Today I spent the day at the PLoS ONE Editorial Board symposium in London. The meeting was well-attended, with about 50 academic editors and 10 PLoS staff members. The meeting was thoroughly enjoyable and I came away feeling extremely positive about PLoS as an organization and the aims of PLoS ONE in particular.
Instead of summarising by session, I will start with the distinctive features of PLoS ONE and how these came up in different talks, and follow with some other interesting other points that came up.
PLoS journals are open access. In the traditional model, the publisher is paid subscriptions by universities, libraries or readers to obtain the content. In the open access model, the authors (or in reality their employers or research funders) pay for the cost of publication, and then anyone in the world can read the article. This has the advantage that people outside (wealthy) universities can benefit from research findings. These can include people working in healthcare, SMEs or universities in developing countries.
This whole area was nicely discussed in the final session, where Dame Janet Finch told us of her experiences in putting together her report for the UK government on open access publication. It was very interesting to find out that the UK government, HE sector and funding councils are now committed to publishing all publicly funded research in open access format. Importantly, there is realization that universities need to have central pots of money to enable academics to publish in such journals – there are too many problems associated with putting such costs directly into research grants.
PLoS is a not-for-profit organisation (in contrast with say Elsevier or Springer). This means that the money they make is being put back into improving their publications – the experience for authors and readers.
PLoS is committed to article-level metrics. There was a great deal of material on article-level metrics in the talks. I found this particularly impressive. It was clear that the overall mood among the academics present (and indeed the majority of my colleagues) that judging someone’s work on the basis of the impact factor of the journals in which they have published is entirely inadequate. Yet, promotions, employment and grant panels continue to do this. PLoS are really leading the way by putting metrics on every article: access statistics (HTML, pdf downloads), citations (on a whole array of services), Mendeley inputs etc. Martin Fenner (PLoS’s technical lead on metrics) was rightly nervous about the use of these metrics for things like promotions – and was keen to emphasise their importance in determining which articles are having an ‘impact’. Nonetheless, moves away from an obsession on journal impact factors are most welcome!
PLoS ONE is committed to publishing science on the basis of its scientific correctness and clarity of its exposition. Articles that meet these criteria are published, and, importantly, articles are not rejected for not being sufficiently ‘important’ or ‘interesting’. I really like this. What this means is that the community decides what is important – not an editorial office. Combined with article level metrics, it becomes clear which of the articles are ‘hits’ and which are not. Interestingly, the PLoS speakers showed us that the top PLoS ONE articles are having more of an impact than the average articles of their more selective journals. This is partly due to weight of numbers (so many more articles are published in PLoS ONE) but it does show that the philosophy of getting articles ‘out there’ and well indexed and searchable then allows the community to work out what is ‘important’ and ‘interesting’.
PLoS connects well with other social media technologies, including Facebook, Twitter, Wikipedia etc. This is also very important. For us scientists to break down the barriers and disseminate our work to a larger and wider audience – and even among other scientists – we do have to embrace social media technologies. For PLoS as publishers to take the lead and use their platform to enable this is a major bonus and shows forward thinking ahead of more traditional publishers rooted in printed media.
Overall, the success of PLoS ONE’s model was demonstrated by the considerable rise in numbers of papers submitted and published. These are rising rapidly and steadily: in November, approximately 4000 papers were submitted, and approximately 2000 published. PLoS have published nearly 50000 papers overall. PLoS ONE is already the largest single journal, and with continued rise in papers submitted (and published), PLoS will quickly become a global academic publishing powerhouse. Here, the not-for-profit agenda is very reassuring. The increase in revenues will be ploughed back into improving PLoS journals.
On the editing itself, it was interesting to discuss experiences with other editors. What was particularly revealing was that most editors found finding referees the most challenging aspect of editing – a fact known to PLoS. In these discussion, PLoS staff made us aware of JANE – the Journal / Author Name Estimator. What a great tool! Type in an abstract, and it will suggest journals, authors or other relevant papers. For an editor, particularly useful for finding possible referees! Also good if you are thinking of relevant journals for your article – though of course, after today, I am feeling particularly inclined to say to people: publish in PLoS ONE. It is the world’s most exciting journal.
The University of Nottingham and the Rothamsted Research Institute are now advertising for 42 fully funded four-year PhD places in their Doctoral Training Partnership. For applicants with a maths, physics or computing background interested in mathematical / computational biology, there are opportunities in all three themes to become involved in world-leading bioscience research. There are three projects on which I would be a second / third supervisor.
Bayesian Inference for Dynamical Systems: From Parameter Estimation to Experimental Design with Theodore Kypraios (maths) as main supervisor. This project will be entirely mathematical / computational.
