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Steps to begin with Brainlife

Owned by Aurore Bussalb (Unlicensed)
Last updated: Jun 25, 2021
2 min read

Here are the steps you should follow to be able to develop Apps on Brainlife:

1. Understand what Brainlife is

  1. Create an account on https://brainlife.io/

  2. Join the Brainlife slack https://brainlife.io/docs/contact/, you need to join the following channels:

    1. #datatype

    2. #brainlife_meeg

    3. #random and #general

    4. you need to ask to be added to #project_nibib_meeg, #brainlife_calendar and maybe later #brainlife_coreteam (they are private channels)

  3. Read the Brainlife documentation : https://brainlife.io/docs/, especially the parts:

    1. Home

    2. Using Brainlife

    3. Developping Apps

You can try to create the Helloworld app. Bear in mind that a Brainlife app is supposed to run on BL but also locally.

You can also check the following Confluence pages:

These pages contain info that I gathered after talking to Giulia Berto and Soichi Hayashi. If you have any trouble regarding Brainlife apps, don’t hesitate to ask them for help.

The key concept to understand on Brainlife is the “datatype” because Apps used it to communicate between each other.

2. Get familiar with the Apps already created

Several MEG/EEG preprocessing and processing apps have already been created. They are still private (meaning they are available for only the BL Users who can access the projects the Apps are registered on) because they have not been tested on many different datasets and they can be still improved (see each description page of the Apps in https://icm-institute.atlassian.net/wiki/spaces/CENIR/pages/1256095775 and https://icm-institute.atlassian.net/wiki/spaces/CENIR/pages/1760231436).

@Maximilien CHAUMON is a maintainer of these Apps on BL, so ask him to add you as a maintainer too. Also, clone the GitHub repositories of these Apps (see https://github.com/AuroreBussalb?tab=repositories)

Don’t hesitate to run these Apps locally, but also on Brainlife. The Python code is fully commented but please check the following Confluence pages to understand better why some code lines are written:

I already ran all of my Apps on Aurore’s default project on Brainlife (ask @Maximilien CHAUMON to be added to this project to see all the tests that were made). The results are discussed here:

To know more about why some decisions have been made, check the Confluence section https://icm-institute.atlassian.net/wiki/spaces/CENIR/pages/1163100184.

3. Get ready to run/create Apps

I strongly recommend you to register your own Brainlife computing resource to be able to test more easily the Apps you created (see https://brainlife.io/docs/resources/register/). To set up your resource, don’t follow the steps described there (Soichi didn’t update this tutorial) but instead check the pages:

If you have any trouble, don’t hesitate to ask Giulia or Soichi.