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ReproNim: A Center for Reproducible Neuroimaging Computation

Welcome to ReproNim!

ReproNim's goal is to improve the reproducibility of neuroimaging science and extend the value of our national investment in neuroimaging research, while making the process easier and more efficient for investigators.

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.

Data flow diagram

Breaking News

  • ReproNim faculty and colleagues lead neuroinformatics neuroimaging sessions in at the INCF Neuroinformatics Assembly (virtual meeting), September 12-16, 2022
  • Our own Yaroslav Halchenko, David Kennedy and Maryann Martone give presentations at the 7th Annual Big Data Neuroscience (BDN) Workshop at the University of Texas in Austin, September 15-16, 2022
  • ReproNim faculty and colleagues presented a half-day OHBM educational course on Sunday, June 19, 2022, in Glasgow, Scotland, called How to Write a Re-executable Publication.
  • 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 provides training for reproducible analyses of big data, using the Adolescent Brain Cognitive Development Study (ABCD)data, in conjunction with instruction on ReproNim-endorsed methods and principles for reproducible data analysis. A supplemental module on Artificial Intelligence/Machine Learning is also included.
    • Although the course is now completed, all lectures and course materials continue to be publicly available online:
  • 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.
    • Next Office Hours Drop-In Session is Thursday December 1, 2022 at 1pm EST.
    • 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.
  • Join us for our new Fall Season! 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, December 2, 2022 at 2pm EST
    • Friday, November 4, 2022 at 2pm EDT
      • ReproNim Collaborator Mike Yassa, along with ReproNim faculty David Keator, join us from UCI for a discussion of Early life adversity and brain development: A case study in imaging insights and challenges.
      • Video presentation and slides will be made available as soon as possible.
    • Friday, October 7, 2022 at 2pm EDT
      • We kick off the new academic year with a special presentation by ReproNim faculty member Maryann Martone (UCSD, INCF), Reflections on progress in open and FAIR neuroscience.
      • Video Presentation is now available.
  • See our ReproNim problem solving series: How would ReproNim do that ?!
  • New Publication: The ReproNim Perspective on Reproducible Neuroimaging

See our ReproNim Publications

News History

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.

Read more.

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.

Read more.

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.

Read more.

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.

Read more.

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.

Read more.

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.

Read more.

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.

Community events

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Contact

Email us at info@repronim.org

Read our blog at https://repronim.wordpress.com/

Find us on Twitter at @ReproNim

Watch us on at YouTube

Catch up on our news in the ReproNim Newsletter

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