From 87e2595648d8601097234b4c7123fb2fad00a958 Mon Sep 17 00:00:00 2001 From: Christian Haselgrove Date: Tue, 9 Jan 2024 13:10:59 -0500 Subject: [PATCH] Add fellows' resources --- css/style.css | 5 + fellows-resources.html | 1071 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1076 insertions(+) create mode 100644 fellows-resources.html diff --git a/css/style.css b/css/style.css index ce4fff3..986278b 100644 --- a/css/style.css +++ b/css/style.css @@ -422,3 +422,8 @@ div.logos img { .main-sub-header-2 { margin-bottom: 2em; } + +div.resource dl { + border: 1px solid #aaa; + padding: 10px; +} diff --git a/fellows-resources.html b/fellows-resources.html new file mode 100644 index 0000000..e98bbc0 --- /dev/null +++ b/fellows-resources.html @@ -0,0 +1,1071 @@ + + + + + + + + + + + Fellows Resources - ReproNim + + + + + + + + + + + +
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ReproNim

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Fellows' Resources

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Resources developed by fellows.

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Title
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A (brief) Introduction to Open and Reproducible Science In Computational Brain Imaging
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Type
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Lecture
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Description
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Audience
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graduate students, postdocs in Psych to electrical engineering
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Keywords
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reproducibility, re-executability, computation, brain imaging, open science, version control, workflows
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Links
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https://github.com/sebastientourbier/openneuroresources/blob/master/lectures/reproducibility_trabit19.pdf
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Fellow
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Sebastien Tourbier
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Title
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Brain Image Processing
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Type
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Workshop
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Description
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Audience
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Keywords
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Links
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Fellow
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Yukai Zou
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Title
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Brainhack NY
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Type
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Event
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Description
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Audience
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Keywords
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Links
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https://brainhack-ny.github.io/
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Fellow
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Xihe Xie
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Title
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BrainIAK
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Type
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Tutorials
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Description
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Audience
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Keywords
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Links
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https://brainiak.org/tutorials/
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Fellow
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Elizabeth McDevitt
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Title
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Carpentries Incubator: SDC-BIDS-diffusion MRI
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Type
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Workshop
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Description
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Audience
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grad students, postdocs, staff
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Keywords
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Links
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https://github.com/carpentries-incubator/SDC-BIDS-dMRI
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Fellow
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Michael Joseph
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Title
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Carpentries Incubator: SDC-BIDS-functional MRI
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Type
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Workshop
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Description
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Audience
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grad students, postdocs, staff
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Keywords
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Links
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https://github.com/carpentries-incubator/SDC-BIDS-fMRI
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Fellow
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Michael Joseph
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Title
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Carpentries Incubator: SDC-BIDS-IntroMRI
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Type
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Workshop
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Description
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Audience
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grad students, postdocs, staff
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Keywords
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Links
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https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI
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Fellow
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Michael Joseph
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Title
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Creating Environments for Reproducible Science
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Type
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Brainhack event
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Description
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Audience
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Undergraduate - faculty
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Keywords
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shell, git/github, python, R, hpc
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Links
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https://github.com/jdkent/incf-fellow-jdkent/blob/gh-pages/index.md
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Fellow
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James Kent
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Title
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Data collection to paper-Git basics, Data Management
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Type
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Workshop
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Description
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Audience
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grad, research staff, postdoc, librarians
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Keywords
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Links
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https://github.com/adswa/mpi-datamanagement-ws
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Fellow
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Lennart Wittkuhn
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Title
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Data Science Basics in Neuroscience
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Type
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Course
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Description
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Audience
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grad, postdoc elective course
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Keywords
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Links
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https://wcm-datascibasics.github.io/
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Fellow
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Xihe Xie
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Title
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Data Science in Communication: Python and Reproducible Research
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Type
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Course
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Description
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COMM 160DS: Data Science in Communication: Python and Reproducible Research (Spring 2023, University of California, Santa Barbara)
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Audience
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Keywords
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Links
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https://github.com/yibeichan/COMM160DS
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Fellow
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Yibei Chen
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Title
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DataLad Course/Handbook
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Type
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Workshop/online course
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Description
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Audience
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researchers all stages
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Keywords
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Links
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Fellow
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Adina Wagner
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Title
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Fundamentals of MRI data
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Type
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Course
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Description
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Audience
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{'undergrad cog sci'}
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Keywords
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Links
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Fellow
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Karolina Finc
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Title
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German Learning platform for DataLad MOOC
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Type
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Course
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Description
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Audience
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researchers all stages
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Keywords
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Links
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https://ki-campus.org/
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Fellow
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Adina Wagner
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Title
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Git for Librarians
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Type
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Course
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Description
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This repository contains the curriculum and material for the Git for Librarians workshop at the VALA Tech Camp.
