In the below interview, Bastian Greshake shares how open research has helped shape his career and what he hopes for the future of open access. This interview was originally published on the ScienceOpen blog. Thanks to ScienceOpen for letting us repost it here!
As academia continues to grapple with how to address the need for cheaper and open access to research, early-career researchers looking to advance in their fields are caught between whether they ought to fulfill traditional publishing expectations or embrace newer open access alternatives. To publish in high Impact Factor journals, or to publish in open access publications with potentially low or no Impact Factor? - that is the question. For Bastian Greshake the answer is simple - he believes in publishing open all the way.
Greshake, bioinformatics PhD candidate at the University of Frankfurt and co-founder of openSNP, which enables customers of direct-to-customer genetics tests to openly publish their test results and compare them to other results as well as current research, has devoted himself to furthering open science and open access in general. In the below interview, which was originally published by ScienceOpen, Greshake shares how open research has helped him develop in his career, his thoughts on obstacles faced by open researchers, and steps he’s taking to advocate for open access.
What is the state of open science in the field of bioinformatics? Do you think it’s progressing faster or frustratingly slower than other fields?
BG: Bioinformatics is a pretty huge field, so I don’t really dare speak for all of it. But, at least for the part 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 with 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 resisting the siren song of Nature/Science and other leading 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.
BG: 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 much as 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.
BG: 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 Journals Impact Factor (JIF), so that discussion comes up virtually every single time when it’s time to submit. 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 communities like OpenCon and FORCE11, which you’re heavily engaged in, impacted upon the global development of open access, open data, and open education?
BG: 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 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 organizations like FORCE11 and OpenCon that foster the intersection of being open, while also trying hard to be committed to fostering global networks.
BG: This comparison always makes me wince, even if I myself use that phrase for comic effect. That one goes back to an article that Fusion ran on me, last year. It was pretty hilarious. The reason for my wincing is that I don’t see how our work on crowdsourcing open data relates 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 these “intellectual property rights.”
BG: 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 color 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 about 2,800 data sets on openSNP we’ve 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, so we got started with the project.
BG: 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.
What do you think the biggest impediments to open research are? How can we collectively combat or overcome them?
BG: 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 extent. If we want to foster openness we need to be more forgiving and accept that no one is without fault.
BG: 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 day 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.
It’s hard to give specific advice on which communities to look at, as that depends heavily on the topics you’re interested in. In general, the already mentioned ones - OpenCon and 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 community.
If you could give one piece of advice to students looking to pursue a research career, what would it be?
BG: 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.