Public Library of Science

Announcing PLoS Pathogens “Pearls”

Patrick Reilly — Fri, 26 Jun 2009 09:53:58 -0700

The PLoS Pathogens editors and staff are thrilled to announce the debut of “Pearls,” a new series in the journal that will begin publishing monthly, starting with this June’s issue.

Each Pearl will be a concise primer on a topic of importance, meant to fill the gap between research articles and textbooks. Pearls will be tailored for graduate students and post-docs, while providing a format accessible to a general readership.

In contrast to the dynamic nature of research articles and textbooks, we hope that Pearls will provide a growing compendium of the “lessons that last,” for everyone from the scientist researching an area outside his or her field, to lay readers looking to learn more about a disease that affects them personally.

The benefit of such widely-accessible (not to mention open access!) introductory articles is clear, as evidenced by the level of enthusiasm we found when soliciting potential authors to write the first batch of Pearls. Under the editorial guidance of Dr. Hiten Madhani (University of California, San Francisco) we have seen Pearls grow from a kernel of an idea into what will soon bring focused educational content to readers of the journal.

More than anything, we’re excited to see all the ways in which Pearls may be used once they’re in the public domain: as lab references, class handouts, lecture slides, and undoubtedly in other ways that haven’t even occurred to us yet. We hope you will keep us informed as you find new ways to use them.

Watch for the first Pearl, by Dr. Michael S. Diamond (Washington University School of Medicine), published Friday, June 26 concurrent with an introductory editorial by Dr. Hiten Madhani.

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The PLoS ONE blog channel is moving

Liz Allen — Mon, 22 Jun 2009 13:42:58 -0700

PLoS ONE now blogs at everyONE, and we won't be posting here any more. We outgrew this site in terms of functionality and ease of use a few months ago and it's time to redirect everyone that visits this channel to our new home. You can sign up for updates from our new blog via RSS or e-newsletter.

The new blog site allows us to incorporate video, podcasts, slide sharing, comic strips and photos into our communications mix. We've also been running a popular blog post of the month event, rounding up our media coverage on a weekly basis (sometimes more frequently for the hottest storie s), answering your questions and updating you on new PLoS projects such as Article Level Metrics. To sum up, the new blog quickly and seamlessly keeps you updated on what gives in our world and allows us to hear from you about what is happening in yours.

Not only do PLoS ONE and PLoS Medicine now have their own blogs, we also have a lively social media program:

@PLoS on Twitter was recommended at the 140 Characters Conference as being "one to watch to learn about science". We have over 1400 followers but we'd like more so please sign up.
We also have a thriving Facebook page with over 4,500 fans, so please join us there too.

Thanks for following us here in the past, we look forward to welcoming you to our new home.

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The PLoS Medicine blog channel is moving

Liz Allen — Mon, 22 Jun 2009 12:49:01 -0700

PLoS Medicine now blogs at Speaking of Medicine, and we won't be posting here any more. We outgrew this site in terms of functionality and ease of use a few months ago and it's time to redirect everyone that visits this channel to our new home. You can sign up for updates from our new blog via RSS or e-newsletter.

The new blog site allows us to stream podcasts from our editorial board members, show a video series from our editor-in-chief, post a daily click (picks of interest from the PLoS Medicine team) and quickly and seamlessly keep you updated on what gives in our world and hear from you about what is happening in yours.

Not only do PLoS Medicine and PLoS ONE now have their own blogs, we also have a lively social media program:

@PLoS on Twitter was recommended at the 140 Characters Conference as being "one to watch to learn about science". We have over 1400 followers but we'd like more so please sign up.

We also have a thriving Facebook page with over 4,500 fans so please join us there too.

Thanks for following us here in the past, we look forward to welcoming you to our new home.

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Announcing the first PLoS Progress Report

Peter Jerram — Mon, 8 Jun 2009 08:25:15 -0700

Today, we’re delighted to share our first Progress Report with you which has the theme of “Liberating research. Accelerating science". We would encourage you to share it with your colleagues, friends and family so that we can spread this information.

Reading it will tell you more about our story, our success and our vision for the future through the voices of many people who have helped us to get where we are today. In it you will find:

Discussions about important questions such as:

Five years after entering the publishing arena, what does the PLoS financial picture tell us? How will PLoS and OA affect STM (science, technology and medical) publishing in the future?
Examples of PLoS articles that have really changed outcomes on the ground: for example some that have improved global health, liberated research, helped scientists advance their careers, protected privacy, unearthed fossils, accelerated science or even changed policy.
Many personal messages from our supporters: “The innovation of PLoS was high-quality; open-access science. The innovation of PLoS ONE in some ways, is even larger because it allows radical reorganizations of scientific knowledge, which can enable new discoveries.” Dr Jesse Ausubel, Director, Program for the Human Environment, The Rockefeller University.
Impressive statistics about the size of the PLoS community: 13,000 peer-reviewers. 26,000 authors, 1,400 board members and millions of unique visitors in 2008.
Information about our diverse portfolio of journals: why each exists and what they do for the organization and the audiences that they serve.
The reasons why PLoS still needs the financial support of our donors: to fuel OA advocacy and fund innovation in new online tools and how you can help us.
Our current financial statement: posted here ahead of our 990 filing on Guidestar, a commonly used resource for finanical information about non profits.
The team: Board of Directors, Senior Staff and Editorial Boards.

