At the Ghent Center for Digital Humanities (GhentCDH) we offer IT-services mainly for researchers in the Humanities at Ghent University. The services range from internal collaborative research tools to publicly facing science communication platforms. Technically, it is a mix of off the shelve software with or without modifications and custom solutions using several technical stacks. It is a challenge to keep these services running, secure and up-to-date for years with a limited budget.
In an attempt to make maintenance of these services more manageable we are in the process of containerizing our software. Running software in containers has advantages. One of the advantages is a guaranteed consistency across environments. Also, isolated software containers can be beneficial for security and stability. It also allows one to run different versions of a stack on the same server without running into compatibility problems.
Next to running software in containers, development in containers also has advantages. It allows you to switch projects easily without needing to install dependencies - e.g a specific database system version - directly on a development machine. The main advantage I see is that containerization promotes developer hygiene. Stereotypically, developers do not have the best hygiene and can use any available help. Containerization forces developers to think about separation of code and configuration, code and data and it forces to be explicit about dependencies and environmental assumptions.
The main disadvantage is that some configuration is needed to get the containers running and that there is a small performance penalty. The following might help with that first part.
Dockerized Python database development
To put the theory to the test my colleagues and I put together a GitHub repository with a dockerized Python development setup. It shows interaction between Python and a PostgreSQL database. The database system runs in a container and the development environment is also kept in a container. Both containers are started with docker compose and configured via a .env file.
The stack uses a recent Python version, PDM to resolve Python dependencies and SQLAlchemy to interact with the PostgreSQL database. The VS code editor allows developers to run and debug software in a container. The video below shows the startup procedure and setting a breakpoint in some Python code.
Vid: Starting a database server and development container. Running and debugging Python code in a container.
Note that this is just an example setup, your setup might look quite different. You might need a different stack, use a different container environment (e.g. podman) or IDE but the principle of container based development could stay the same.
I have put off using containers for quite a while and I am quite a late convert, but now that I am doing more technical work in a small team I do see the advantages of an easy-to-set up, controlled, containerized development with explicitly defined dependencies. If you have no experience with containers yet, I would encourage you to at least try container based development out and see where it could help you!
A couple of months ago, OnTracx, a Ghent University sports-tech spin-off launched with the ‘dream of a world where every runner can stay injury-free’. That dream is based on a firmly grounded interdisciplinary research project, which I was fortunate to contributed to. The research project - headed by the UGent sports science department - developed a music-based bio-feedback system to reduce footfall shock while running with the aim to lower common running-related injury risk. I fondly remember soldering and programing the first cluncky prototypes, now already eight years ago!
In my role, I contributed to several key papers that form the foundation of OnTracx. Notably, the ‘validity and reliability’ paper, which has become the most cited work in my academic portfolio, which at least indicates academic interest. The main author of the paper is now doing a post-doc in Harvard, so he must have been doing something right! Additionally, I am also recognized as co-inventor on a patent related to the system.
Van den Berghe, P., Lorenzoni, V., Derie, R., Six, J., Gerlo, J., Leman, M., & De Clercq, D. (2021). Music-based biofeedback to reduce tibial shock in over-ground running: A proof-of-concept study. Scientific reports
Fig: schema of the low impact runner research system. Foot-fall impact is measured with wearable sensors and music-based feedback is given to the runner with the aim to avoid high impact.
The journey from research to commercial realization is always thrilling. As OnTracx steps into the market, I am filled with hope and anticipation for its success, mirroring and potentially exceeding the fruitful research track.
My ex-girlfriend and current wife likes maps. While looking for a gift for the new-years I got the idea to give her a 3D map of the nearby historic city center of Ghent with its three iconic towers. I have a 3D printer at home but still need to find a printable 3D model of Ghent.
Luckily, a couple of days ago a piece of software appeared to capture Google Earth tiles -cubes- into a single 3D file. There you can select an area of interest via google maps and download a GLTF file which captures the landscape in 3D. The software needs an API key which can be requested via the Google Developer tools.
After downloading a GLTF file, the 3D model needs to be made 3D-printable. There are online GLTF to STL converters but a bit of care needs to be taken to end up with an actually printable STL. My selected area of interest only has slight height differences in the landscape which are handled by placing the STL file on a base which compensates for these differences. Your 3D slicer can also generate structure to support inclinations in the landscape.
The 3D model generated by Google Earth is quite noisy and can contain floating parts and holes. It may be needed to edit the STL mesh directly. Selecting a slightly shifted area of interest may also solve problems with the edges of the print: take care to chop less buildings in two.
Have fun printing your own piece of the world!
Fig: a 3D model for the Ghent city center visualized with an Three.js STL viewer.
UGent
