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<!DOCTYPE html>
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<h1 class="logo"><a href="index.html">ReproNim</a></h1>
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<li><a href="do.html">Do</a></li>
<li><a href="teach.html">Teach</a></li>
<li><a href="fellowship.html">Fellowship</a></li>
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<h1 class="promo-text">ReproNim: A Center for Reproducible Neuroimaging Computation</h1>
</div>
</section>
<section class="section-2">
<div class="container">
<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>
</div>
<div class="col-md-8">
<img class="overview" src="ReproNimAlignment.png" alt="Data flow diagram" />
</div>
</div>
</div>
</div>
<div class="container">
<div class="row">
<div class="col-md-12">
<p>
</p>
<h3>Breaking News</h3>
<p>
<ul>
<li><a href="https://datascience.nih.gov/nih-data-sharing-and-reuse-seminar-series">NIH Office of Data Science Strategy : Data Sharing and Reuse Seminar Series</a>, July 12, 2024, 12-1pm EDT</li>
<ul>
<li>ReproNim faculty member <a href="https://mcgovern.mit.edu/profile/satrajit-ghosh/">Satra Ghosh</a> discusses <em>The Transformative Potential and Challenges of Open Data and Technologies in Neuroscience</em> </li>
<li>Open to the Public, <a href=" https://scgcorp.zoom.us/webinar/register/WN_4Yukd63mRX6EDAd5zLIVBQ#/registration">Registration</a> required</li>
</ul>
<li><a href="https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=4229">OHBM 2024 | Organization for Human Brain Mapping Annual Meeting</a>, June 23-27, 2024, Seoul, South Korea</li>
<ul>
<li> ReproNim folks were in Seoul for OHBM!</li>
<ul>
<li><a href="https://ohbm.github.io/hackathon2024/">OHBM Brainhack 2024</a> (June 20-22)</li>
<li><a href="https://www.repronim.org/fellowship.html">ReproNim/INCF Fellowship 2024</a> kickoff </li>
<li><a href="https://ww6.aievolution.com/hbm2401/index.cfm?do=ev.viewEv&ev=1620">OHBM Conference Symposium</a> (June 24) <em> David Kennedy, organizer</em></li>
<ul>
<li>Symposium Title:<strong></strong>“In the beginning…Advances in fetal and infant Imaging”</strong></li>
</ul>
<li>We were at the <a href="https://www.nitrc.org/">NITRC</a> and <a href="https://centerforopenneuroscience.org/">Center for Open Neuroscience</a> Booths as well! </li>
</ul>
</ul>
<li>ReproNim was at the <a href="https://sobp.org/">2024 Society of Biological Psychiatry (SOBP) Annual Meeting</a>, May 9-11, 2024 (JW Marriott, Austin, Texas)</li>
<ul>
<li><a href="https://www.repronim.org/SOBPHack-052024/">SOBP BrainHack</a>, May 7-8, 2024, University of Texas Austin (in person)</li>
<ul>
<li>ReproNim faculty, collaborators, colleagues and friends initiated a very productive two-day SOBP BrainHack event!</li>
<ul>
<li><em>Hackathon</em>: Open Collaboration on participant projects</li>
<li><em>Unconference</em>: Presentations and Panel Content, organized on site by attendees</li>
<li><em>Learn</em>: Basic software and Data Analysis Skills through live lectures, hands-on tutorials</li>
<li><em>Community Building</em>: Meet, greet, socialize and network</li>
</ul>
</ul>
<li><a href="https://sobp.societyconference.com/conf/#sessions/conf10011">SOBP Conference Symposium</a>, Thursday, May 9, 2024 (JW Marriott, Austin, Texas)</li>
<ul>
<li>ReproNim faculty, collaborators and colleagues addressed the topic of<a href="https://sobp.societyconference.com/conf/#sessions/conf10011"><strong><em> "Big Data in Psychiatry: Does It Solve the Reproducibility Problem?" </em></strong></a>in a special symposium (<a href="https://profiles.umassmed.edu/display/130002/">David Kennedy</a>, <em>Chair</em>, <a href="https://profiles.sc-ctsi.org/neda.jahanshad">Neda Jahanshad</a>, <em>Co-Chair</em>): </li>
<ul>
<li>BABS in Action: Merging Reproducibility and Scalability for Large-Scale Neuroimaging Analysis with BIDS App (<a href="https://gablab.mit.edu/team/chen-yibei/">Yibei Chen</a>, <em>presenter</em>) </li>
<li>Nilearn and Big Data Facilitates Transdiagnostic Brain Biomarkers (<a href="https://criugm.qc.ca/en/chercheurs/wang-hao-ting/">Hao-Ting Wang</a>, <em>presenter</em>)</li>
<li>Continuous Contributions to Psychiatric Neuroimaging Through the ENIGMA Consortium (<a href="https://profiles.sc-ctsi.org/neda.jahanshad">Neda Jahanshad</a>, <em>presenter</em>) </li>
<li>Meta- And Multiversal Analytics in Big Data Neuroimaging: Challenges and Potential Solutions (<a href="https://case.fiu.edu/about/directory/profiles/laird-angela.html">Angela Laird</a>, <em>presenter</em>) </li>
</ul>
</ul>
</ul>
<li><a href="https://neurohackademy.org/apply">Applications</a> are now closed for the <a href="https://neurohackademy.org/">2024 Neurohackademy</a> summer school program in neuroimaging and data science based at the University of Washington eScience Institute, Seattle. This is a two-week program offered in hybrid format, July 29 – August 10, 2024). ReproNim faculty and collaborators are long time participants in this program!