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Audience
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Keywords
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Links
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https://git-for-librarians.netlify.app/
https://github.com/likeajumprope/Git_for_librarians
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Fellow
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Johanna Bayer
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Title
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Git Workshop
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Type
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Workshop
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Description
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Audience
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Researchers, Infrastructure managers
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Keywords
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Links
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https://1drv.ms/b/s!AgJAAJz1ThiGms0Z1FcP8964X7sAxw?e=ZpBDCi
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Fellow
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Julian Kosciessa
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Title
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Gitlab, Docker
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Type
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Tutorial
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Description
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Audience
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postdocs, Neuroimaging grad students
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Keywords
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Links
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Fellow
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Avery Van De Water
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Title
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Guidelines for hosting plus teaching resources
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Type
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Workshop
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Description
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Audience
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undergrad/grad students, postdoc, faculty
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Keywords
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Links
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https://github.com/brainhack-uiowa/2020-brainhack
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Fellow
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James Kent
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Title
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How to Analyze IQMs
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Type
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Educational notebook
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Description
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Audience
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masters students from physics and bio, Researchers- neuroimaging, machine learning
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Keywords
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Links
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Fellow
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Celine Provins
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Title
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Image to Inference
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Type
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Course
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Description
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Audience
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undergrad, scientists, MD, postdoc
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Keywords
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Links
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https://crnl.readthedocs.io/psyc589888/#overlay-context=
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Fellow
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Chris Rorden
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Title
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Individualized training, DataLad and Data consumption
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Type
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Video tutorial
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Description
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Audience
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Keywords
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Links
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Fellow
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Felix Hoffstaedter
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Title
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Interpretability of the Image Quality Metrics (IQMs) of MRIQC
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Type
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Book chapter
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Description
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Audience
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masters students from physics and bio, Researchers- neuroimaging, machine learning
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Keywords
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Links
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https://www.nipreps.org/qc-book/auto-qc/iqms_intepretability.html
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Fellow
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Celine Provins
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Title
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Intro to Open and Reproducible Science in Computational Brain Imaging
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Type
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Lecture
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Description
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Audience
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Keywords
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Links
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https://github.com/sebastientourbier/openneuroresources/blob/master/lectures/reproducibility_trabit19.pdf
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Fellow
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Sebastien Tourbier
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Title
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Intro to Reproducibility Tools and Foundations
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Type
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Workshop
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Description
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Audience
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grad students, human cog neuro labs
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Keywords
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Links
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https://brainhack-princeton.github.io/handbook/
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Fellow
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Elizabeth McDevitt
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Title
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Introduction to ReproNim
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Type
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Lecture
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Description
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Audience
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Keywords
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Github, DataLad, YODA
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Links
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https://github.com/myyoda/talk-principles
https://github.com/DavidEWarrenPhD/INCF-Fellow-DavidEWarren
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Fellow
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David Warren
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Title
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Managing Your Reproducible Experiments with DataLad and Boutiques
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Type
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Workshop
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Description
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Audience
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upper-level undergraduates and graduate students in the sciences
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Keywords
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reproducible computational workflows data management, data processing
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Links
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https://github.com/gkiar/Repronim-GSAN
https://docs.google.com/document/d/12vvV_Vx9Jw03mr-gmAuSt2QnaByVXfhtoDPjObPGf4o/edit#heading=h.fv7xzjeknb2
https://docs.google.com/document/d/12vvV_Vx9Jw03mr-gmAuSt2QnaByVXfhtoDPjObPGf4o/edit#heading=h.pmutzjv87s05
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Fellow
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Greg Kiar
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Title
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MRI Analysis & ReproNim Reproducibility Imaging
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Type
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Course
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Description
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Audience
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Target Audience: graduate students, novices
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Keywords
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Shell, fMRI basics, BIDS, FAIR, Statistics
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Links
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https://github.com/eroesch/2019-20-PYM0FM
https://docs.google.com/spreadsheets/d/1VVsCPr4BS1Jc7TL6F7E9rJJsJ1_2PJojODq9uHUTb1A/edit#gid=0
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Fellow
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Etienne Roesch
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Title
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Open & Reproducible Neuroimaging Data Science
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Type
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Annual Workshop
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Description
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Audience
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Graduate students/postdocs in neuroimaging
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Keywords
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Keywords: Linux, version control, python, data science, FAIR, reproducible basics
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Links
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https://github.com/mick-d/repronim-fcbg
https://docs.google.com/document/d/1iSJYKgCTs7gCOIxc3T2V5Nrzfc349R3X708-rx8EVvg/edit
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Fellow
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Michael Dayan
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Title
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Open and Reproducible Computational Modeling
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Type
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Lecture series
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Description
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Audience
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Keywords
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Links
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Fellow
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Paula Sanz-Leon
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Title
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Princeton Handbook for Reproducible Neuroimaging (fMRI)
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Type
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Document
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Description
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Audience
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Target Audience: graduate students, postdocs in psych and neurobio
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Keywords
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best practices for building reproducible workflow, BIDS, data management, data analyses
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Links
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https://brainhack-princeton.github.io/handbook/
https://github.com/brainhack-princeton/handbook
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Fellow
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Sam Nastase
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Title
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Reproducibility science and methodologies
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Type
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Course
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Description
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Audience
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grad students, post docs
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Keywords
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Links
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https://docs.google.com/document/d/1I4U9E_5fvJ2BSSAux_PPQvr6QavR6g1burSyIACXuKI/edit#heading=h.qm1rn5lf4l02
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Fellow
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Jennifer Legault
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Title
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Reproducible Computation Environments
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Type
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Video tutorial
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Description
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Audience
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postdocs, Neuroimaging grad students
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Keywords
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Links
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https://uicapture.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0640440b-c7ab-46c7-9bca-afdc00f914e6
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Fellow
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Avery Van De Water
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Title
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Reproducible Data Management with DataLad
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Type
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Talk
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Description
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Audience
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Researchers, Infrastructure managers
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Keywords
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Links
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https://onedrive.live.com/?authkey=%21AFsNiGzveqZ750s&id=86184EF59C004002%21416672&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp
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Fellow
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Julian Kosciessa
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Title
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Reproducible Data Management with DataLad
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Type
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Talk
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Description
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k.
