Reproducibility

Open science practice for reproducibility spans advocacy and norms, pre-registration and protocol sharing, computational provenance, model sharing, and research software citation.

Advocacy and frameworks

GFRN coordinates national reproducibility networks across disciplines, advocating for open and rigorous research practices. ReproducibiliTea is a grassroots journal club initiative for open and reproducible research with chapters at 128+ institutions in 31 countries. The Turing Way is a community-led open handbook covering reproducible research, project design, collaboration, and research ethics. ECoC is the EC-recognised standard for research integrity across all Horizon-funded projects, updated in 2023 to address open science practices and GDPR-aligned data management. Center for Open Science develops infrastructure and norms for open, reproducible research, operating OSF as its primary platform and coordinating the TOP Guidelines, a modular eight-standard framework for publication transparency adopted by over 5,000 journals.

Pre-registration and protocols

OSF provides the infrastructure for pre-registration and Registered Reports, in which peer review and provisional acceptance occur before data collection, making acceptance conditional on study design quality rather than outcome. arXiv, founded in 1991, established the preprint model for immediate open sharing of scientific work prior to peer review. This practice is now central to open science and has been adopted across biology and medicine through bioRxiv and medRxiv. The quantitative biology section of arXiv (q-bio.NC) is a widely used preprint venue for theoretical and computational neuroscience. Protocols.io provides a platform for sharing versioned, citable step-by-step research protocols, addressing the methods reporting gap that contributes to irreproducibility in published research.

Computational provenance

Computational reproducibility infrastructure centres on ReproNim, which develops NIDM as a PROV-O-based provenance standard and integrates DataLad for distributed dataset versioning and re-executable workflows. DataLad itself is co-produced by INM Jülich and the Center for Open Neuroscience (CON) at Dartmouth, which also co-leads the DANDI Archive. Its director serves on both the BIDS Steering Committee and the NWB technical advisory committee, making CON a central node in the reproducibility tooling ecosystem. BrainLife.io implements this stack in a cloud environment, applying automatic provenance tracking to neuroimaging pipelines run against BIDS-organised data. Together, PROV-O, NIDM, and DataLad constitute the provenance layer that makes computational workflows machine-readable and re-executable independent of local infrastructure.

Computational model sharing

ModelDB and OpenSourceBrain are the primary open resources for computational model deposit and collaborative development. NeuroML provides the simulator-independent format standard and SWC covers morphological reconstructions. For the full format and archive landscape, see Computational.

Research software and code sharing

Making analysis code FAIR requires addressing citation, licensing, and long-term preservation as distinct steps. CITATION.cff is a machine-readable file placed at the root of a code repository that specifies how to cite the software. It is supported by GitHub, Zenodo, and Software Heritage. SPDX identifiers provide standardised, machine-readable licence tags enabling automated licence compliance checking. Zenodo assigns a DOI to any GitHub or GitLab repository release via its direct integration, making a specific version of analysis code citable alongside a dataset. Software Heritage provides long-term archival of source code with persistent SWHIDs that remain valid regardless of what happens to the original hosting location, and integrates directly with HAL for French researchers. These practices together address the software pillar of FAIR Principles for research code.

For pre-registration and data management planning, see Study Registration and Data Management. For a practical guide to open data deposit across modalities, see Sharing your data.