NeuroDesk - A scalable and easy to use data analysis environment for reproducible neuroimaging

stebo85 commented 3 years ago

Project info

Title: NeuroDesk - A scalable and easy to use data analysis environment for reproducible neuroimaging

Project lead: @stebo85

**[Timezone] Brisbane UTC+10

Description: Neuroimaging researchers require a diverse collection of bespoke command-line and graphical tools to analyse data and answer research questions. Installing and maintaining a neuroimaging software setup is challenging and often results in un-reproducible environments. Package managers and software repositories can help with this and NeuroDebian is a well-known example that drastically improves the neuroscience software distribution. However, a limitation of NeuorDebian is the inability to install neuroscientific software on Linux flavours commonly used on high performance computing systems or Windows and Macintosh computers. Researchers therefore still struggle to get access to the required software or to move analyses between different computing platforms due to the setup work required - ultimately limiting interoperability and reproducibility and impeding the broad sharing of analysis pipelines with the community. Container technology, such as docker or singularity, enables the execution of software on different operating systems and could aid in distributing scientific software. We are developing NeuroDesk, a platform build on container technology for processing and analysing neuroimaging data with the aim to lower the barrier of using various neuroimaging software in a reproducible environment, so that researchers spend less time on setting up and maintaining an analysis environment.

Two minute video introducing the project: https://youtu.be/JLv_5fycugw

Link to project: https://github.com/NeuroDesk

Mattermost handle: @sbollmann_mri

Goals for the OHBM Brainhack:

develop an electron user interface for Mac/Linux/Win that manages the docker setup in the background and provides a VNC/RDP client with clipboard support

Good first issues:

run NeuroDesk on your system and let us know what problems you run into and where usability could be improved
Open an issue for tools that you would like to see in NeuroDesk: https://github.com/NeuroDesk/caid/issues

Skills:

ideas for improving usability for non-technical users
electron/node.js/webassembly
github actions
linux admin skills
docker/singularity containers
building neurodocker recipes

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

Image for the OHBM brainhack website PXQHthA-_400x400

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

[x] Link to your project: could be a code repository, a shared document, etc. See here
[x] Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
[x] Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
[x] Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
[x] Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
[x] Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
[x] Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

[ ] Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
[ ] Number of participants, cf. here
[ ] Twitter-size summary of your project pitch, cf. here
[ ] Set up a kanban board on your repository to better divide the work and keep track of things, cf here
[x] Project snippet for the OHBM Brainhack website, cf. here

title: "NeuroDesk - A scalable and easy to use data analysis environment for reproducible neuroimaging" image: https://user-images.githubusercontent.com/4021595/119743595-9312fb80-becd-11eb-9718-68239c08d085.jpg details: "NeuroDesk is a platform build on container technology for processing and analysing neuroimaging data with the aim to lower the barrier of using various neuroimaging software in a reproducible environment, so that researchers spend less time on setting up and maintaining an analysis environment."
More information here"

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

[ ] Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
[ ] Provide links to onboarding documents if you have some.

QMENTA has agreed to sponsor the event and provide computational resources through their platform.

[ ] Get in touch with QMENTA through their Brain Innovation Hub Slack space, if you think your project would benefit from their support.

stebo85 commented 3 years ago

hi @ohbm/project-monitors: My project is ready!

stebo85 commented 3 years ago

@matteomancini - I see the project is in the "Needs revision" stage, but I can't find what I should change? Can you point me to the revisions required?

tiborauer commented 3 years ago

The revision is what we do. :) We notify you if there are any suggestions.

tiborauer commented 3 years ago

Can you, please, specify the optional and the recommended points or untick the corresponding box(es)?

I assume the documentation is contained within the repo.

Have you also contacted QMENTA?

stebo85 commented 3 years ago

Dear @tiborauer - I unticked the boxes for the optional components. I am not planning on contacting QMENTA.

shawnrhoads commented 3 years ago

FYI, this project is currently listed as "Learn and Enhance BrainIAK Tutorials: From Basics to Advanced fMRI Analyses" on the website

tiborauer commented 3 years ago

Sorry! I have just updated the repo. The website should also reflect it soon.

aswinnarayanan commented 3 years ago

Updated mattermost channel is here https://mattermost.brainhack.org/brainhack/channels/virtual-neuro-machine-vnm

ohbm / hackathon2021