Although this report is as transparent and as complete as we could make it, a single document can never do justice to all our dedicated staff, supporters, authors, users and friends who make PLoS such a vibrant organization. To all of them, I would like to say a big thank you, without you we could not have come this far, this quickly.

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PLoS Computational Biology at ISMB/ECCB 09

Evie Browne — Mon, 1 Jun 2009 10:37:13 -0700

As an official journal of the International Society for Computational Biology, PLoS Computational Biology is once again delighted to be participating in the ISMB/ECCB conference for 2009, this year held in Stockholm, Sweden, June 27^th – July 2^nd, where you’ll find us at Booth 12 in the exhibition hall.

This year we’ll be presenting two sessions:

1. Future of Scientific Publishing (Monday, June 29^th 14:15 – 18:45 pm)

This year, BioLINK—a special interest group run for many years in association with ISMB—has devoted the final part of their program to PLoS Computational Biology and the ISCB Publications Committee to discuss developments and desires in scientific publishing. Our four distinguished speakers will be David Shotton (Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article), Anita de Waard (From Proteins to Hypotheses—Some Experiments in Semantic Enrichment), Dietrich Rebholz-Schuhmann (ELIXIR Scientific Literature Interdisciplinary Interactions), and PLoS Computational Biology Editor-in-Chief Philip E. Bourne (OpenID vs. ResearcherID). This afternoon session is open to BioLINK and ISMB/ECCB delegates and will be followed by a Publishers’ Panel discussion with representatives from major publishers, including PLoS, Oxford University Press, Nature, Wiley-Blackwell, Cambridge University Press, and BioMed Central.

You can also read more about the session here.

2. Special Session on Advances and Challenges in Computational Biology (Wednesday, July 1^st 10:45 am – 12:40 pm)

Brought to you through the eyes of three of PLoS Computational Biology’s editors, this session covers recent scientific advances made possible by computation and mathematics in different fields—Synthetic Biology (Adam Arkin), Computational Neuroscience (Abigail Morrison), and Infectious Diseases (Christophe Fraser). Addressing themes such as drivers of research directions, scientific impact, reproducibility, model validation, co-operation amongst researchers, the need for tools to enable sharing (such as common description languages), and interfacing with scientists who are not focused on computational approaches, this session aims to provide a wide-reaching overview of common issues faced by computational biologists in different areas.

Meet the Team—Booth 12

PLoS Computational Biology team members Evie Browne, Publications Manager, and Rosemary Dickin, Publications Assistant, will answer your questions about PLoS, open access, the NIH Public Access Policy, and publishing your work in PLoS Computational Biology, the leading journal in its field. Don't forget to visit us at Booth 12 and collect some FREE PLoS goodies:

T-Shirts—Sign up for our e-mail content alerts and receive our 2009 t-shirt (while supplies last).
Buttons/Badges designed for our authors, editorial board members, readers, and supporters.
Postcards, to remind yourself and your colleagues why you should publish in PLoS Computational Biology.

We look forward to seeing you very soon.

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World Hepatitis Day: Prospects for the Future - Guest blog by Paul Klenerman and colleagues

Andrew Hyde — Tue, 19 May 2009 07:41:34 -0700

"World Hepatitis Day...does not usually make the headlines in the same way that World AIDS day does, but viral hepatitis affects about half a billion people globally (perhaps 1 in 12 of the global population) and so the relative publicity associated with World Hepatitis Day does not accurately reflect the importance of hepatitis as a public-health problem.”

In this World Hepatitis Day blog ahead of the formal publication of their Perspective article in PLoS Medicine, Paul Klenerman, Vicki Fleming and Ellie Barnes of the University of Oxford describe research by Christian Drosten and colleagues about a new low-cost diagnostic test for Hepatitis C for use in developing countries. The research was recently published in PLoS Medicine.

The Perspective article by Paul Klenerman and colleagues will be formally published in PLoS Medicine on 16th June 2009.

What Are the Prospects for Controlling Hepatitis C?

Paul Klenerman*, Vicki Fleming, Ellie Barnes

May 19 this year marked World Hepatitis Day [1].This event does not usually make the headlines in the same way that World AIDS Day does, but viral hepatitis affects about half a billion people globally (perhaps one in 12 of the global population), and so the relative publicity associated with World Hepatitis Day does not accurately reflect the importance of hepatitis as a public health problem.