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Audience
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Researchers, Infrastructure managers
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Keywords
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Links
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https://onedrive.live.com/?authkey=%21AANsp4ZosaSOK2o&id=86184EF59C004002%21416988&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp
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Fellow
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Julian Kosciessa
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Title
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Reproducible Neuroimaging - open source guide
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Type
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Guide
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Description
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Reproducible neuroimaging guide in Polish.
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Audience
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Keywords
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Links
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Fellow
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Karolina Finc
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Title
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Reproducible Neuroimaging w/Connectome Mapper 3 Training
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Type
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Workshop
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Description
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Audience
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postdocs -psych to electr engineering, phd students
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Keywords
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Links
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https://drive.google.com/file/d/1BkZvAyGpRXpgOPtt9wOVjaWIRNquQOjl/view
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Fellow
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Sebastien Tourbier
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Title
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Reproducible Neuroimaging, tutorial guide
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Type
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Tutorial
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Description
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Audience
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cog sci students
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Keywords
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Links
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https://github.com/compneuro-ncu/reproducible-neuroimaging
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Fellow
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Karolina Finc
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Title
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ReproNim concepts
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Type
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Workshop
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Description
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Lap workshop on ReproNim.
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Audience
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Keywords
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Links
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Fellow
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David Smith
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Title
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ReproRehab: Reproducible Rehabilitation Research Education Program
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Type
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Course
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Description
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Audience
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MS and PhD students, Rehab researchers
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Keywords
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Links
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https://www.reprorehab.usc.edu/
https://github.com/npnl/OT699
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Fellow
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Sook-Lei Liew
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Title
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Research Data Management workshop at MPI Berlin
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Type
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Workshop recording
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Description
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Audience
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researchers all stages
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Keywords
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Links
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https://www.youtube.com/watch?v=fL3DWzSWFL8
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Fellow
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Adina Wagner
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Title
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Research Imaging Informatics
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Type
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Course
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Description
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Audience
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grad students biomed informatics
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Keywords
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imaging, informatics, workflows, containers, analytics, FAIR, data sharing
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Links
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https://docs.google.com/document/d/1J-wCg62yIJNCdZd_bTDYkOWCXn0eqD1j7l17MQlE4qM/edit
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Fellow
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Aaron Kemp
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Title
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Reusable (big) data management with DataLad
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Type
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Talk
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Description
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Audience
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Researchers, Infrastructure managers
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Keywords
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Links
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https://1drv.ms/b/s!AgJAAJz1ThiGms0Vdo-WifbI8FKPOA?e=ourGa2
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Fellow
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Julian Kosciessa
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Title
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syllabus for creating Univ.Del. Reproducibility Handbook
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Type
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Workshop syllabus
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Description
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Audience
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Keywords
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Links
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https://docs.google.com/document/d/1VBMtoBSuviYTDY5AdaoqIFBrHlBt6NmBToDVGkTexG4/edit#heading=h.g63wsqcq2bbh
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Fellow
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Jennifer Legault
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Title
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Version Control of Code and Data
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Type
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Online course
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Description
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Audience
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Keywords
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Links
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https://lennartwittkuhn.com/version-control-book/
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Fellow
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Lennart Wittkuhn
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Title
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Workshop/tutorial series in reproducibility
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Type
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Workshop
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Description
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Audience
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grad students, postdocs
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Keywords
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Links
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https://docs.google.com/document/d/1I4U9E_5fvJ2BSSAux_PPQvr6QavR6g1burSyIACXuKI/edit#heading=h.qm1rn5lf4l02
https://docs.google.com/document/d/1JAz10xCdWw2ifOzcV-KQhmqz9Vq7PCF1CBq868aaXvQ/edit?usp=sharing
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Fellow
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Julie Schneider
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  • Copyright © ReproNim 2016-2024
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  • Support: NIH-NIBIB P41 EB019936
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  • Site theme: themewagon.com
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