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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

  • We are pleased to announce that applications are now being accepted for our fourth year of the ReproNim/INCF Fellowhsip Program.
    • Applications are now open, with a submission deadline of January 31, 2024.
    • We will then review and select the 2024 ReproNim/INCF Fellows by March 1st, to allow folks to make pre-registration discounts for OHBM.
  • The 2023 Neuro-Irv and Helga Cooper Foundation Open Sciences International Prize was recently awarded to the Brain Imaging Data Structure (BIDS) as an impactful global community initiative driving international data standards for neuroimaging. ReproNim faculty member and BIDS Steering Committee member Yaroslav Halchenko represented BIDS at the 5th Open Science in Action Symposium (November 30, 2023 in Montreal, Canada)
  • Society for Neuroscience 2023 Annual Meeting, November 11-15, 2023
    • In-person at the Walter E. Washington Convention Center, Washington, D.C., (also includes a virtual component)
    • ReproNim faculty were there, including representation at the following exhibitor booths:
      • DANDI: Distributed Archives for Neurophysiology Data Integration (Booth #3316)
      • INCF: International Neuroinformatics Coordinating Facility (Booth #3323)
      • NIF: Neuroscience Information Framework (Booth #3417)
  • Center for Open Science, Virtual Event: "Helping Others Use Your Data: Lessons from the Field of Neuroscience"
    • Virtual Event, Wednesday, November 8, 2023 at 11am ET
    • Event Recording now available.
    • Speakers included ReproNim Faculty member David Keator and collaborator Karl Helmer
  • Join us for our 2023-2024 'First Fridays' ReproNim Webinar Series, at 2pm, Eastern Time
    • Webinars are held on the first Friday of every month during the academic year, from 2-3pm Eastern Time, and are open to the public.
    • Featured topics will include important efforts in reproducibility, from both ReproNim and others
      • Friday, February 2, 2024
        • Nikola Stikov (University of Montreal) discusses NeuroLibre and various aspects of publishing to include essential materials for reproducibility, in his presentation on NeuroLibre Reproducible Preprints: Going Beyond the PDF.
        • Webinar presentations are open to the public, Register in advance for videoconference.
        • Video Presentation and Slides will be made available as soon as possible thereafter.
      • Friday, January 5, 2024 - Cancelled due to unforeseen circumstances
      • Friday, December 1, 2023
        • Daniel Asay joins us from the Harvard University Center for Brain Science. He discusses his work with Tim O'Keefe and colleagues on open-source quality control pipelines (XNAT 1.8+ plugins), particularly for diffusion weighted imaging, in his presentation: DWIQC: Diffusion Imaging Quality Control Pipeline
        • Video Presentation and Slides are now available.
      • Friday, November 3, 2023 at 2pm EDT
        • We welcome Anisha Keshavan, Senior Data Scientist from Octave Bioscience, for a discussion of 'Reproducible Data Science Practices at Octave.'
        • Video Presentation is now available.
      • Friday, October 6, 2023 at 2pm EDT
        • Rudolph Pienaar joins us as guest speaker to kickoff our fall season! He shares his expertise and insights on the development and applications of an open source platform for computational research and medicine (ChRIS), with a presentation on "The Challenges of Medical Computing in the Age of AI and Clouds – how ChRIS can help."
        • 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.
    • Office Hours Drop-In Sessions at 1pm Eastern Time
      • Thursday January 4, 2024 Cancelled for January 4th
        • Drop-in Office Hours are cancelled for January 4, 2024, but we will gladly meet individually by appointment, please contact us at info@repronim.org to schedule an appointment
      • Thursday February 1, 2024
      • Thursday March 7, 2024
      • Thursday April 4, 2024
    • 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.
  • ReproNim faculty members Maryann Martone, Yaroslav Halchenko, and Jeff Grethe gave lectures in the INCF Short Course: Introduction to Neuroinformatics at the University of Washington Seattle, October 2-4, 2023
  • The 2023-2024 Reproducible Rehabilitation Research Education Program (ReproRehab) kicked off its second year under the leadership of ReproNim Fellow Sook-Lei Lew, joined by ReproNim Faculty members David Kennedy and JB Poline. University of Southern California, Los Angeles, CA. September 29-30, 2023
  • ReproNim had strong representation at the INCF Neuroinformatics Assembly 2023! (virtual event, September 18-20, 2023). Both JB Poline and Maryann Martone led sessions in this year’s assembly, organized around the theme of ‘Transparency in FAIR neuroinformatics’ and were joined by several ReproNim faculty:
    • Session 1: A FAIR roadmap for knowledge graphs and ontologies
        JB Poline, (chair, speaker), Jeff Grethe (speaker), Fahim Imam (speaker)
    • Session 3: Streamlining Cross-Data Platform Integration: Processes and Solutions for Rapidly Developing an Integrated Workflow Across Independent Systems for the US BRAIN Initiative Cell Census
      • Maryann Martone (co-chair, speaker), Yaroslav Halchenko
  • This year’s Make Data Count (MDC) Summit: The Time is Now to Advance Data Metrics, Washington DC (September 12-13, 2023) included a presentation by ReproNim Faculty member JB Poline in the session on ‘Incorporating Data Metrics in Tenure & Promotion.’
  • Both David Kennedy and JB Poline participated as instructors in the Neurohackacademy summer school program in neuroimaging and data science, (hybrid event, August 7-18, 2023) based at the University of Washington eScience Institute, Seattle, WA
  • We are very excited about our third year of the ReproNim/INCF Training Fellowship
    • We also know that inquiring minds would like to know! We anticipate opening applications in January 2024 for our fourth year of the fellowship, with a start date in June, 2024
  • The 2022 ABCD-ReproNim Course has ended. However, lectures and course materials are still publicly available, see our News Archive for details.
  • See our ReproNim problem solving series: How would ReproNim do that ?!
  • 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.

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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