Bastian Greshake – “At least no one is seriously using MatLab”

The latest Open Science Stars interview couldn’t be better timed, as I’m sitting here with the interviewee, Bastian Greshake at OpenCon in Washington DC! Let’s get right to it!

Hi Bastian, and thanks for joining us here! Could you start off by letting us know a little bit about your background?

Sure! Right now I’m working on my PhD in bioinformatics at the University of Frankfurt, the city in the middle of Germany that is famous for having a more or less working airport. Before I transferred into being an armchair/standing desk biologist I did a Master’s degree in Ecology & Evolution. Much of my, maybe let’s say “traditional”, research is about how evolution has shaped the genomes of the funny living things around us. And then there’s the whole open* shebang, which we’ll probably talk about later.


When did you first hear about open access/data/science? What were your initial thoughts?

I’m not really sure whether it was before or during my undergrad studies. I was certainly experimenting with open source software since I was 15 or so. For the open access-part I at least vividly remember one of the computational biology nerds sporting an open access-shirt, so I guess that way of advertising works. In any case, in my naivety I was puzzled and shocked that open science and science aren’t the same thing yet (c.f. this), as I would have assumed that academics would be progressive, being on the frontier of knowledge and all (boy, was I wrong!).

What is the state of ‘open science’ in the field of bioinformatics? Do you think it’s progressing faster or more frustratingly slower than other fields?

Bioinformatics is a pretty huge field, so I don’t really dare to speak for all of it. But at least for the part that I’m meddling in I think we’re doing a pretty good job open science-wise. Much of the data people generate is ending up in open repositories, virtually everything is programmed in open source programming languages and much of the written code ends up being open sourced as well. And there are some decent open access journals, with pre-prints becoming more and more accepted as well. Of course, it’s not perfect yet. Many people still seem to have a hard time to resist the siren song of Nature/Science publications and unfortunately it’s also the case that people still use and publish closed source and commercial software for their analysis. But hey, at least no one is seriously using Matlab.

Many people still seem to have a hard time to resist the siren song of Nature/Science

How has practising ‘open science’ sculpted your development as a junior researcher?

Having been dragged away from the pure wet lab biology into the mystic arts of bioinformatics I guess I was doing some level of open science right from the start of my active research career. So I’d say my open* evangelism hasn’t been actively harmful so far, which I’ve heard is a risk, as much political activism is. But at least for the traditional academic pathways, it also hasn’t been much of a direct boost as far as I can tell. Having said this, doing open* and being vocal about it definitely helped in finding and establishing international collaborations early on, largely thanks to social media (c.f.

What sort of obstacles have you faced so far as an open researcher, and how have you resolved them?

Openly sharing data has never been an issue so far, thanks to well-established rules for sharing, enforced by journals etc. And even without rules in place, sharing code never was one either. The biggest issue has been on the decisions on where to publish. As I mentioned earlier, people are still pretty much in love with the useless JIF, so that discussion comes up virtually every single time when it’s time to submit/write up. Unfortunately all the lobbying in the world often isn’t enough to convince all the co-authors to take the high road of open access.

How have you found other researchers and friends/colleagues to respond to your advocacy and practices? Are they generally accepting or resilient?

There are the people who fully support all the open* stuff, others are more resilient (c.f. publishing open access). And I think many people are smugly making a bit fun of all the weird activism and refuse to see the point (yes, that’s you, who accidentally found the link on Facebook and are now smiling!).

Bastian also runs the #ScienceIsGlobal campaign. Source

How have communities like OpenCon and FORCE11, which you’re heavily engaged in, impacted upon the global development of open access, open data, and open education?

I think the biggest achievement of both FORCE11 and OpenCon is how they are building a diverse community by connecting young researchers from across the globe. Too often our open* work is still pretty much grounded in the things we know from our own experiences. Which, far too often, are based on our Europe/North American-centric view of the world. By bringing together very different communities we can learn so much from each other. And I honestly think that we’re in dire need of this kind of cross-pollination, if we want open* to succeed. As such it’s great that we’re having organisations like FORCE11 and OpenCon that foster the intersection of being open* while also trying hard to be committed to fostering global networks.

