Contributors
We try to update this page based on the git commit history:
- Neurodesk Contributors
- Neurocommand Contributors
- Neurocontainers Contributors
- Neurodesk Website Contributors
- Transparent Singularity Contributors
Core team: Steffen, Aswin, Ashley, Josh, Xincheng, Thuy, Moni, Michèle, Marshall
Steffen Bollmann (stebo85)
Section titled “Steffen Bollmann (stebo85)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Funding: Oracle Cloud (114k AUD), ECR Knowledge Exchange & Translation Fund (42k AUD), ARDC (CI for $566k AUD)
- System architecture
- CVMFS container deployment
- Initial desktop container prototype
- Container build scripts
- Application containers (afni, aslprep, code, convert3D, freesurfer, hdbet, minc, mriqc, romeo, spm12, tgvqsm, bart, fatsegnet, fsl, itksnap, lcmodel, mritools, niistat, qsmxt, root, slicer, trackvis, ants, cat12, conn, diffusiontoolkit, gimp, mricrogl, mrtrix3, rstudio, slicersalt, surfice, vesselapp, bidstools, clearswi, connectomeworkbench, dsistudio, fmriprep, julia, mrtrix3tissue, palm rabies, spinalcordtoolbox)
- Migrating container recipes and bugfixes to neurodocker upstream (fsl, ants)
- Documentation
- Tutorials (QSM, SWI, Unwrapping, lcmodel, freesurfer)
- Google Colab support
- Outreach (e.g. Mastodon, talks at conferences, YouTube videos)
Aswin Narayanan (aswinnarayanan)
Section titled “Aswin Narayanan (aswinnarayanan)”National Imaging Facility, Australia
Section titled “National Imaging Facility, Australia”- Funding: ARDC (CI for $566k AUD)
- Neurocontainer devops
- Neurodesktop development
- Neurocommand installer rewrite
- Neurodesk Play and Kubernetes implementation
- Jupyter notebook support
- Hugo website build and documentation
University of Queensland, Australia
Section titled “University of Queensland, Australia”- Application search tool with lunr
- Platform-independent GUI application (Neurodeskapp)
- Application container development (civet)
- Documentation (GitHub workflow)
- Automated building and testing of example documentation from Jupyter notebooks
- Development of interactive container building tool
Joshua Scarsbrook (Vbitz)
Section titled “Joshua Scarsbrook (Vbitz)”University of Queensland, Australia
Section titled “University of Queensland, Australia”build.shtobuild.yaml- Neurocontainers
Oren Civier (civier)
Section titled “Oren Civier (civier)”Swinburne University of Technology, Australia
Section titled “Swinburne University of Technology, Australia”- Funding: ARDC Australian Electrophysiology Data Analytics PlaTform (AEDAPT) (CI for $566k AUD), contributing to initial conceptualisation, EOI writeup, scope of project, proposal writeup, teaming up with the Australian Imaging Service (AIS), recruiting collaborators, assisting collaborators with case studies
- Design: leading the Virtual Neuro Machine (VNM) hackathon project in the 2020 OHBM BrainHack, where the first version of Neurodesktop was developed
- Development: allowing Neurodesk containers running in Neurodesktop to access sshfs mounts
- Development: template for container recipe documentation
- Development: software application containers (developer): bidscoin, MATLAB; in progress: MMVT
- Development: software application containers (facilitator): Fieldtrip, running arbitrary scripts using compiled MATLAB containers; in progress: SOVABIDS
- Documentation: for developers (contribution to “add tools”, configuring GitHub)
- Documentation: for users (copy and paste troubleshooting, accessing storage, installation on different platforms, using ARDC Virtual Desktop Service, screenshots)
- Documentation: Neurodesk’s original logo
- User testing: HPC, NECTAR, Mac, Linux, ARDC Virtual Desktop Service
- User testing: VNC and RDP interfaces, including multiple concurrent users
- Outreach: providing assistance to nodes of the Australian National Imaging Facility with installing/using Neurodesk
- Administration: one of Neurodesk/AEDAPT representatives in ARCOS, AIS and NECTAR Interactive Analytics committees and working groups
- Papers: co-author Neurodesk manuscript (in preparation; contribution to initial outline, input on first draft), co-author proceedings of the OHBM Brainhack 2021 (to be published in Aperture)
Tom Johnstone (TomEmotion)
Section titled “Tom Johnstone (TomEmotion)”Swinburne University of Technology, Australia
