Fellows Resources

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: Southampton Brain Image Processing Workshops
Type: Workshop
Description
Audience: academics and clinicians developing image processing and data analysis methods for neurological disorders
Keywords
Links: https://sotnir.github.io/svg
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

ReproNim

Fellows' Resources

Resources developed by fellows.