German Center for Diabetes Research
Working at German Center for Diabetes Research as IT-cook-general. In this project Tim is developing and coordinating the data import pipeline.
What is your professional background?
Back in the old days I started as an apprentice in IT system integration at Siemens. Setting up enterprise telecommunication systems and side hustling as a Webdesigner/-developer earned me my first few bucks. This helped to have some beers and pizzas on the weekend, in spite of the major city rent.
After realizing that this stuff bored me to death (the “telecommunication system at Siemens”-thing, not the “beer and pizzas”-thing), I stumbled into a biotech company to work as a system admin. There I spent a good amount of time underground fostering a huge, room-sized cluster computer, which calculated molecular models for some brilliant molecular modeler guys. This job sparked my interested in computational biology and the use of my good old IT craftsmanship to support scientist doing their sciency things.
From there I switched more and more from being an administrator to being a developer. After my first biotech company, I was hooked and I started to work as a full stack developer for another small biotech consultant company. Here I leveled up my relational-database-game and made my descend into web app developing hell (which I survived, but got a little bit nuts on the way).
After realizing that this stuff bored me to death (the “consultant company”-thing, not the “coding”-thing) stumbled into public science.
What are you currently doing, what experience do you bring along?
Despite the boredom that the beginnings brought me, today I profit from my background knowledge. I work in public science at the German Center for Diabetes Research (DZD) as (wannabe-) bio-informatician, developer, system-administrator, helpdesk-support and whatever else I know.
I work together with Alexander Jarasch, who is our team leader. Our overall task is to synchronize all DZD scientists on the data level. But there is always a sideshow that provides us with new adventures and adds some more aspects to our overall mission … CovidGraph enters the stage
There are many facets in CovidGraph that overlap with our main mission at the DZD. From the most obvious like Neo4j (we used Neo4j extensively at the DZD before CovidGraph already), to the main goals like helping scientists create knowledge from data, to the details like sharing many of our homebrew Python tools between projects (which is no problem at all thanks to open source)
Oh btw: I am not bored to death at all right now …
Do you have a special hobby, passion - what do you like to do most in your free time?
I my spare time I enjoy working on projects that connect the physical world with the digital world. 3D printing for example is a great tool to achieve this, or the ESP32 is a great SoC to easily connect both worlds. Also some good old woodwork coming in handy from time to time.
Right now, I am trying to build my own 4K projector, and I am failing at every damn step. Well, that’s part of the fun.
Another recent project is the breeding of my own ant colony. I use it as inspiration for my code to create an algorithm to simulate an ant colony. Again here: fail at every damn step. At least the ant colony is still alive and slowly growing 🙂
Why did you join the project - what motivated you and still inspires you today?
Martin Preusse, who is an external member of our team at the DZD, asked me if I was interested in a Covid19 coding challenge, the CORD19 (COVID-19 Open Research Dataset Challenge). I agreed and started coding some prototypes to get the data from CORD19 and transfer it to a Neo4j database.
On the way there, we picked up more and more people until we started thinking about how to organize ourselves. Faster than we could imagine, there was a community of people working on a potentially big open source project.
Later, our employer gave us the OK to invest time in CovidGraph also during work, and now CovidGraph and the team are part of my recent life.
I am still amazed by this whole story today 🙂
Have there been any “uh-huh moments” or surprises during the last months (since the project started)?
I am still surprised on how we were able to gather so many people in such a short time. At the same time the crowd managed to organize itself. A nice example of swarm intelligence and the benefits of open source.
What are the challenges of the project for you?
Creating a solid basis for CovidGraph is my task at the moment. My aim is to make the graph reproducible for everyone. I am also responsible for the infrastructure on which the graph runs. It should be reasonable, not complex and at the same time perfomant.