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<!DOCTYPE html>
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<h1 class="promo-text">ReproNim: A Center for Reproducible Neuroimaging Computation</h1>
</div>
</section>
<section class="section-2">
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<h2 class="section-heading text-center">Welcome to ReproNim!</h2>
<p>
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.
</p>
<div class="row">
<div class="col-md-4">
<p>
</p>
<p>
ReproNim delivers a reproducible analysis framework comprised of components that include:
</p>
<ul>
<li>data and software discovery</li>
<li>implementation of standardized description of data, results and workflows</li>
<li>development of execution options that facilitates operation in all computational environments</li>
<li>provide training and education to the community</li>
</ul>
<p>
All components of the framework are intended to foster continued use and development of the reproducible and generalizable framework in neuroimaging research. See our <a href="https://repronim.wordpress.com/">Blog Post</a> for more discussion of ReproLake and ReproPond.
<ul>
<a href ="https://www.repronim.org/about_us.html"><strong>Meet the Team</strong><a/>, our <a href ="https://www.repronim.org/community.html#collaborating-projects"><strong>Collaborators</strong></a>, and our <a href ="https://www.repronim.org/eab.html"><strong>External Advisory Board</strong></a>
</p>
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<img class="overview" src="ReproNimAlignment.png" alt="Data flow diagram" />
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<p>
</p>
<h3>Breaking News</h3>
<p>
<ul>
<li><a href="https://sobp.societyconference.com/v2/">2025 Society of Biological Psychiatry (SOBP)</a> is coming up!</li>
<ul>
<li><a href="https://www.repronim.org/SOBPHack-042025/">2025 SOBP BrainHack</a> (before the annual meeting) April 22-23, 2025 in Toronto, Canada
<ul>
<li> <em></em>Organizers</em>: <a href="https://profiles.umassmed.edu/display/130002">David Kennedy</a> (UMass Chan Medical School) and <a href="https://psychiatry.utoronto.ca/faculty/erin-dickie">Erin Dickie</a> (Univeristy of Toronto), <em>Leads</em></li>
<li> BrainHack <a href="https://www.repronim.org/SOBPHack-042025/">Program</a> </li>
<li> BrainHack <a href="https://www.eventbrite.com/e/sobp-brain-hack-2025-tickets-1258326421199?aff=oddtdtcreator">Registration</a> </li>
<li> For more information, contact us: [email protected] or see our <a href="https://www.repronim.org/SOBPHack-042025/">website</a></li>
</ul>
<li><a href="https://sobp.org/2025-sobp-annual-meeting/">2025 SOBP Annual Meeting</a>, April 24-26, 2025 in Toronto, Canada</li>
<ul>
<li><em>Artificial Intelligence and Mental Health: A new landscape for research and practice</em></li>
<li>Conference <a href="https://sobp.societyconference.com/v2/">Home Page</a></li>
<li>Conference Location: Sheraton Toronto, Toronto, Canada</li>
</ul>
</ul>
<li>Announcing <a href="https://www.reprorehab.usc.edu/">ReproRehab - 2025-2026</a>! Reproducible Rehabilitation (ReproRehab) research education program</li>
<ul>
<li>ReproRehab Applications now open for both Students and Teaching Assistants!
<ul>
</li>General Application Information <a href="https://www.reprorehab.usc.edu/apply">Here</a></li>
<li>Students - <a href="https://docs.google.com/forms/d/e/1FAIpQLSfwvhfyMzWiaWSdZ7ti9Qx0KmmUmSDbPF-QuSrglhjKyq-ylw/viewform">Apply Here</a></li>
<li>Teaching Assistants - <a href="https://docs.google.com/forms/d/e/1FAIpQLSfwvhfyMzWiaWSdZ7ti9Qx0KmmUmSDbPF-QuSrglhjKyq-ylw/viewform">Apply Here</a></li>
<li>May 2, 2025: Applications close</li>
<li>May 23, 2025: Decision letters sent</li>
</ul>
</ul>
<li><strong>Congratulations</strong> to our <a href="https://www.repronim.org/fellowship.html">2024 ReproNim/INCF Fellowship Program Awardees</a></li>
<li><strong><a href="https://www.repronim.org/webinar-series.html">ReproNim Webinar Series</strong></a><strong> ~ Join us!</strong> </strong> </li>
<ul>
<li> 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.
