Last week, we kicked off a series interviewing some of the top ‘open scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’ve got something completely different, with Daniel Shanahan of BioMed Central who recently published a really cool PeerJ paper on auto-correlation and the impact factor.
Hi Daniel! To start things off, can you tell us a bit about your background?
I completed a Master’s degree in Experimental and Theoretical Physics at University of Cambridge, but must admit I did my Master’s more to have an extra year to play rugby for the university, rather than a love of micro-colloidal particles and electron lasers. I have always loved science though and found my way into STM publishing, albeit from a slightly less than traditional route.
Open science is a rapidly evolving field, with a huge diversity of actors involved. We want to highlight some of the superstars helping to spearhead the evolution of scholarly communication, who are real positive forces for change. The first of these is with Joanne Kamens PhD, who currently is the Executive Director for Addgene, a repository for the life sciences. We asked her about open science, the impact this can have on diversity in research, and the value of repositories. Here’s her story!
Hi Joanne! So can you tell us a little bit about your background to get things started?
After graduating University of Pennsylvania I went directly to graduate school in the Harvard Medical School Division of Medical Sciences where I received a PhD in genetics. For you historians, it was the first year that the Division existed allowing students to move around PIs in many departments. I defended my thesis while 6 months pregnant and had my son while still working in that lab. I had a great mentor in Dr. Roger Brent (now at the Fred Hutchinson Center in Seattle). I studied transcription using yeast and helped demonstrate that an acidic domain of the Rel protein was activating when brought in proximity to the promoter region. Again for historical perspective, PCR was invented while I was in grad school and I got to beta test the first MJ research PCR machine (M worked on my floor) which had no outsides. Roger Brent’s lab was one of the labs that created the yeast two-hybrid screening system and I have always been a lover of molecular biology technology which serves me well at Addgene.
We have new Collections coming out of our ears here at ScienceOpen! Last week, we saw two published on the bacterium Shewanella, and another on the Communication Through Coherence theory. Both should represent great platforms and resources for further research in those fields.
The latest is on the diverse field of Atomic Force Microscopy. We asked the Editor, Prof. Yang Gan, to give us a few details about why he created this Collection.
This collection is to celebrate the 30th anniversary of atomic force microscopy (AFM). March 3, 1986 saw publication of the land-marking paper “Atomic force microscope” by G. Binnig, C. G. Quate and C. Gerber (Phys Rev Lett, 56 (1986) 930-933, citations >8,800) with the motivation to invent “a new type of microscope capable of investigating surfaces of insulators on an atomic scale” with high force and dimension resolution. This can be used to measure local properties, such as height, friction, and magnetism, so has massive implications for science.
Since then, AFM has given birth to a large family of scanning probe microscopy (SPM) or SXM where X stands for near-field optical, Kelvin, magnetic, acoustic, thermal, etc. More than 100,000 journal papers, ~6,000 papers/yr since 2008, have been published if one searches the Scopus database with “atomic force microscopy” or “force microscope”. On ScienceOpen, there are over 6,000 article records if one searches using the keywords “atomic force microscopy” too. Nowadays, many disciplines — physics, chemistry, biology, materials, minerals, medicine, geology, nanotechnology, etc — all benefit greatly from using AFM as an important and even key tool for characterization, fabrication and processing.
ScienceOpen Collections are thematic groups of research articles that transcend journals and publishers to transform how we collate and build upon scientific knowledge.
What are Collections
The modern research environment is a hyper-dimensional space with a vast quantity of outputs that are impossible to manually manage. You can think of research like a giant Rubik’s cube: you have different ‘colours’ of research that you have to mix and match and play around with to discover how the different sections fit together to become something useful.
We view Collections as the individual faces of a Rubik’s cube. They draw from the vast, and often messy, pool of published research to provide an additional layer of context and clarity. They represent a new way for researchers to filter the published record to discover and curate content that is directly relevant to them, irrespective of who published it or what journal it appears in.
Advantages of Collections
Perhaps the main advantage of Collections to researchers is that they are independent of journals or publishers and their branding criteria. Researchers are undoubtedly the best-placed to assess what research is relevant to themselves and their communities. As such, we see Collections as the natural continuing transformation of the concept of the modern journal, acting in almost full cycle to return them to their basic principles.
