Covering the bioinformatics niche and much more

SciView: Part 4, Interview With Rosie Redfield

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Dr Redfield, from the University of British Columbia is a microbiologist and an advocate of Open Science, a rather recent movement that is trying to open the doors (and computers) of every scientific lab. I took the opportunity to ask her about her views of Open Science and why to create an scientific diary online. I would like to thank Dr Redfield for the opportunity.

My initial questions are about Open Science. What are the main benefits of opening your whole scientific life to the public? And the drawbacks of doing this? How is the best way to manage a lab under Open Science?

RR: There are practical consequences and philosophical consequences to doing open science the way we are. So far the practical consequences have been good – I get helpful suggestions from people I’ve never met. And I can tell people who wonder what we’re doing to take a look at the stuff on our web pages. I’d love to also be able to say that our open approach has attracted collaborators and new lab members, but that hasn’t happened yet. Another big practical consequence is that writing blog posts about the research I’m working on helps me think clearly about it. So whenever I’m feeling muddled I post the problem on my blog.

Philosophically it just feels right. Science is fundamentally a collaborative endeavour; we all build on what others have done. Just as the web gives us new and better ways to publish our findings in peer-reviewed journals, it lets us find out communicate about our work in progress. Furthermore, the taxpayer pays for our work, and deserves to be able to see what’s going on. So I like to think of random people stumbling onto my blog and thinking “Hmm, so that’s what a scientist really does.”.

Also, openness is much easier and more comfortable than secrecy. In my teaching (mostly first-year biology) I give only open-book exams, and it’s much easier for me than worrying about cheaters.

I can see on your webpage that you have grant applications, results and even future plans listed. Do you fear having your ideas and plans “stolen”? You might have some data and results that end up on the webpage/blog only after the publication or everything is uploaded as soon as it out of the oven?

RR: I blog about the day-to-day research we’re doing, and I post our grant proposals as soon as they’re submitted. So everything is open from the start.

I don’t worry much about people stealing our ideas, but it’s not a big risk because nobody else is working on what we’re working on. And most of the people doing related work seem to think I’m more-or-less misguided in my interests and approaches. I try not to post exactly the same figures I’m putting into a manuscript (only because I fear the journal editors might get cranky), but otherwise my goal is to give anyone who’s interested an accurate picture of what we’re doing.

The visibility of scientific blogs has increased considerably in the past years. Yours is up for almost an year now (at least your archives go back to August 2006) and it seems that you support that your whole group of students and post-docs do the same. What have influenced you to start recording your daily routine on a website? Does it help the interaction in the lab since everyone has its own personal page?

RR: I started blogging about research in response to a post by Pedro Beltrao (http://pbeltrao.blogspot.com/2006/07/opening-up-scientific-process-during.html) about the desirability of opening up the scientific process (I found it through Tangled Bank #59). As soon as I read it I realized that I wanted to have a blog about my lab’s research.

After a couple of weeks I told everyone in my lab that I wanted them to have blogs too. I love reading their blogs – they have such thoughtful things to say about their research. They don’t always post as often as I’d like them to; they say it’s because they feel there’s a high standard that they can only sometimes reach. But I’d like them to at least scribble a few lines every day.

From your blog it is easy to see some frustration with bioinformatics. How important is bioinformatics in your research and what the major problems that you have with it?

RR: It’s a collection of important tools and resources, and I love what I can do. And I enjoy learning new things, like babytalk Perl and standalone BLAST. But Unix has always driven me crazy – I keep hoping to attract a Unix/Perl geek to the lab, but no luck so far.

My bioinformatics frustrations arise in two ways. First, it’s only part of what we do, so I’m not doing it nearly enough to get really good at it. If bioinformatics was the main focus of our work I would invest more of my brain in improving my skills. But we’re primarily an experimental lab (we get our hands wet). And each time I go back to it, NCBI or TIGR has changed their interfaces.

The other source of frustration is that we’re always trying to do new things, that nobody has ever done before, Sometimes we can find existing tools that can do these things, but sometimes we have to write our own and we don’t really know what we’re doing. For a while we were lucky enough to have Mario Pineda-Krch working with us, but he’s gone on to better things (see http://pineda-krch.com/).

Another question that is already favourite of this interview series is about computer graphic interfaces. From what I could see your lab generates most of its scripts in Perl, but some work is done with graphical interfaces. What do you and your group look for in a program and its graphic interface? What are the main drawbacks of the command line interface that could be easily mitigated by a GUI?

RR: By graphic interfaces do you mean things like the web interfaces for BLAST? Basically we’ll take whatever we can get. If the resource has a nice point-and-click interface, great. If we have to submit a string of instructions to get what we need, we can cope. If we’d need to write some software ourselves, we usually move on to a different problem unless we’re highly motivated and the problem looks simple. I hate the frustration of not getting line commands exactly right, so much prefer menu-driven interfaces.

The only good interface we’ve generated was done by Mario, working on the fabulous hotspot paradox.

How do you see the “publish or perish” in science, with the increasing number of retracted papers, fake results, rushed publications and sometimes publication of extremely similar results in different papers and journals? Being an advocate of Open Science, do you think this new movement can help alleviate some of the known problems of the “publish or perish” culture?

RR: There’s always been a lot of bad science mixed in with the good; I’m not convinced that the proportion has gotten higher as the total number of papers has increased.

Do you have an advice for the young scientist? And, as you are the first woman interviewed here, any special advice for the girls that are considering a scientific career?

RR: Work by women is unconsciously but systematically undervalued by everyone (including the women who do it), so don’t go into science for the glory. But if you love doing research it’s wonderful. I’m still delighted that I can get paid to do this.

What in your opinion is your most important publication?

RR: That’s a hard one. I don’t get much recognition for what I think is important, mostly because my conclusions don’t fit what others want to hear.

I would like to thank again for Dr Redfield’s answers. I am planning some changes to SciView soon.

If you want to follow the RRResearch blog, here is the link.