<li> Featured topics will include important efforts in reproducibility, from both ReproNim and others
<ul>
<li><strong> Friday, May 2, 2025 at 2pm EDT</strong> </li>
<ul>
<li>We welcome <a href="https://www.med.upenn.edu/cbica/aibil/gerus.html"><strong>Guray Erus</strong></a> (UPenn/Perelman Sch. Med), Director of Research at the <a href="https://www.med.upenn.edu/cbica/faculty.html">Center for Biomedical Image Computing & Analytics</a> for a presentation on NiChart. </li>
<li>Video Conference open to the public, <a href="https://umassmed.zoom.us/meeting/register/v5Ikce2qrzkjF_dnGYL7_CeVQ_JqodcCrA">Register</a> in advance for videoconference connect details</li>
<li>Presentation will be recorded, and both Video and Slides will be posted as soon as available.</li>
</ul>
</ul>
<ul>
<li><strong> Friday, April 4, 2025 at 2pm EDT</strong></li>
<ul>
<li> ReproNim/INCF Fellowship Alum <a href="https://github.com/neurolabusc"><strong>Chris Rorden</strong></a> is our featured speaker this month, with a presentation on <em>"<a href="https://reporter.nih.gov/search/dNfNq05F10WBBWtJH_hp0A/project-details/10724895">NiiVue Visualization</a>,</em>" a highly innovative web-based tool for community driven data visualization for all stages of neuroimaging.</li>
<li><a href="https://youtu.be/EElbiLkF0Yk">Video Presentation</a> and <a href=" https://drive.google.com/drive/folders/1whQjhHIvvxfxYk-Pjjdpum2wpV-vKhCG">Slides</a> are now available.</li>
</ul>
</ul>
<ul>
<li><strong> Friday, March 7, 2025 at 2pm EST</strong></li>
<ul>
<li>Our own <a href ="https://profiles.umassmed.edu/display/130002"><strong>David Kennedy</strong></a> (<a href ="https://www.umassmed.edu/news/news-archives/2022/02/david-kennedy-awarded-$6-million-repronim-brain-imaging-grant/">PI, ReproNim</a>), provides an update on <em>‘The State of the ReproNim 3.0 – The Way of the Future’</em>! </li>
<li><a href="https://youtu.be/7EvcrEQdCV8">Video Presentation</a> and <a href="https://docs.google.com/presentation/d/1iSDI-T65wa7GOy_txFwNpExu46xLslpbZDiGca1d9Jg/edit#slide=id.g2e3b9d04b56_0_20">Slides</a>are now available.</li>
</ul>
</ul>
<ul>
<li><strong> Friday, February 7, 2025 at 2pm EST</strong></li>
<ul>
<li>Special guest speaker <a href="https://eccl.mit.edu/team-profiles/melissa-kline-struhl"><strong>Melissa Kline Struhl</strong></a> (Research Scientist, MIT) joins us from the <a href="https://eccl.mit.edu/">Early Childhood Cognition Lab</a>, where she serves as the Executive Director for the Lookit Team, and Director of <a href="https://childrenhelpingscience.com/">Children Helping Science</a>. </li>
<li><a href="https://youtu.be/dnMW_xipxJo">Video Presentation</a> is now available.</li>
</ul>
</ul>
<ul>
<li><strong> Friday, January 3, 2025 ~ No Webinar ~ Happy New Year!</strong> </li>
</ul>
</ul>
<li><strong>ReproNim Office Hours Program</strong> Drop-In for virtual Office Hours on the <strong>First Thursday of each month at 1pm Eastern Time</strong>,
or contact us anytime by email at <em>[email protected]</em> to schedule a session.
<ul>
<li>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.
<li>Open to all levels of user, whether you are new to reproducibility methods or an established investigator.
<ul>
<li><strong>Spring 2025 Virtual Drop-in Office Hours</strong></li>
<ul>
<li>Thursday, January 2, 2025 ~ <em>cancelled</em> ~ please contact us if you would like to schedule an appointment</li>
<li>Thursday, February 6, 2025 </li>
<li>Thursday, March 6, 2025 </li>
<li>Thursday, April 3, 2025</li>
<li>Thursday, May 1, 2025 </li>
<li>Thursday, June 5, 2025</li>
</ul>
<li>Sessions are accessible via Gathertown meeting space:
<ul>
<li>If you are new to <a href="https://gather.town/app/ESJPNXX7CVirKett/nmind"> Gathertown</a> 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.
</ul>
</ul>
<li>The <a href="https://abcd-repronim.org">2022 ABCD-ReproNim Course</a> has ended. However, lectures and course materials are still publicly available, see our <a href="https://www.repronim.org/news_archive.html">News Archive</a> for details.
<li> See our ReproNim problem solving series: <a href="https://how-would.repronim.org/"><strong>How would ReproNim do <em>that</em> ?!</strong></a>
<ul>
<li> In this series, we will look at a number of real world analytic, computational, data capture, management and data sharing problems in neuroimaging research.
<li> <a href="https://how-would.repronim.org/en/latest/vol01/localcontainer.html">How Would ReproNim Do a Local Container Analysis</a><em>* includes a companion Jupyter notebook</em>
<li> <a href="https://how-would.repronim.org/en/latest/vol02/publishdata.html">How Would ReproNim Publish a Dataset?</a>
<li> <a href="https://how-would.repronim.org/en/latest/vol04/freesurferpond.html">How Would ReproNim Manage Local FreeSurfer Results?</a><em>* includes a companion Jupyter notebook</em>
<li> <a href="https://how-would.repronim.org/en/latest/vol06/abcdanalysis.html">How Would ReproNim Do an Analysis on ABCD Data?</a>
<li> <a href="https://how-would.repronim.org/en/latest/vol09/containerizeworkflow.html">How Would ReproNim Containerize a Workflow? (ENIGMA Container for Shape Analysis)</a>
</ul>
<li> For a ReproNim Overview, see our paper: <a href="https://www.frontiersin.org/articles/10.3389/fninf.2019.00001/full">The ReproNim Perspective on Reproducible Neuroimaging</a>
</ul>
</p>
<p><a href="https://www.repronim.org/publications.html"><em>See our </em><strong> ReproNim Publications</strong></a>
</p>
<p><a href="news_archive.html"><strong>News Archive</strong></a>
</p>
<h3>Use cases</h3>
<p>
ReproNim tools and services are intended to support a wide range of users with varied background, from <em>applied users</em> with minimal or extensive experience in image analysis, physics, and computer science to <em>technology developers and software engineers</em>.