<ul>
<li>Applications no longer being accepted</li>
</ul>
<li><strong>Congratulations</strong> and a big Welcome to our new <strong>2024 ReproNim/INCF Fellowship Program Awardees!</strong></li>
<li><strong><a href="https://www.repronim.org/webinar-series.html">ReproNim Webinar Series</strong></a><strong> ~ Join us for our new Fall Season!</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, December 6, 2024 at 2pm EST</strong></li>
<ul>
<li>ReproNim/INCF Fellowship alum <a href="https://nl.linkedin.com/in/johanna-bayer">Johanna Bayer</a> (Donders Institute for Brain Cognition and Behavior, The Netherlands) presents some of her recent work. Details to follow.</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>Session will be recorded for those unable to attend, and both Slides and Video Presentation will be made available</li>
</ul>
<li><strong> Friday, November 1, 2024 at 2pm EDT</strong></li>
<ul>
<li>We welcome <a href="https://cris.maastrichtuniversity.nl/en/persons/stefano-moia"><strong>Stefano Moia</strong></a> and colleagues <strong>Inês Esteves</strong> (Instituto Superior Técnico, Universidade de Lisboa - Lisbon), <strong>Rebecca Clemens </strong>(Northwestern University - Chicago), <strong>Mary Miedema</strong>(McGill University - Montreal), and <strong>Marie-Eve Picard </strong>(Université de Montréal - Montreal) for a special introduction to the <a href="https://physiopy.github.io/">PhysioPy </a>project:<em> The <strong>physiopy Community</strong>: working towards accessible and reproducible physiological data integration in neuroimaging studies</em></li>
<li><a href="https://youtu.be/4euIogu-TnA"> Video Presentation</a> is now available</li>
</ul>
<li><strong> Friday, October 4, 2024 at 2pm EDT</strong>
<ul>
<li>Our special guest speaker this month is <a href="https://childmind.org/bio/michael-p-milham-md-phd/"></strong>Mike Milham</a>, who joins us from the Child Mind Institute. Mike’s work spans brain development, child and adolescent psychiatry, and the advancement of neuroimaging data sharing initiatives and implementation of big data all in the service of understanding how functional & structural connectivity in brain may underlie mental illness. He discusses some of his very recent work with a presentation on <em>"Moving beyond processing- and analysis-related variation in resting-state functional brain imaging."</em> </li>
<li><a href="https://youtu.be/d_xHVSW8oZQ"> Video Presentation</a> is now available</li>
</ul>
<li><strong> Friday, September 6, 2024 at 2pm EDT</strong>
<ul>
<li>We are excited to kick off the new academic year with special guest speaker <a href="https://biosciences.lbl.gov/profiles/chris-mungall/">Chris Mungall</a>! Chris joins us from Berkeley National Lab & Univ. California, where he leads the Biosystems Data Science group. Chris has very considerable expertise in large systems-level computation modeling, systems biology, data science, reusable and interoperable software, machine learning and knowledge graphs, and shares his remarkable perspective with a presentation on <em>"Creating AI-ready datasets using LinkML and biomedical ontologies.</em></li>
<li><a href="https://youtu.be/pH4hiUaknow"> Video Presentation</a> is now available</li>
</ul>
</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>info@repronim.org</em> to schedule a session.
<ul>
<li>Do you have a reproducibility question, challenge or problem?
<li>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.
<li><strong>Our next Office Hours Drop-In Session is November 7, 2024 </strong> at <strong>1pm Eastern Time</strong>
<ul>
<li><strong>Thursday November 7, 2024</strong> </li>
<ul>
<li>Virtual Drop-in Office Hours</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">
<div class="row">
<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>
</div>
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</div>
</section> <!-- section-2 -->
<section class="section-4">
<div class="container">
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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>
</section>
<section class="section-5">
<div class="container">
<div class="row">
<div class="col-md-12">
<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>
<section class="section-6">
<div class="container">
<div class="row">
<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:info@repronim.org">info@repronim.org</a>. Someone from ReproNim will be in touch to see how we can work together.
</p>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3 class="section-heading text-center">Community events</h3>
<div id="events">Loading events...</div>
<div id="more_events"><a href="events.html">See more...</a>.</div>
</div>
</div>
</div>
</section>
<div class="section-7">
<div class="container">
<div class="row">
<div class="col-md-12">
<h2><a class="fragment-identifier" name="contact-us">Contact</a></h2>
<p><b>Email us</b> at <a href="mailto:info@repronim.org">info@repronim.org</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>
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