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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 will be presenting a half-day OHBM educational course on Sunday, June 19 called How to Write a Re-executable Publication. Join us by signing up on the OHBM web site.
  • ReproNim celebrates NIBIB-funded 5-year Center Grant Renewal
  • We are very excited about our upcoming third year of the ReproNim/INCF Training Fellowship.
    • A big Congratulations and Welcome to our new Fellows!
    • Thank you to all who applied, and for those not admitted this year, please know that you are welcome to re-apply in the future.
  • The 2022 ABCD-ReproNim Course is now underway, and all materials are publicly available.
  • Introducing our new ReproNim Office Hours Program! Do you have a reproducibility question, challenge or problem? 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.
    • 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 June 2, 2022 at 1pm EDT.
    • 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 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, June 3, 2022 at 2pm EDT
      • Special guest speaker Ted Satterthwaite joins us from the Lifespan Informatics and Neuroimaging Center at UPenn, with a presentation on Reproducible Image Curation and Processing for Large-scale Studies of Brain Development.
      • Video Conference open to the public, Register in advance for videoconference connect details
      • Session will be recorded for those unable to attend, and both Slides and Video Presentation will be made available
    • Friday, May 6, 2022 at 2pm EDT
      • Special guest speaker Eugenio Iglesias joins us from MGH to share his expertise in a presentation on Synth*:Domain Randomization for out-of-the box Brain Analysis with Enhanced Reproducibility.
      • Slides and Video Presentation will be made available.
    • Friday, April 1, 2022 at 2pm EDT
      • Tim Errington joins us from the Center for Open Science, with a presentation on Reproducibility in Preclinical Cancer Research - Lessons from the Reproducibility Project: Cancer Biology. This project underscores valuable insights and perspective on reproducibility that translate widely across scientific disciplines.
      • Slides and Video Presentation will be made available.
    • Friday, March 4, 2022 at 2pm EST
      • Guest speaker and ReproNim Affiliate Peer Herholz discusses the topic of machine/deep learning with a presentation on "Everything Matters...also in Machine Learning: Some Pointers from ReproNim."
      • Video Presentation is now available. Slides will be made available as soon as possible.
    • Friday, February 4, 2022 at 2pm EST
      • Sebastian Urchs joins us from McGill to discuss linked data principles and how they can be used to integrate data via metadata, with an illuminating presentation on Annotation 101: Linked Data 101 and the Semantic Web.
      • Video Presentation and Slides are now available.
    • Friday, January 7, 2022 at 2pm EST
      • Special guest speaker Dorit Kliemann discusses Opportunities and Challenges of a preregistration: Functional Connectivity of the Amygdala in Autism.
      • Video Presentation and Slides are now available.
    • Friday, December 3, 2021 at 2pm EST
      • We welcome guest speaker Neda Jahanshad from the ENIGMA consortium for a presentation on The Evolving Landscape of Structured Multisite Neuroimaging Analyses: Observations and Opportunities from the ENIGMA Consortium.
      • Video Presentation and Slides are now available.
  • Introducing 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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