PeerJ has recently launched a collection on Bioinformatics Software Tools. This collection is collating the most interesting and relevant articles on bioinformatics tools which have been published in PeerJ and PeerJ Computer Science. The bioinformatics community has long shown a strong commitment to open research practices and the sharing of both data and open source software and so it is not surprising that they are starting to publish in PeerJ in large numbers. This collection offers a space to look across different developments in the field and provides valuable recognition for the contributions these tools have brought to the scientific community.
To mark the launch, we caught up with Claus Wilke and Keith Crandall, Senior Academic Editors at PeerJ and the editors responsible for the curation of this new Collection.
Interview with Senior Editors Claus Wilke and Keith Crandall #PeerJBioinfo
Can you give us a bit of background about yourself?
CW: I am Professor of Integrative Biology at The University of Texas at Austin. I’ve been a computational biologist for almost 20 years. My main areas of interest are molecular evolution, protein biochemistry, and virology. Much of my work happens at the interface of two or three of these areas.
KC: I’m the Founding Director of the George Washington University’s Computational Biology Institute. I got into bioinformatics the old fashioned way – through a double major in Mathematics and Biology with a number of computer science courses as an undergraduate at Kalamazoo College in Michigan. My lab develops methods for sequence analysis, especially centered around phylogenetic and microbiome (metagenomic) analyses. Then we apply methods in both natural history studies (especially crustacean systematics and evolution) and infectious disease studies (especially population genetics, phylodynamics).
What has your involvement been with PeerJ until now, and what attracted you to get involved further?
CW: I have been an author and editor since the very beginning. In fact, I think my lab published the first software article in PeerJ (M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80).
I strongly believe in open access and in the need to bring down publication costs without sacrificing quality. I think PeerJ is providing great quality at an excellent price, and therefore I want to help strengthen it in any way I can.
KC: I’ve been an Academic Editor at PeerJ from the beginning because I really like the central concept of much more affordable publishing mechanism for academic research. I am further attracted to the journal because of the exceptional look and feel of the web-based journal. The articles are really exceptionally beautiful!
What was this initial reason for pulling together this collection and why is having these articles in one place important?
KC: We wanted to pull together a collection of bioinformatics articles for a couple of reasons. First, to help readers find these exceptional resources a bit more easily and to explore related resources published in PeerJ. Second, we wanted to let the bioinformatics community know of the great infrastructure at PeerJ for publishing quality, beautiful articles in bioinformatics where you can really describe your methods, develop appropriate visualizations, and find an eager readership.
How do you see the bioinformatics community reacting to Open Access in general?
CW: The bioinformaticians are generally at the forefront of open access in biology. I assume that’s because they are used to open source code, and hence find it natural to make their articles freely available as well. Bioinformaticians are also generally pro-preprints. We have seen a growing number of bioinformatics submissions to PeerJ. I think this means that this community can recognize the value that PeerJ provides.
You have both published in PeerJ before – how was your experience and what do you see as our strengths for authors in the field?
CW: I have published 5 articles in PeerJ, and two more manuscripts have received at least one round of reviews. These articles cover a wide range of different topics, from computational peptide biochemistry to virology to cancer genomics. Every time I’ve been surprised how quick the review process was, and how good the quality of the peer reviews.
What are the unique needs of ‘bioinformatics tools’ authors?
CW: First, the journal must actually accept and value articles about software tools. Those articles often don’t contain a discovery or novel result, and therefore many journals don’t want them. They act more as an advertisement for the actual product, which is the software.
However, bioinformaticians need these articles so that people using their tools have something to cite. And contrary to the opinion of some, I believe the community needs these articles as well, because they often provide an additional layer of explanation and detail to the software tool that is missing from the documentation. While documentation is good to explain *how* a tool is used, the paper is usually a good place to explain *why* it was written in the first place, and why it works the way it does.
In your opinions, what makes a great article in this field? How can authors strengthen their Bioinformatics Tools articles?
KC: In my view, the best bioinformatics papers 1) develop a new method for data analysis, 2) implement the method in open-source software, 3) test the method with simulated and real data, and 4) demonstrate the method with an interesting biological application. Great papers in bioinformatics have all of these elements.
CW: I think the journal article serves a different purpose from a tool manual. It should explain the why, and also describe any specific theory or new algorithms that went into the development of the code. The journal article should complement the manual, not replace it. A good manual needs to exist separately.
Which articles in this Collection stand out to you so far?
KC: I really like the PhyloSift software because it offers a novel analysis approach in some relatively easy to use software and really provides a wonderful example of what I think a constitutes the essential elements of a ‘great’ article (see above).
For authors who are considering submitting their articles to PeerJ, what message would you give them?
Both: Do it.
The PeerJ Bioinformatics Software Tools Collection can be found here. Share your thoughts on the Collection on Twitter at #PeerJBioInfo. For more info on how to submit to this collection, guidelines for PeerJ submissions can be found here.