NeuroDesk -A flexible, scalable, and browser-based data analysis environment for reproducible neuroimaging

[stebo85]

Title

NeuroDesk -A flexible, scalable, and browser-based data analysis environment for reproducible neuroimaging

Leaders

Steffen Bollmann
github: @stebo85
mattermost: @sbollmann_mri
mastodon: https://masto.ai/@Sbollmann_MRI

Aswin Narayanan
github @aswinnarayanan
mattermost: @aswinnarayanan

Collaborators

No response

Brainhack Global 2022 Event

Brainhack Australasia

Project Description

• What are you doing, for whom, and why?
  Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data. Analysis pipelines for neuroimaging data typically rely on specific versions of packages and software, and are dependent on their native operating system. These dependencies mean that a working analysis pipeline may fail or produce different results on a new computer, or even on the same computer after a software update.

• What makes your project special and exciting?
  Neurodesk provides a platform in which anyone, anywhere, using any computer can reproduce your original research findings given the original data and analysis code.

• How to get started?
  https://www.neurodesk.org/docs/neurodesktop/getting-started/play/

• Where to find key resources?
  https://www.neurodesk.org/

Link to project repository/sources

https://github.com/NeuroDesk

Goals for Brainhack Global

• make container contribution ALOT easier (ideas: interactive container building on the neurodesk play platform itself - no install required; generating docker recipes based on the interactive install steps recorded)
• running Neurodesk on ARM and Apple M1/2 chips
• Develop Notebook experience of Neurodesk: the unerlying jupyter instance could be used to develop pipelines directly in jupyter without requiring the full desktop experience: https://play-sydney.neurodesk.org/v2/gh/neurodesk/jupyter-neurodesktop-image/main - for this we would like to develop a better user experience and example notebooks

Good first issues

1. issue one:
   Contribute a new container for Neurodesk of your favorite tool: https://www.neurodesk.org/developers/new_tools/add_tool/

2. issue two:

Communication channels

https://mattermost.brainhack.org/brainhack/channels/virtual-neuro-machine-vnm

Skills

• Python
• Bash
• Github

Onboarding documentation

No response

What will participants learn?

Building software containers

Data to use

No response

Number of collaborators

more

Credit to collaborators

Contributions are listed here: https://www.neurodesk.org/developers/contributors/

Image

Type

coding_methods, documentation, method_development, pipeline_development, visualization

Development status

2_releases_existing

Topic

reproducible_scientific_methods

Tools

other

Programming language

containerization, documentation, Python, shell_scripting

Modalities

not_applicable

Git skills

3_continuous_integration

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.

[stebo85]

Hi @brainhackorg/project-monitors my project is ready!

[stebo85]

Mastodon sized project pitch: Neurodesk provides a containerised data analysis environment to facilitate reproducible analysis of neuroimaging data and with this provides a platform in which anyone, anywhere, using any computer can reproduce research findings given the original data and analysis code.