fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

A workflow for reproducible and open scientific articles

A lightweight, AI-native training framework for large language models. Designed for fast iteration, reproducible experiments, and modular configuration across SFT, RLVR, and evaluation workflows.

Plan-Validate-Solve (PVS) Agent for accurate, reliable and reproducable workflow automation

PLynx is a domain agnostic platform for managing reproducible experiments and data-oriented workflows.

doped is a Python software for the generation, pre-/post-processing and analysis of defect supercell calculations, implementing the defect simulation workflow in an efficient, reproducible, user-friendly yet powerful and fully-customisable manner.

Flexible and scalable template based on PyTorch Lightning + Hydra. Efficient workflow and reproducibility for rapid ML experiments.

DAAF, the Data Analyst Augmentation Framework: An open-source, extensible workflow for Claude Code that allows skilled researchers to rapidly scale their expertise and accelerate data analysis by as much as 5-10x -- without sacrificing the transparency, rigor, or reproducibility demanded by our core scientific principles.

A tool that supports one-button reproducible workflows with the Jupyter Notebook and Scons.

pytask is a workflow management system that facilitates reproducible data analyses.

A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

Reproducible Data Analysis Workflow in Jupyter

Data Analysis Workflows & Reproducibility Learning Resources

Easy, reproducible Metashape photogrammetry workflows

Working reverse-engineered Claude Code CLI rebuilt from source analysis to reproduce the original terminal workflow

Unified specification for defining and executing ML workflows, making reproducibility, consistency, and governance easier across the ML pipelines

Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

Build and verify byte-for-byte reproducible Rust packages using a Cargo-based workflow

A short and to-the-point summary of a reproducible data science workflow

The Bioinformatician’s Interactive Lab Notebook (BILN) is a smart, dynamic system for tracking experiments, datasets, and workflows. Designed for bioinformaticians, it ensures reproducibility, structured logging, and AI-readiness. Export logs, collaborate seamlessly, and let BILN become your interactive companion in computational biology.

moai is a PyTorch-based AI Model Development Kit (MDK) created to improve data-driven model workflows, design and reproducibility.

CK automation actions to let users implement portable, customizable and reusable program workflows for reproducible, collaborative and multi-objective benchmarking, optimization and SW/HW co-design:

a Graphical Interface for Reproducible Analysis oF workFlow Experiments

Quadra: Effortless and reproducible deep learning workflows with configuration files.

Collective Knowledge workflow for the MILEPOST GCC (machine learning based compiler). See how it is used in the collaborative project with the Raspberry Pi foundation to support collaborative research for multi-objective autotuning and machine learning techniques, and prototype reproducible papers with portable workflows:

Textbook that provides JavaScript and Python code to create open reproducible remote sensing analyses and workflows in Google Earth Engine.

teemi: A Python package for reproducible and FAIR microbial strain construction. Simulate the entire dbtl-cycle, generate genetic parts, design libraries, and track samples. Open-source Python platform for workflow flexibility and automated tasks, accelerating metabolic engineering. Try teemi with our Google Colab notebooks!