The advantage of using Collections is that they provide researchers with the power to filter and select from the published record and create what is in essence a highly-specialised virtual journal. This means that Collections are not pre-selective, but instead comprise papers discriminated only by a single criterion: research that is relevant to your peers, and also deemed relevant by them.
Filtering for Collections occurs at different levels depending on scope or complexity of research. For example, Collections can be designed to focus on different research topics, lab groups or research groups, communities, or even departments or institutions. Collections can also be created for specific conferences and include posters from these, published on ScienceOpen. Youdefine the scope and the selection criteria.
Traditional models of peer review occur pre-publication by selected referees and are mediated by an Editor or Editorial Board. This model has been adopted by the vast majority of journals, and acts as the filter system to decide what is considered to be worthy of publication. In this traditional pre-publication model, the majority of reviews are discarded as soon as research articles become published, and all of the insight, context, and evaluation they contain are lost from the scientific record.
Several publishers and journals are now taking a more adventurous exploration of peer review that occurs subsequent to publication. The principle here is that all research deserves the opportunity to be published, and the filtering through peer review occurs subsequent to the actual communication of research articles. Numerous venues now provide inbuilt systems for post-publication peer review, including ScienceOpen, RIO, The Winnower, and F1000 Research. In addition to those adopted by journals, there are other post-publication annotation and commenting services such as hypothes.is and PubPeer that are independent of any specific journal or publisher and operate across platforms.
One main aspect of open peer review is that referee reports are made publicly available after the peer review process. The theory underlying this is that peer review becomes a supportive and collaborative process, viewed more as an ongoing dialogue between groups of scientists to progressively asses the quality of research. Furthermore, it opens up the reviews themselves to analysis and inspection, which adds an additional layer of quality control into the review process.
This co-operative and interactive mode of peer review, whereby it is treated as a conversation rather than a selection system, has been shown to be highly beneficial to researchers and authors. A study in 2011 found that when an open review system was implemented, it led to increasing co-operation between referees and authors as well as an increase in the accuracy of reviews and overall decrease of errors throughout the review process. Ultimately, it is this process which decides whether research is suitable or ready for publication. A recent study has even shown that the transparency of the peer review process can be used to predict the quality of published research. As far as we are aware, there are almost no drawbacks, documented or otherwise, to making referee reports openly available. What we gain by publishing reviews is the time, effort, knowledge exchange, and context of an enormous amount of currently secretive and largely wasted dialogue, which could also save around 15 million hours per year of otherwise lost work by researchers.
Open peer review has many different aspects, and is not simply about removing anonymity from the process. Open peer review forms part of the ongoing evolution of an open research system, and the transformation of peer review into a more constructive and collaborative process. The ultimate goal of traditional peer review remains the same – to make sure that the work of authors gets published to an acceptable standard of scientific rigour.
There are different levels of bi-directional anonymity throughout the peer review process, including whether or not the referees know who the authors are but not vice versa (single blind review), or whether both parties remain anonymous to each other (double blind review). Open peer review is a relatively new phenomenon (initiated in 1999 by the BMJ) one aspect of which is that the authors and referees names are disclosed to each other. The foundation of open peer review is based on transparency to avoid competition or conflicts born out through the fact that those who are performing peer review will often be the closest competitors to the authors, as they will tend to be the most competent to assess the research.
It’s not too hard to see that the practices of and attitudes towards ‘open science’ are evolving amidst an ongoing examination about what the modern scholarly system should look like. While we might be more familiar with the ongoing debate about how to best implement open access to research articles and to the data behind publications, discussions regarding the structure, management, and process of peer review are perhaps more nuanced, but arguably of equal or greater significance.
Peer review is of enormous importance for managing the content of the published scientific record and the careers of the scientists who produce it. It is perceived as the golden standard of scholarly publishing, and for many determines whether or not research can be viewed as scientifically valid. Accordingly, peer review is a vital component at the core of the process of research communication, with repercussions for the very structure of academia which largely operates through a publication-based reward and incentive system.
Openness in scholarly communication takes many forms. One of the most commonly debated in academic spheres is undoubtedly open access – the free, equal, and unrestricted access to research papers. As well as open access, there are also great pushes being made in the realms of open data and open metrics. Together, these all come under an umbrella of ‘open research’.
One important aspect of open research is peer review. At ScienceOpen, we advocate maximum transparency in the peer review process, based on the concept that research should be an open dialogue and not locked away in the dark. We have two main peer review initiatives for our content: peer review by endorsement, and post-publication peer review.
