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Getting started on BEAR

This page collects tutorials and examples for neuroimaging analyses to run on BlueBEAR. This is intended to extend the main Bear Technical Documentation pages.

Here we provide a set of links, tips and tricks for getting started. Mostly linking out to other places.

Step 0: Linux

Bear provide a Introduction to Linux guide. Many computing services on bear rely on linux. There are in-person workshops and an online canvas courses available on this page.

Step 1: BlueBEAR

Bear also provide a Introduction to BlueBEAR course. There are in person workshops and an online canvas course.

Step 2: RDS Projects

You'll need to be a member of a Bear project and have a Bear linux account to use BlueBEAR. Your PI and lab can help with this. A detailed guide for accessing BEAR is provided on the technical docs.

Step 3: Bear Portal

BEAR Portal provides web-based access to a range of BEAR services, such as JupyterLab, RStudio, and various other GUI applications. BEAR Portal is only available on campus or using the University Remote Access Service.

Step 4: Launching interactive sessions

From BEAR Portal there are three options for launching an interactive analysis session.

  • Some software packages have GUI Apps installed on BlueBEAR that can be launched from the Bear Portal - the main example for neuroimaging analysis is Matlab.

  • JupyterLab and RStudio are installed as standalone apps that can be launched from BEAR Portal. (ote that only packages installed on Bear Apps are available to load in JupyterLab).

  • A complete Linux Desktop can be launched as the BlueBEAR GUI. BlueBEAR GUI is effectively a blank-slate linux desktop, into which you can load the modules for various applications, specify environment variables etc. by using the built-in Terminal client (see image below), and then ultimately launch the interface for the application that you require.

Step 5: Running cluster jobs with Slurm

There are two ways to submit a cluster job - the bluebear terminal and the job submission page on Bear Portal

BlueBEAR Terminal Once you have prepared a submission script, you can go to that location in the BEAR-Portal file browser and click 'Open in termnal' in the top. This will open a terminal session from which you can submit, monitor and (optionally) cancel your job using sbatch, squeue and scontrol.

Note

These terminal sessions are ONLY intended for submitting and monitoring cluster jobs - not for active analyses. This should be carried out on BEAR GUI or similiar.

BlueBEAR Job Composer this is a GUI page which helps you to write a new job to submit to blue-bear using the job composer.