Fellows' Resources

Resources developed by fellows.

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