Section titled “Swinburne University of Technology, Australia”- Funding: ARDC (PI for $566k AUD)
- Application container (sigviewer)
Monika Doerig (MoniDoerig)
Section titled “Monika Doerig (MoniDoerig)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Interactive notebook examples (workflows: MRIQC, pyBIDS, Nipype on Neurodesk, RISE Slideshow of a Jupyter Notebook; structural imaging: brain extraction with different software packages; diffusion imaging: MRtrix; functional imaging: AFNI, FSL, FSL’s fMRI Data Analysis via Nipype)
- Co-organisation of the Neurodesk Workshop in Zurich, Switzerland (2024), and presentation of “Nipype on Neurodesk”
Michèle Masson-Trottier (micmas)
Section titled “Michèle Masson-Trottier (micmas)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Redesigning the Neurodesk logo
- Redesigning neurodesk.github.io
- User documentation
Nikhil Kumar Jangamreddy (jnikhilreddy)
Section titled “Nikhil Kumar Jangamreddy (jnikhilreddy)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Language models
- Container building
Akshit Beniwal (akshitbeniwal)
Section titled “Akshit Beniwal (akshitbeniwal)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Cloud infrastructure and testing
Kyle Mapue (kylemaps)
Section titled “Kyle Mapue (kylemaps)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Cloud infrastructure
Edan Hamilton (Edan-Hamilton)
Section titled “Edan Hamilton (Edan-Hamilton)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Cloud infrastructure
- Cyber security
Angela Renton (air2310)
Section titled “Angela Renton (air2310)”University of Queensland, Australia / École Polytechnique Fédérale de Lausanne, Switzerland / Université de Genève, Switzerland
Section titled “University of Queensland, Australia / École Polytechnique Fédérale de Lausanne, Switzerland / Université de Genève, Switzerland”- Tutorials (MNE-Python, tutorial template)
- Graphics for website (layer diagram)
- Documentation
- User testing
- Neurodesk paper lead author
Thomas Shaw (thomshaw92)
Section titled “Thomas Shaw (thomshaw92)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Windows, Mac, Linux startup scripts
- Initial transparent singularity prototype
- Application container development (LASHiS, ASHS)
- User testing
Fernanda Ribeiro (felenitaribeiro)
Section titled “Fernanda Ribeiro (felenitaribeiro)”Justus-Liebig University Giessen, Germany; University of Queensland, Australia
Section titled “Justus-Liebig University Giessen, Germany; University of Queensland, Australia”- Application container development (deepretinotopy)
- Documentation
Ashley Stewart (astewartau)
Section titled “Ashley Stewart (astewartau)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Application container development (qsmxt)
- Presentation of Neurodesk at OHBM Brainhack 2022 and OHBM educational course 2022
Xincheng Ye (yexincheng)
Section titled “Xincheng Ye (yexincheng)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Application container development (delphi, slicer, deepretinotopy)
Marshall Xu (KMarshallX)
Section titled “Marshall Xu (KMarshallX)”University of Queensland, Australia
Section titled “University of Queensland, Australia”- Application container development (VesselBoost)
Swinburne University of Technology, Australia
Section titled “Swinburne University of Technology, Australia”- Application container development (Brainstorm, eeglab, fieldtrip)
Yaroslav Halchenko (yarikoptic)
Section titled “Yaroslav Halchenko (yarikoptic)”Dartmouth College, USA
Section titled “Dartmouth College, USA”- DataLad neurocontainers
Martin Grignard (MartinGrignard)
Section titled “Martin Grignard (MartinGrignard)”University of Liège, Belgium
Section titled “University of Liège, Belgium”- Initial neurocommand prototype and menu system builder, including
apps.jsonidea
Akshaiy Narayanan (Akshaiy91)
Section titled “Akshaiy Narayanan (Akshaiy91)”The University of Auckland, New Zealand
Section titled “The University of Auckland, New Zealand”- Bugfixes in neurodesktop, added tool for diskusage, checking of new version script
Kelly Garner (garner-code)
Section titled “Kelly Garner (garner-code)”University of New South Wales, Australia; The University of Queensland, Australia
Section titled “University of New South Wales, Australia; The University of Queensland, Australia”- Tutorials (fmriprep, mriqc, physio batch)
- User testing on macOS