The role of a novel zinc uptake system (C1265-7) in uropathogenic E. coli, with Jon Hobman as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.
Tunable zinc responsive bacterial promoters for controlled gene expression in E. coli, with Phil Hill as main supervisor. This project will be mostly experimental, but could involve a mathematical modelling component should the student be interested.
For more information, please visit the advert site on findaphd.com
Dorota’s second paper has just been published in PLoS ONE as:
Herman, D., Thomas, C.M. and Stekel, D.J. 2012. Adaptation for Protein Synthesis Efficiency in a Naturally Occurring Self-Regulating Operon. PLoS ONE7(11): e49678.
We are particularly pleased with this work, and had some very nice comments from the reviewers. The quotes (from two different reviewers) here are reproduced with permission from PLoS ONE:
“the kinds of questions the authors address appear to be the most rewarding uses of computational/mathematical uses in biology”
“I found this paper important because it investigates a system with biological plausible parameters, thus, revealing whether the results of previous purely theoretical studies are biologically plausible.”
We are hoping for that sort of reception more generally in the community!
The abstract of the paper is:
The korABoperon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed investigation of the role of the regulatory mechanism using a biologically grounded mechanistic multi-scale stochastic model that includes plasmid gene regulation and replication in the context of host growth and cell division. We use the model to compare four hypotheses for the action of the regulatory mechanism: increased robustness to extrinsic factors, decreased protein fluctuations, faster response-time of the operon and reduced host burden through improved efficiency of protein production. We find that the strongest impact of all elements of the regulatory architecture is on improving the efficiency of protein synthesis by reduction in the number of mRNA molecules needed to be produced, leading to a greater than ten-fold reduction in host energy required to express these plasmid proteins. A smaller but still significant role is seen for speeding response times, but this is not materially improved by the cooperativity. The self-regulating mechanisms have the least impact on protein fluctuations and robustness. While reduction of host burden is evident in a plasmid context, negative self-regulation is a widely seen motif for chromosomal genes. We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis.
We are delighted that the Universities of Birmingham and Nottingham have awarded a Strategic Collaboration Fund award to Josh Rappoportand myself. The project is titled “Experimental analysis and modeling of occludin trafficking during epithelial polarization and wound healing”. We will be looking at the modelling end, developing an ODE model and fitting to data from Josh’s lab using Monte Carlo techniques. The funding awarded is £20,000 and we will be looking for a short-term post-doctoral research fellow for a two month period to carry out the work – to start at some point in 2013 (further details to be posted).
We are very much looking forward to collaborating with Josh and others on this project.
Applications are invited for the above posts specialising in Advanced Data Analysis, with a particular emphasis on bioinformatics. The successful candidates will carry out multi-disciplinary data analysis as part of the newly formed Advanced Data Analysis Centre (ADAC: http://www.nottingham.ac.uk/adac) at the University of Nottingham.
The persons appointed will be aligned with the bioinformatics research group housed at the school of veterinary medicine and science (http://www.nottingham.ac.uk/vet/) and will be associated with other researchers in the Advanced Data Analysis Centre.
Candidates must hold a PhD (or equivalent) in a relevant subject; experience of multi-disciplinary data analysis and a proven ability to apply a wide range of bioinformatics, statistical and computational data analysis approaches in order to analyse a variety of biological/biomedical data. It is desirable that candidates have the ability to both apply existing techniques and develop new techniques in languages such as ‘R’, ‘PERL’ or ‘Python’, have experience of data generated by high throughput techniques such as DNA sequencing or proteomics, and have an interest in broadening multi-disciplinary collaboration across academic disciplines.
Informal enquiries may be addressed to Dr Richard Emes, tel: +44 (0)115 951 6583 or email:firstname.lastname@example.org. Please note that applications sent directly to this email address will not be accepted. Further information about the School of Veterinary Medicine and Science is available at:http://www.nottingham.ac.uk/vet/.
The link to the job on the University of Nottingham vacancies site is here.
Congratulations to Dorota Herman who had her PhD viva today and passed with no corrections! This is a real testament to all her hard work and effort. The viva only lasted 1 hour 40 minutes. Dorota is now working as a PostDoc Bioinformatician at the VIB in Ghent.
Today the University of Nottingham launches the Advanced Data Analysis Centre – ADAC. This represents an investment of £492,000 of University funding over a five year period. ADAC will support University of Nottingham’s research and discovery by assisting in research grant applications and by analysis of large and complex data sets. The centre will employ seven data analysts over a 5 year period who will be based in the Vet School in the Sutton Bonington Campus and in the School of Computer Science in the Jubilee Campus. ADAC has three directors: Richard Emes, who is Director of Bioinformatics; Jon Garibaldi, who is director of Informatics; and myself.