James Thomas

@jatonline.uk

177 Followers 507 Following

Data Scientist at the Jean Golding Institute, University of Bristol. Working on Urban Analytics. https://jatonline.uk

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Title card for the video: Can others reproduce your conda results? Using pixi in a Python data analysis project. By James, Thomas, Jean Golding Institute, University of Bristol
VS Code error messages showing: Process Execution: ~/anaconda3/envs/defaultwork/bin/python 09:12:06.174 [error] Failed to request kernel info [Canceled: Canceled at Ah. value /Users/~/. vscode/extensions/ms-toolsai.jupyter-2025 3
Screenshot of the Wagtail and Django release timeline, filtered for releases prior to June 2025, with security support at least until today (22 April 2025). Shows Wagtail 7.0 LTS (in the future), and current supported versions (in order): Django 5.2 LTS, Wagtail 6.4, Wagtail 6.3 LTS, Django 5.1, Wagtail 5.2 LTS and Django 4.2 LTS. Wagtail 5.2 LTS support ends soon.
Screenshot of a terminal session. The terminal says: Project was started with: uv init -- lib $ tree * README. md * pyproject. toml * uv. lock * notebooks * example_notebook.ipynb * src * my_project * __ init __. py * probability.py 4 directories, 6 files
Will Chapman presenting a slide at the Health Data Research Network. The slide says: Purpose of this session We want to understand the current processes) for getting routine data for research from our local NHS - "Easy data" that is fast to specify and extract - Structured data that needs transformation before transfer - Multi-modal data that can't be created through the right query, eg images, vitals We want to understand what it took to get (routine) data for health research via the Trusts - Which parts of the process went well, with good support from UoB/NHS? - Which parts of the process were lengthy or painful? This will feed into a project to streamline health data pipelines for both the SDE and our usual research platforms
Ben Elsworth talks about research at Our Future Health at the Health Data Research Network. The slide says: What our participants donate to Our future Health Complete a baseline questionnaire (demographics & household, work & education, lifestyle, family history, personal health history) Physical measurements taken at clinic appointment (height, weight, waist circumference, blood pressure, heart rate) A blood sample for genotyping and for long-term storage of plasma, buffy coat, and DNA DNA is genotyped using a custom array that captures 700k up-to-date variants of interest for optimal research insights Provide permission for data linkage to health-related datasets (e.g., primary care, secondary care, cancer, death) Provide permission to be recontacted for further surveys/biospecimens/assessments and to be invited to additional studies/trials
Richard Welpton presenting a slide at the Health Data Research Network. The slide says: Other key lessons Researchers work collaboratively. TREs should support this. Invest in tech, invest in people: Automate the repetitive and mundane. TREs and researchers need to understand each other. Invest in specialist support
Fiona Booth presenting a live survey at the Health Data Research Network. The slide says: What do you think makes research reproducible? published methods methodology is robust open code access honesty accessible code good code base publications readability visibility clear datasets open data open reporting access to data documentation curated data robust data sets version control open source consistently must be desired openness code access to code transparency reusable script accurate reporting sharing code common methods detailed meta data method is available
Damon Chow giving a live demo of the Health Data Research Gateway website at the Health Data Research Network.
Rachel Denholm presenting a slide at the Health Data Research Network. The slide says: What is a secure data environment (SDE?) (= trusted research environment (TRE)) Data access process Accredited researcher proposes project → Request approval from one advisory group → Access via a remote portal. Cannot copy or download data. Outputs exported only after checked by an independent researcher → End of project, access removed
Programme for the Health data Research Netowrk workshop on 12th March 2025. 10.10 Rachel Denholm, Senior Lecturer, Bristol Medical School, UoB, and Co-Director of Health Data Research UK South West The Rise of New English Secure Data Environments 10.30 Damon Chow, Business Data Analyst, HDR UK The Health Data Research Gateway 11.10 Fiona Booth, Data integrity & Quality Assurance Programme Director, UoB Commercial vs. academic research approaches to reproducibility 11.30 Richard Welpton, Head of Data Service Infrastructure, Economic and Social Research Council Improving the experience of accessing sensitive data for research 11.50 Ben Elsworth, Lead Data Engineer, Our Future Health Processing and releasing genetic data at Our Future Health 12.20 Will Chapman, Data Scientist, Jean Golding Institute Routine data for health research 12.40 Q&A and round table Challenges in health data research: aims for the HDRN
Pau Erola presenting a slide at the Health Data Research Network. The slide says: What will we do? The HDRN will organize workshops every month that will discuss about specific topics on health data science. The events will be an opportunity to share knowledge, discuss and agree best practices, and networking. Taking inspiration from The Turing Way and Data Hazards, each workshop will be reflected in a chapter of a live, collaborative book on standard practices for health data science.