A new project has been launched recently, the Peer Reviewers Openness Initiative (PROI). Similarly to ScienceOpen, is grounded in the belief that openness and transparency are core values of science. The core of the initiative is to encourage reviewers of research papers to make open practices a pre-condition for a more comprehensive review process. You can read more about the Initiative here in a paper (open access, obviously) published via the Royal Society.
Data should be made publicly available.All data needed for evaluation and reproduction of the published research should be made publicly available, online, hosted by a reliable third party. [I’m an author; help me comply!]
Stimuli and materials should be made publicly available.Stimulus materials, experimental instructions and programs, survey questions, and other similar materials should be made publicly available, hosted by a reliable third party. [I’m an author; help me comply!]
In case some data or materials are not open, clear reasons (e.g., legal, ethical constraints, or severe impracticality) should be given why. These reasons should be outlined in the manuscript.[I’m an author; help me comply!]
Documents containing details for interpreting any files or code, and how to compile and run any software programs should be made available with the above items.In addition, licensing or other restrictions on their use should be made clear. [I’m an author; help me comply!]
The location of all of these files should be advertised in the manuscript, and all files should be hosted by a reliable third party.The choice of online file hosting should be made to maximize the probability that the files will be accessible for many years, and to minimize the probability that they will be lost for trivial reasons (e.g., accidental deletions, moving files). [I’m an author; help me comply!]
Stephanie Dawson, CEO of ScienceOpen, and Jon Tennant, Communications Director, have signed the PROI, both on behalf of ScienceOpen and independently, respectively, joining more than 200 other researchers to date. Joining only takes a few seconds of your time, and would help to solidify a real commitment to making the peer review process more transparent, and helping to realise the wider goal of an open research environment.
Hello there, and Happy New Year from the new Communications Director of ScienceOpen!
My name’s Jon, and I’m currently finishing up my PhD at Imperial College London, where I’m a palaeontologist! (think Ross from Friends..) This year, I’ve been fortunate enough to join the ScienceOpen team to help grow their communications and networking abilities, and continue to realise the benefits of their pretty cool open research networking platform.
Those of you who know me will be aware that open access and more broadly, open science and communications, is something that I’ve been quite active in over my short career as a researcher. Some of the more ‘open-related’ projects I’ve been involved with include the writing of the Open Research Glossary, as well as challenging the AAAS on non-optimal publishing practices. For those of you lucky enough not to have met me yet, I’m highly interested in a whole array of factors that influence scholarly communication, including:
Publishing and disruptive technologies and innovation
Access to raw data and reproducibility
Community building and the power of social networks
Social media for researchers
Science communication, public engagement and outreach
Academic assessment and altmetrics
I’ll be taking over the reins from Liz Allen, who will shortly announce her new non-profit role. Rest assured that she will continue to spread the word about the importance of open. On behalf of the ScienceOpen team, I’d like to take this opportunity to thank Liz for helping to establish our brand and offering her personal support as I get up to speed with the nuances of the job. Over the next few months (and onwards), I hope to help to raise awareness of what ScienceOpen does, and why it should be part of the essential toolkit for researchers, along with a host of other innovative applications that are bringing research into the digital age.
Why ScienceOpen? Well, apart from the obvious name, I support their ideals that science deserves to be open, transparent, and equal in every way. This essentially is the inverse of the traditional method of scholarly communication of publishing via journals, which are closed, opaque, and beset by inequalities on all fronts, the foremost being financial. ScienceOpen offers a valuable service that doesn’t replace traditional publishing, but compliments it through having a community aspect of driving open peer review, which is still the golden standard of acceptability for published research. Combine this with a hefty archive of both open and non-open research articles, and you have a valuable platform for developing research networks and building upon the published literature in an open, transparent, and community-driven way. For me, this is just one of the many ways in which the way we conduct research and disseminate those results is changing for the better, by harnessing the power of the Web and the opportunities it gives us for greater inter-operability throughout academia.
Alongside my activities here, I’ll be continuing my research and finishing the dreaded thesis, as well my science communication activities, in particular for the PLOS Paleo network which is great fun! So essentially combining my three favourite things: research, science communication, and open science policy and communications. Yay!
You can contact me on Twitter, or drop me an email if you wish. I look forward to working with ScienceOpen, and with them the global research community!