ReproNim

ReproNim delivers a reproducible analysis framework comprised of components that include:

data and software discovery
implementation of standardized description of data, results and workflows
development of execution options that facilitates operation in all computational environments
provide training and education to the community

All components of the framework are intended to foster continued use and development of the reproducible and generalizable framework in neuroimaging research. See our Blog Post for more discussion of ReproLake and ReproPond.

Meet the Team

, our

Collaborators

External Advisory Board

Breaking News

ReproNim celebrates NIBIB-funded 5-year Center Grant Renewal
We are very excited about our third year of the ReproNim/INCF Training Fellowship
- A big Congratulations and Welcome to our new Fellows!
The 2022 ABCD-ReproNim Course has ended. However, lectures and course materials are still publicly available, see our News Archive for details.
Join us for our 2022-2023 program! ReproNim Webinar Series, ‘First Fridays’ at 2pm, Eastern Time
- Webinars are held on the first Friday of every month, from 2-3pm Eastern Time
- Featured topics will include important efforts in reproducibility, from both ReproNim and others
- Friday, March 3, 2023 at 2pm EST
  - Special guest speaker Pradeep Raamana joins us from the University of Pittsburgh to share his expertise in the development of automated QA tools for MRI protocol compliance, including open datasets, in Neuroimaging Quality Control (niQC): critical yet overlooked part of neuroscience."
  - Both video conference presentations are open to the public, Register in advance for videoconference connect details
  - Video presention is now available. Slides will be posted as soon as possible.
- ~ Special Time/Day ~ Thursday, February 2, 2023 at 6pm EST (live) and Friday, February 3 at 2pm EST (re-broadcast)
  - Special guest speaker Steffen Bollmann joins us from University of Queensland with a presentation on Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging.
  - Video presention is now available. Slides will be posted as soon as possible.
- Friday, January 6, 2023 at 2pm EST
  - Our own David Kennedy (ReproNim PI, UMass Chan Medical School) and members of the ReproNim Team discuss The State of the ReproNim: An Update on Center Activities.
  - Video presentation and Slides are now available.
ReproNim Office Hours Program Drop-In for virtual Office Hours on the First Thursday of each month at 1pm Eastern Time, or contact us anytime by email at info@repronim.org to schedule a session.
- Do you have a reproducibility question, challenge or problem?
- ReproNim faculty are available to provide support and guidance on implementation of reproducibility principles and technologies in your work.
- Open to all levels of user, whether you are new to reproducibility methods or an established investigator.
- Please Note March 2023 Virtual Drop-In Office Hours are cancelled, but please contact us if you would like to schedule an appointment in March and we will gladly arrange a time. Drop-In office hours will resume in April as regularly scheduled
- Office Hours Drop-In Sessions at 1pm Eastern Time
  - Thursday April 6, 2023
  - Thursday May 4, 2023
  - Thursday June 1, 2023
  - Thursday July 6, 2023
- Sessions are accessible via Gathertown meeting space:
  - If you are new to Gathertown you will be prompted to join (which involves creating a username and password) and an avatar will be created for you that allows you to navigate the space. Upon entering, look for 'ReproNim Dave' in the 'attendees' list on the left, and follow, find, or message him.
See our ReproNim problem solving series: How would ReproNim do that ?!
- In this series, we will look at a number of real world analytic, computational, data capture, management and data sharing problems in neuroimaging research.
- How Would ReproNim Do a Local Container Analysis* includes a companion Jupyter notebook
- How Would ReproNim Publish a Dataset?
- How Would ReproNim Manage Local FreeSurfer Results?* includes a companion Jupyter notebook
- How Would ReproNim Do an Analysis on ABCD Data?
- How Would ReproNim Containerize a Workflow? (ENIGMA Container for Shape Analysis)
For a ReproNim Overview, see our paper: The ReproNim Perspective on Reproducible Neuroimaging

See our ReproNim Publications

News Archive

Use cases

ReproNim tools and services are intended to support a wide range of users with varied background, from applied users with minimal or extensive experience in image analysis, physics, and computer science to technology developers and software engineers.

Discover

On-demand access (discovery) for widely distributed web-based data, publication and software resources, with highly refined search tools. There are two broad classes of product we envision:

Tools to help researchers Publish their data, making it discoverable
Tools to help researchers Discover published data.

These tools are designed to facilitate data sharing, use and discovery. ReproNim is developing an integrated application, NeuroBLAST, that will powerfully enable user-specified search and publish functions to data repositories, published studies, versioned software packages, study-related questions, and content.

Describe

Reproducible description based on recording, reporting, and reusing experimenter procedures from start to finish. Machine-captured experimental metadata from scanner (data acquisition) to methods, analyses, and results.

Tools to help researchers record (describe) experimental procedures
Tools to help researchers define and semantically describe workflow.

ReproNim is developing BrainVerse to help researchers manage, track and share information in a comprehensive format.

Do

Efficient management of data and scripts while capturing the history and details of changes and analyses execution in a fashion that facilitates inspection, comparison, modification, sharing, and re-execution. We provide

Support, maintenance, and promotion of platforms (e.g., NeuroDebian) and tools (e.g., Singularity and DataLad) for efficient and reproducible computation and data management
Tools and materials to establish reproducible computation across all stages of the neuroimaging research

ReproNim is developing ReproIn framework for turnkey collection of BIDS datasets straight from the scanner, and ReproMan to help researchers track and manage computation resources that they have available and to use them in a reproducible and scalable way.

Teach

An increasing body of evidence point to some issues in reproducibility in biomedical or life sciences. The issue of lack of reproducibility has been now described in several scientific domains and for several years, raising concerns in the scientific community. ReproNim has developed a curriculum that will give researchers the information, tools and practices to perform repeatable and efficient research and a map of where to find the resources for deeper practical training.

Tools

We have many tools designed to help the user work through a more reproducible version of their data analysis tasks. These toold support areas such as Data processing, Data ingestion, Standardization, Search, Data Management, Computation, Testing, etc.

Community

ReproNim is only as successful as the neuroimaging community itself. We encourage active participation and engagement in our efforts. See our current community collaborator and service projects.

Join us! If you have a project that could benefit from a collaborative relationship with ReproNim let us know your interests and needs via email at info@repronim.org. Someone from ReproNim will be in touch to see how we can work together.