</p>
<p><a href="use_cases.html">Read more</a>.</p>
</div>
</div>
</div>
</section>
<section class="section-3">
<div class="container">
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<div class="col-sm-4">
<h3><a href="discover.html">Discover</a></h3>
<p>
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:
</p>
<ul>
<li>Tools to help researchers Publish their data, making it discoverable</li>
<li>Tools to help researchers Discover published data.</li>
</ul>
<p>
These tools are designed to facilitate data sharing, use and discovery. ReproNim is developing an integrated application, <strong>NeuroBLAST</strong>, that will powerfully enable user-specified search and publish functions to data repositories, published studies, versioned software packages, study-related questions, and content.
</p>
<p><a href="discover.html">Read more.</a></p>
</div>
<div class="col-sm-4">
<h3><a href="describe.html">Describe</a></h3>
<p>
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.
</p>
<ul>
<li>Tools to help researchers record (describe) experimental procedures</li>
<li>Tools to help researchers define and semantically describe workflow.</li>
</ul>
<p>
ReproNim is developing <strong>BrainVerse</strong> to help researchers manage, track and share information in a comprehensive format.
</p>
<p><a href="describe.html">Read more.</a></p>
</div>
<div class="col-sm-4">
<h3><a href="do.html">Do</a></h3>
<p>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</p>
<ul>
<li>Support, maintenance, and promotion of platforms
(e.g., <a href="http://neuro.debian.net">NeuroDebian</a>) and
tools (e.g., <a href="http://singularity.lbl.gov">Singularity</a>
and <a href="http://datalad.org">DataLad</a>) for efficient and
reproducible computation and data management
</li>
<li>Tools and materials to establish reproducible computation across
all stages of the neuroimaging research</li>
</ul>
<p>
ReproNim is developing <strong>ReproIn</strong> framework for turnkey
collection of BIDS datasets straight from the
scanner, and <strong>ReproMan</strong> to help researchers
track and manage computation resources that they have available and to
use them in a reproducible and scalable way.
</p>
<p><a href="do.html">Read more.</a></p>
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<h2 class="section-heading text-center"><a class="fragment-identifier" name="training">Teach</a></h2>
<p>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. </p>
<p><a href="teach.html">Read more.</a></p>
</div>
</div>
</div>
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<section class="section-5">
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<h2 class="section-heading text-center"><a class="fragment-identifier" name="training">Tools</a></h2>
<p>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. </p>
<!-- <p><a href="reprostack.html">Read more.</a></p> -->
<p><a href="https://docs.google.com/document/d/1I1qFuo6aemiZRUGS4KLJF2qieNXGQS1Gr-u_ti8ZK78/">Read more.</a></p>
</div>
</div>
</div>
</section>
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<div class="col-md-12">
<h2 class="section-heading text-center">Community</h2>
<p>
ReproNim is only as successful as the neuroimaging community itself. We encourage active participation and engagement in our efforts. See our current <a href="https://www.repronim.org/collaborators.html">community collaborator and service projects</a>.
</p>
<p>
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 <a href="mailto:[email protected]">[email protected]</a>. Someone from ReproNim will be in touch to see how we can work together.
</p>
</div>
</div>
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<h3 class="section-heading text-center">Community events</h3>
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<div id="more_events"><a href="events.html">See more...</a>.</div>
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<h2><a class="fragment-identifier" name="contact-us">Contact</a></h2>
<p><b>Email us</b> at <a href="mailto:[email protected]">[email protected]</a></p>
<p><b>Read our blog</b> at <a href="https://repronim.wordpress.com/">https://repronim.wordpress.com/</a></p>
<p><b>Find us on Twitter</b> at <a href="https://twitter.com/repronim">@ReproNim</a></p>
<p><b>Watch us on </b> at <a href="https://www.youtube.com/channel/UCGX2sXmEgDuUGWHDSiT1NdQ/videos">YouTube</a></p>
<p><b>Catch up on our news</b> in the <a href="https://mailchi.mp/5c9f52b3883b/repronim-newsletter-5">ReproNim Newsletter</a></p>
<p><b>Get updates</b> by <a href="https://google.us3.list-manage.com/subscribe?u=dc2b7706a7fe29c44ca3d4580&id=1330cff2b6">signing up for our mailing lists</a></p>
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