022.06.30.498314
des_sharing_lit_review
Systematic scoping review paper for healthcare DES model sharing.
arco-era5
Recipes for reproducing Analysis-Ready & Cloud Optimized (ARCO) ERA5 datasets.
https://github.com/HugoBlox/hugo-blox-builder
⚡ Hugo Blox: Markdown sites in minutes. Academic/resume/lab/portfolio for AI researchers & startups. Premium templates. Deploy to GitHub Pages now in 1-click 👇
pydar
A Python package to access, download, view, and manipulate Cassini RADAR images in one place
muller-eot
A Python package for M. Müller implementation of the "Equation of Time - Problem in Astronomy" to calculate the Equation of Time based on the individual effect of eccentricity and obliquity
wb-reproducible-research-repository
This repository supports the World Bank's Reproducible Research Repository
obofoundry.github.io
Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
lingvan-voice
Supplementary materials for "Corpus linguistic and experimental studies on the meaning-preserving hypothesis in Indonesian voice alternations" (published in Linguistics Vanguard).
disciplines-differencies-hal
Différences disciplinaires en contexte de Science ouverte
python-package-guide
Python packaging made simple. Recommendations & guidance curated by the pyOpenSci community
os_strategy_nhmw
Open Science in Museums - Strategy of the "Naturhistorisches Museum Wien"
RBIEN
Tools for accessing the Botanical Information and Ecology Network (BIEN) database
https://github.com/alleninstitute/mouse_connectivity_models
Python package providing mesoscale connectivity models for mouse.
https://github.com/alleninstitute/neuroglia
a Python machine learning library for neurophysiology data
NitrogenUptake2016
R package containing data and source code from Hill et al. 2018a (DOI: https://doi.org/10.1016/j.jembe.2018.07.006) and Hill et al. 2018b (DOI: https://doi.org/10.1016/j.dib.2018.09.133)
https://github.com/danielvartan/open-science-pres
🔎🔓 Opens Science Presentation for the Sustentarea Research and Extension Center
https://github.com/crsh/psych-transparency-guide
Supplementary material for "A practical guide for transparency in psychological science" (find the paper at https://psyarxiv.com/rtygm/)
https://github.com/abitter/ptos
Practices and Tools of Open Science: Topic Modeling
neurotic
Curate, visualize, annotate, and share your behavioral ephys data using Python
knowledge-commons
Knowledge Commons research group's repository
https://github.com/aaronpeikert/reproducible-research
A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker
https://github.com/hauselin/docdata
R package to generate dataset documentation semi-automatically https://hauselin.github.io/docdata/
stars-reproduce-anagnostou-2022
Assessing the computational reproducibility of Anagnostou et al. 2022 as part of STARS.
https://github.com/arunbodd/portfolio
I am a Bioinformatics Scientist by Profession, AI enthusiast by Curiosity and a Technologist by skillset. To know more about me Click the below link
An Introduction to prismAId
An Introduction to prismAId: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews - Published in JOSS (2025)
sim-tools
Tools to support the Discrete-Event Simulation process for education and practice.
mrisharingguide
We developed a guide for researchers in the Netherlands who want to share brain MRI data to help them get started.
12
Try to observe with a microscope what is making an UV/Vis spectroscopy method fail
eyeris
🧠 Advanced reproducible pupillometry preprocessing in R | Interactive reports, BIDS-compliant, High-throughput database tooling out-of-the-box | Actively developed by cognitive neuroscientists at Stanford University
beatmonitor
Naturalistic measurement of multi-person cardiac activity using open source smartwatch technology
humidityproject
Research Compendium for the preprint DOI: https://doi.org/10.1101/2022.06.30.497551
https://github.com/arvkevi/openhumansimputer
Imputation pipeline for Open Humans
wolf-sheep
example reproducible ABM + RMarkdown analysis pipeline based on the NetLogo wolf-sheep predation model
alembica
Open science package for LLM-powered semantic synthesis and precise extraction of information from unstructured texts.
https://github.com/assert-kth/decompilercmp
Dataset and tool to analyse and compare java bytecode decompilers
constructional-equivalence
Repository of supplementary materials and RStudio project for the paper on corpus-based approach to measuring constructional equivalence.
stars-reproduce-hernandez-2015
Assessing the computational reproducibility of Hernandez et al. 2015 as part of STARS.
stars-reproduce-lim-2020
Assessing the computational reproducibility of Lim et al. 2020 as part of STARS.
stars-reproduce-kim-2021
Assessing the computational reproducibility of Kim et al. 2021 as part of STARS.
dataprivacyhandbook
Repository for the Data Privacy Handbook @UtrechtUniversity, a practical guide on handling personal data in scientific research
quarto-project-example
Project Example for the Lesson: Introduction to Reproducible Publications with Quarto
1
When determining equilibrium constants of multi-substrate / multi-product reactions, their ratios affect the uncertainty of the result.
same-version
Automatically ensures your software version metadata is consistent across key project files.
9
Compare the results from eQuilibrator (component contribution) or group contribution methods with experimental results from nucleoside phosphorolysis
semproducible
Generates R code for your lavaan models automatically, which helps with reproducible open science
ols2-cohort-talks-and-transcripts
Cohort calls/talks and their transcripts for OLS 2
template
My "Farm of Ideas" is supposed to store ideas I would like to develop into scientific progress some day. This is the template for all ideas in this Farm.