[July '20]

Bastian makes FOSS and takes our Twitter mic from July 01 to 08. Thank you, Bastian!

Tell us about yourself

I’m a biologist/bioinformatician by training, and have been a big proponent of open science pretty much since my first steps into doing research as an undergrad. Since around 2010 I have been working on different aspects of open science: Promoting open access to scientific publications; making research software available and releasing them as open source code; open data sharing; etc.).

In the last few years, since finishing my PhD, I decided to switch things up a bit and started working full time in the growing field of citizen/community science. The principles of FOSS are maybe even more important there, as the goal is to have people from outside of traditional academia to engage in doing research side by side with academic researchers. Which makes equity in access, reuse, even more important in my opinion.

What are you working on right now?

Since last year I’m an independent research fellow at the Center for Research & Interdisciplinarity in Paris. My lab specifically works on the question of how we an apply the same principles of commons-based peer-production that we see in FOSS and projects like Wikipedia to the design of citizen science projects. Traditionally citizen science projects operate rather hierarchical with most of the power being held by the academic researchers, so the question is: How can we move towards a truly peer-based citizen science?

I’m also the Director of Research for the Open Humans Foundation, a platform for enabling self-research based around our own personal data (be it from wearables, GPS records, social media usage, etc). We aim to allow people to scale their individual self-research to peer-based group-projects and create shared knowledge and expertise. Of course we’re highly interested to apply the peer-production principles there too.

What is most interesting about that?

To me the most interesting aspect of this work is that it’s right in the middle between pure FOSS technology development and the social impact that the design decisions have. By design and out of principle all of our technology we develop is open source and relies heavily on other open source projects. Just recently we integrated our own JupyterHub deployment into Open Humans to allow people to analyze and explore the data they collect. Based on this we wrote some new Jupyter plugins to allow people to easily share their notebooks with other community members.

On the research side we aim to implement the principles of peer-production (modularity, lack of hierarchies, being not for profit, re-use) throughout the larger design at the project. To enable this we’re engaging in user research and collaborative design with our community for all of our implementations. All of this together allows us to have a shared sense of ownership and a wide variety of contributions.

How did you first discover FOSS?

I have to blame the field of bioinformatics at large. Overall bioinformaticians are really good at releasing their code and making it open source, to a point where in many sub-disciplines it’s the norm rather than the exception. And the same is true for the sharing of data. As a result I got to appreciate started contributing to FOSS early on. In fact, already back in 2011 I started openSNP together with Philipp Bayer. openSNP is a crowdsourced open data repository for personal genomes (e.g. as analyzed by 23andMe and ancestry). Members release their own genomes into the public domain using the Creative Commons Zero public domain declaration and all of our code is open source too.

Since then over 5,000 members have shared their data sets through openSNP - making it one of the worlds largest databases of its kind. We also got some great interns to work with us through the Google Summer of Code and the data is widely used in academic research, used for teaching in classes, and even for open source machine learning competitions.

Why should others get involved with FOSS?

For me personally FOSS was a great way to learn a whole range of new skills that are extremely valuable. Despite having a PhD in Bioinformatics I had virtually zero lectures on computer science, coding or any related things during my studies. A gap that I could fill thanks to the wealth of open learning resources and learning from/contributing to FOSS. Plus there are some wonderful FOSS communities that are just a pleasure to be a part of. Besides that it is a great way to improve the software you are using and relying on. Many of the contributions I’ve made came out of the need to fill some gaps in features etc!

What difficulties and limitations do you see with FOSS?

One big problem I see, especially in the field of academically created FOSS projects, is the question of sustainability and maintenance. Too often these projects end up dying due to the academic incentive structure: Academics need to publish research findings and once a project is published there is very little reason to keep maintaining it.

At the same time it’s often nearly impossible to get research funding to improve or maintain projects, as funding goes to “the next shiny thing” instead of maintaining central infrastructure. So people need to move on, leaving behind slowly decaying tool chains. I think this is especially problematic in the case of infrastructure on which many people have come to rely.

How can they be solved?

The incentive structure needs to change. We need to acknowledge all the hard work that goes into creating and maintaining such projects instead of just looking at the number of research papers that academics publish and how often they are cited. Helping to maintain FOSS software that is used daily by thousands of researchers around the globe should be at least as important. Similarly, funders need to come to understand that maintaining FOSS projects is something worth supporting, instead of throwing away money to reinvent the wheel.

What does a perfect day off look like?

That’s hard to generalize, but something along these lines: Sleeping in, reading a good book in bed before getting up, going out for a walk and to do some photography and then meeting some friends for dinner.