By bringing together very different communities we can learn so much from each other

Rumour has it that you’re the “The Mark Zuckerberg of Open Source Genetics” – what’s the story here?

This comparison always makes me wince, even if I myself sometimes use that phrase for comic effect. That one goes back to an article that fusion ran on me, last year. After they did a profile on our work on openSNP, they also ran one on me as an individual. It was pretty hilarious. The reason for my wincing is that I don’t see our work on crowdsourcing open data related to what Facebook is doing in any form or shape. We’re completely non-profit and give away all of what we do, including all of these “intellectual property rights”.

We’re completely non-profit and give away all of what we do, including all of these “intellectual property rights”

You co-founded the openSNP What’s this for, and what was your motivation behind it?

The elevator-pitch is that openSNP enables everyone who’s having access to their personal genome to donate it into the public domain, fostering the free and global re-use of human genetics data. With over 2.5 million people having done personal genomics testing that’s a potentially huge data source, especially if people start annotating the data with their phenotypes (think hair/eye colour but also “did you have breast cancer”?)! And as data and source code are completely open there’s no way our project can go all Google and turn evil, because everyone can spin off a clone. With now ~2800 data sets on openSNP we’re managed to go around 0.1% of the way, it’s baby steps. The main motivation for starting the project was rather personal: I wanted to donate my own data, to enable researchers everywhere to use it. Unfortunately, back then there was no good place to put my data to, so we got started with the project.


How do you think ‘open science’ feeds into broader issues to do with ‘open culture’ or ‘open society’?

I think all of these are pretty much interconnected, after all science is part of culture and society. That’s why I always like to use the open* notation, as most of the challenges of open science are also true for society, culture and whatever comes to your mind. Personally I feel that both science and culture (in a narrower sense of the term) have an obligation to challenge traditions, get us to reflect about our world and as such need to be positive role models. From my experience being open facilitates all these things.

I feel that both science and culture have an obligation to challenge traditions

What do you think the biggest impediments to open research are? How can we collectively combat or overcome them

There’s our own vanity, wanting to publish in Cell/Nature/Science, because of the fame and reputation we hope to get from it. This is also tied to the incentive structure we still face in many fields. Jobs, grants etc. are still being awarded for being successful, and this success is measured by exactly those vain standards. The first might be harder to change, but we can certainly tackle the incentive structure. We do see some change in rewarding openness, which goes into the right direction I think. Lastly there’s fear. People fear that they might have made honest mistakes in their work and will be ostracized for them if found out. Not being open protects from this to some extend. If we want to foster openness we need to be more forgiving and accept that no one of is without fault.

If we want to foster openness we need to be more forgiving and accept that no one of is without fault.

What other or platforms would you recommend to researchers looking to get into open science?

Personally I find tools a bit boring to be honest. Yes, I’ve co-written one tool, and I use many of the open science tools. Git is great, open data repositories are great, tools x, y and z are great. But at the end of the data it’s a change of mind-set, of culture, that’s really important. Culture doesn’t exist in a vacuum, but is driven by communities. So my recommendation is: Try to find others to do open science with. It’s not only much more fun, it’s also much easier to learn something new if you’re part of a community. And last but not least: The bonds you will form and the lessons learned are – at the end of the day – much more lasting than the tools you will use.

The bonds you will form and the lessons learned are much more lasting than the tools you will use.

It’s hard to give specific advice which communities to look at, as that depends heavily on the topics you’re interested in. In general the already mentioned ones, OpenCon & FORCE11, aren’t too bad a start. And if you want to go into tools: Try to bond with projects that are close to your interests and see what’s going on there. So you can have your cake and eat it too: nerd out about open tools and find a community.

If you could give one piece of advice to students looking to pursue a research career, what would it be?

Be wary of anyone telling you that research needs to be performed in a certain way, especially if the claim is that things have always been done that way. Much of the really interesting science does not (and can not) happen in the trodden ways.