Paris Lyons
Section titled “Paris Lyons”Swinburne University of Technology, Australia
Section titled “Swinburne University of Technology, Australia”- Design of the first Neurodesk logo
- Project management of AEDAPT project
Lars Kasper (mrikasper)
Section titled “Lars Kasper (mrikasper)”University of Toronto, Canada; University of Zurich and ETH Zurich, Zurich, Switzerland
Section titled “University of Toronto, Canada; University of Zurich and ETH Zurich, Zurich, Switzerland”- Tutorials (physio)
- Application container (physio)
Judy D Zhu (JD-Zhu)
Section titled “Judy D Zhu (JD-Zhu)”Macquarie University, Australia
Section titled “Macquarie University, Australia”- Application containers (fieldtrip)
- Tutorials (fieldtrip)
Korbinian Eckstein (korbinian90)
Section titled “Korbinian Eckstein (korbinian90)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Documentation
- Application container development (qsmxt, mrsi)
Stefanie Evas (neuro-sevas)
Section titled “Stefanie Evas (neuro-sevas)”University of Adelaide, Australia; CSIRO, Australia
Section titled “University of Adelaide, Australia; CSIRO, Australia”- Documentation
- Application containers
The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Application container development (oshyx)
Korea Advanced Institute of Science & Technology, South Korea
Section titled “Korea Advanced Institute of Science & Technology, South Korea”- Tutorial (DataLad)
Jakub Kaczmarzyk (kaczmarj)
Section titled “Jakub Kaczmarzyk (kaczmarj)”Stony Brook University, USA
Section titled “Stony Brook University, USA”- Proof of concept contributions
Alan Hockings (ahockings)
Section titled “Alan Hockings (ahockings)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Application container development (mricron)
Arjen Lentz (arjenlentz)
Section titled “Arjen Lentz (arjenlentz)”Software freelancer
Section titled “Software freelancer”- Discussion on software licensing
Kexin Lou (Kaxnn)
Section titled “Kexin Lou (Kaxnn)”The University of Queensland, Australia
Section titled “The University of Queensland, Australia”- Application container development (mne/torch, esilpd)
Laurentius (Renzo) Huber (layerfMRI)
Section titled “Laurentius (Renzo) Huber (layerfMRI)”National Institutes of Health, USA
Section titled “National Institutes of Health, USA”- Application container development (laynii)
Marcel Zwiers (marcelzwiers)
Section titled “Marcel Zwiers (marcelzwiers)”Radboud University, Netherlands
Section titled “Radboud University, Netherlands”- bidscoin
Farwa Abbas (Farwa-Abbas)
Section titled “Farwa Abbas (Farwa-Abbas)”Adelaide University, Australia
Section titled “Adelaide University, Australia”- Initial container setup for nftsim
- Testing and validation for nftsim
- Institutional profile
Steering Committee members without code contributions
Section titled “Steering Committee members without code contributions”- Ryan Sullivan, University of Sydney: Key User, Steering Committee
- Thomas Close, University of Sydney: Key User, Scientific/Subject Expert Advisory Board
- Wojtek Goscinski, Monash University: Steering Committee, Technical Advisory Board
- Tony Hannan, Florey Institute of Neuroscience and Mental Health: Scientific/Subject Expert Advisory Board
- Gary Egan, Monash University: Steering Committee
- Paul Sowman, Macquarie University: Key User, Scientific/Subject Expert Advisory Board
- Marta Garrido, University of Melbourne: Key User, Scientific/Subject Expert Advisory Board
- Patrick Johnston, Queensland University of Technology: Key User, Scientific/Subject Expert Advisory Board
- Aina Puce, Indiana University: Key User, Scientific/Subject Expert Advisory Board
- Franco Pestilli, Indiana University: Technical Advisory Board
- Levin Kuhlmann, Monash University: Key User, Scientific/Subject Expert Advisory Board
- Gershon Spitz, Monash Epworth Rehabilitation Research Centre: Key User, Scientific/Subject Expert Advisory Board
- David Abbott, Florey Institute of Neuroscience and Mental Health: Key User, Scientific/Subject Expert Advisory Board
- Megan Campbell, The University of Newcastle: Key User, Scientific/Subject Expert Advisory Board
- Nigel Rogasch, University of Adelaide: Key User, Scientific/Subject Expert Advisory Board
- Will Woods, Swinburne University of Technology: Key User
- Satrajit Ghosh, Massachusetts Institute of Technology: provision of advice only