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Editor of PLoS Computational Biology Says It s Time to Move Beyond Methods


Phil Bourne, professor in the department of pharmacology at the University of California, San Diego, co-director of the Protein Data Bank, and former president of the International Society for Computational Biology, has recently taken on a new role as founding editor-in-chief of the upcoming journal PLoS Computational Biology. The open-access journal, to be jointly published by the Public Library of Science and ISCB, is scheduled for launch in June, at ISCB’s 13th annual Intelligent Systems for Molecular Biology conference.

BioInform spoke to Bourne recently to discuss the scope of the journal, and its role within the context of the field’s other peer-reviewed publications, which include Bioinformatics, Briefings in Bioinformatics, BMC Bioinformatics, and others.

Why launch a new bioinformatics journal? Is there room for another peer-reviewed publication in the field?

There are a significant number of journals out there, but first of all, the activity in this field is such that there’s a huge number of papers coming into the area. I’m also associate editor of Bioinformatics and Proteins: Structure Function, so I see that not just from the perspective of this new journal, but from other journals as well.

So I think there’s certainly room for this. I also think that we’ve defined this to actually fill what we think is an important niche, because there are good journals that deal with methods in bioinformatics and computational biology, but in terms of the biological outcomes associated with new or existing computational methods, right now, they don’t go to the traditional bioinformatics journals, which are primarily methods journals. They get peppered around, depending on their quality, in journals like Cell, Science, Nature, [and] in a few cases [in] PNAS, and then other journals, like the Journal of Molecular Biology, and so on. And what we wanted to do was have a showcase for computational biology where there are indeed significant biological outcomes from these methods.

So the readership is very much biologists, and the idea is to get them engaged, or further engaged, in using computational methods based on outcomes that they see that others are doing.

Will PLoS Computational Biology focus primarily on biological discoveries using computational methods, or will it also publish methods papers?

Well, the ideal paper would be [about] a compelling new method that has biological outcomes. However, if it’s an existing method with biological outcomes, that’s appropriate as well.

The other important aspect is that it transcends biological scales. So typically, you have more and more bioinformatics papers now appearing in JMB, for example. But they’re only at the molecular level. And yet there are large amounts of computational work being done, for example, at the cellular level, at the population level — across all biological scales. And what we want to do is to point out to people in different areas that, indeed, a method that’s being used in one area on occasion can be applied to a completely different area focusing on a different biological scale.

Have there been many papers submitted so far?

There are about 50 papers in the system, and we’re getting submissions every day. People are treating this journal very seriously because PLoS Biology already has an outstanding reputation after only one or so years of existence, so that’s important. We’re leveraging that, and it’s also being published in partnership with the International Society for Computational Biology, so there’s that credibility aspect to it as well. That’s certainly being reflected in the quality of the manuscripts that we’re getting. I can’t say too much about them, but so far it’s looking really good.

Associated with the research articles, there will be invited perspectives, which are relatively short — invited perspectives on different areas of the field — and reviews, which are also invited. And that’s going well as well.

I think the other aspect of this that’s not directly related to the science is that it’s clear that more and more scientists are getting behind the whole open-access movement. That’s being done by other journals as well, so it’s not a unique component, but we feel it’s very important. It also allows us more flexibility in the presentation material. What’s happening more and more now is you almost get a snapshot of a very good research paper, and the bulk of it is in supplementary material. We will have that too, but there will be the opportunity to publish both a high-impact short paper as well as long papers. So that’s a consideration.

If you look at the editorial board [for PLoS Computational Biology], it’s absolutely stellar, it’s got many of the best people in the field, and I think that’s partly because they see the need for the kind of journal I just described. They’re also increasingly behind the whole open-access movement, and the NIH, with some of its recent announcements, is pushing in that direction as well.

There are many different sub-communities within bioinformatics — from text-mining to protein structure prediction to biosimulation. You mentioned that there are more papers now in the field, which is leading to more journals. Do you envision more specialized journals addressing these sub-domains at some point?

Yes, potentially. First of all, there are actually some very poor journals [in bioinformatics] as well. It’s clear to me now that launching a successful journal is a huge endeavor by a large number of people, and the PLoS organization is just absolutely spectacular. They have some outstanding people who are running the journals, so all of that really helps. It may be that there will be [more specialized journals]. Already, for example, in areas like computational neuroscience, that’s not an area that’s traditionally addressed by any of the existing bioinformatics-oriented journals — so it may be that that will happen later. In the interim, what we see here is that if you look at Science and Nature, they have categories that they publish in, but they’re extremely broad, whereas what ties [PLoS Computational Biology] together are categories that involve computational methods in biology, as opposed to delving into other areas like geology and everything else, but it’s at the same time broader than any existing [bioinformatics] journal from a biological perspective — many of them, anyway.

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