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Oliver G The helpers that keep the community running smoothly. UKB Community team Data Analyst

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Activity overview

Latest activity by Oliver G

  • Oliver G created an article,

    Parallelising on UKB‑RAP: How to balance speed and cost

    When you run analyses on UKB-RAP, you can choose how your compute is set up. Two settings can significantly impact time and cost: how many jobs you run in parallel, and whether you choose spot or o...

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  • Oliver G created a post,

    Swiss Army Knife + Docker - Env set up & retrieving outputs

    I've recently stumbled across a wrinkle using the Swiss Army Knife with a docker image where I want to source an environment setup script at initialisation.This docker run statement is organised as...

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  • Oliver G commented,

    Hi Maddalena,This should be a case of: running a ttyd instance on UKB RAP downloading and installing the mango papaya code. Instructions on how to build are on the papaya GitHub. loading images for...

  • Oliver G commented,

    Hi Meghana and Maddalena,We have recently included a 3D Slicer image visualisation tool in the RAP tool library. Here's a link to the article describing how to use it:https://community.ukbiobank.ac...

  • Oliver G created an article,

    Using MONAI on UKB-RAP

    UK Biobank provides access to a rich and diverse set of imaging data, including brain, heart, and body scans. These datasets are available in formats such as NIfTI and DICOM, and more information c...

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  • Oliver G created an article,

    Viewing images on UKB RAP with 3D Slicer

    The UKB-RAP now has a 3D Slicer application. This application starts a web browser accessible interactive session with the 3D Slicer volume visualization and annotation tool.  Use cases View DICO...

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  • Oliver G commented,

    Hi Vineet,Apologies for the confusion, the ID contained in the filename of the .zip file accurately represents the identity of the files contained therein.Kind regards,Ollie

  • Oliver G commented,

    Hi Natalie,The JupyterLab doesn't have a built in “display” for the GUI to work with and therefore the answer to your question is no/not simply. We are looking at additional ways that DNAnexus that...

  • Oliver G commented,

    The GitHub notebook "Access the Sleep Questionnaire data" provides two methods for extracting the accurate data and a note on how to join the accurate encoding meanings to the raw encoded values.

  • Oliver G commented,

    Hi both,After being uploaded to Showcase, new data is added into the UKB-RAP by our partners at DNAnexus as a part of a new UKB-RAP Data Release Version. This results in a lag between the UKB-RAP a...