HIC Knowledge Base
Introduction
Welcome to the Health Informatics Centre (HIC) Knowledge Base about our Trusted Research Environment (TRE). You can search for topics below, or see a full list of articles using the menu on the left. Hopefully these how-to guides help you start using the TRE and working on your project.
How-to search
Getting started
Here are a few starting articles to begin working with the TRE:
https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803696
https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803812
https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803109
Working patterns
Our routine maintenance window is 07:00 to 09:00 every Tuesday morning. This should not normally impact your ability to use the TRE- we aim to give notice in advance if we think this might happen.
How should I get support? We are continually developing this HIC Knowledge Base. However, if you do need help, email HICSupport@dundee.ac.uk and we will aim to provide support as quickly as possible.
Below is a table to signpost you to the most frequently asked questions, exploring commonalities amongst TRE users.
We keep track of changes to the Service Workbench and workspace types on our TRE Change Log page.
FAQs
FAQ | Overview | Links to relevant Knowledge Base articles |
|---|---|---|
What software is available? | This should be touched on in project initiation meetings, but most statistical or image processing tools and software can be made available (e.g. R, Python), dependent on licensing (e.g. Matlab). | https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802422 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802599 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803475 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803475 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802273 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803143 |
Where is my data? | This depends on your workspace and the set-up storage, but generally - Linux (Ubuntu): ‘studies’ folder under home directory Windows: D:\ drive
| https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803150 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802305 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803905 |
What is a SQL database? | Structured Query Language (SQL) is a way of storing data that requires users to query the raw data. SQL and Python are often used for big data analysis on the cloud. When we provision data, we have 2 copies - read-only access to a database, and a ‘working’ database that you can edit as you wish.
| https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802305 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802963 |
Is there an option for more powerful processing? | Our ‘standard offering’ will satisfy most research projects, however, those studies that use AI/ML may require more powerful compute. High Performance Computing (HPC) can be provisioned and you can create your own cluster to potentially use Slurm as a workload manager. | https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802599 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1803073 https://hicservices.atlassian.net/wiki/spaces/HKB/pages/1802273 |