The two major hepatitis viruses—hepatitis C virus (HCV) and hepatitis B virus (HBV)—share a number of features. Both viruses are readily spread through the transfer of infected blood or blood products. Both cause persistent infections and share an insidious progression after decades of asymptomatic carriage that creates a huge burden of end-stage liver disease and liver cancer. Thus, both viruses are major public health problems across the globe. However, there are substantial differences between these infections in terms of the risk groups affected, the geographical distribution of the viruses, and the tools at our disposal to deal with them.

Prospects for Controlling HBV and HCV

For HBV we have a well-established vaccine and an emerging panel of well-tolerated oral agents for the treatment of chronic infection. Although there is still a massive burden of complex and severe infection to tackle, the pathway towards effective combination therapy has already been trodden in HIV, and careful clinical trials in this area for HBV should bring some clarity. Delivery of such drug combinations in resource-poor settings where the prevalence of carriage is high will create its own significant challenges.

For HCV we have no current vaccine, and current therapies are toxic, complex, and expensive, as well as only partially effective. Treatment is further complicated by HIV coinfection, which is increasingly encountered in some risk groups [2]. So why is the prevention and treatment of HCV infections apparently so far behind that of HBV infections? One reason is that HCV was only identified in 1989, and only successfully cultured in 2005 [3,4]. However, the major biological hurdle to controlling HCV is the hTuge diversity of the virus, both within patients and among populations [5].

HCV is an RNA-based virus with a variable genome and the capacity to evolve over time to evade drug and immunologic pressure. HCV has coevolved with human populations for centuries, if not millennia [6], and has diversified widely over this period (Figure 1). By comparison, the phylogenetic tree of HIV is much more compact because this virus has had less than a century in which to diversify in humans.

The net result of this diversification is the existence of seven major genotypes of HCV (the last added very recently) that share less than 80% sequence homology with one another, and more than 50 HCV subtypes [7]. Although these genotypes may have arisen over long periods as endemic strains in geographically distinct regions (e.g., genotype 6 in southeast Asia [8]), most have now spread globally. Genotype 1 is particularly common in western Europe and the United States, although genotype 3 is also now very common in the United Kingdom as a result of its spread through intravenous drug–using populations and through immigration from the Indian subcontinent.

Multiple genotypes occur in many other viruses, including HBV, but their importance in HCV is particularly high because both the duration and success rate of current treatments for HCV infection (pegylated interferon-alpha and ribavirin) are highly genotype dependent. Thus, genotypes 2 and 3 are typically associated with much greater response rates than genotypes 1 and 4 (70%–80% long-term clearance versus 40%–50%) and require shorter treatment periods (six months versus one year) [9]. The biological basis for these differences is unclear—the genomes of these genotypes are so diverse that such differences could result from multiple complex changes. Even within a single genotype (e.g., genotype 1), the fundamental mechanisms behind relative resistance to treatment of different HCV subtypes are not fully defined, although an interferon-sensitivity determining region has been described [10].

The Role of Nucleic Acid Tests for HCV

Given these important clinical and virologic differences between HCV genotypes, robust and sensitive nucleic acid tests for HCV have a major role to play in virus detection and in guiding treatment and thus are at the core of current clinical practice in developed countries. However, these tests are relatively complex molecular tests and are therefore not universally available. Additionally, they may not be equally sensitive at detection of all genotypes. In a recent article in PLoS Medicine, however, Christian Drosten and colleagues described a new approach to nucleic acid testing in HCV [11].

The authors generated a test based on a highly conserved region in the 3? end of the virus (most current tests are based on the 5? end) and validated their assay to show that it was sensitive in detection of a wide range of genotypes from geographically diverse populations. They also attempted to reduce the overall cost of their approach and have thus provided a novel system that uses an open (i.e., nonproprietary) protocol that might be particularly appropriate for resource-poor settings. This new assay is potentially an important step forward for laboratories in such regions and, if rolled out effectively, could provide novel information relevant to the prevalence, clinical impact, and treatment response of HCV genotypes that are currently poorly studied—most clinical analyses, and vaccine and treatment trials have focused on genotype 1.

Although very simple and cost-effective tests to detect, quantify, or genotype HCV in resource-poor areas could be of great value in future, the overall costs and usefulness of any such test in comparison to other methods and in relation to other public health priorities in such regions will need to be considered carefully. Thus, although conventional PCR methods as used by Drosten and colleagues look promising, non-PCR-based methods such as loop-mediated isothermal amplification (LAMP) also need to be considered, since little specialist equipment is required for LAMP and the sensitivity appears to be high [12]. In the end, however, the definitive test for any new method of HCV analysis will be clinical utility in the field.

The Extreme Viral Diversity of HCV

As we mark World Hepatitis Day, the recent paper by Drosten and colleagues once more draws our attention to one of the key features of HCV: its extreme viral diversity, which brings enormous challenges for the future. The capacity for HCV to evolve creates a complex target for both vaccine and drug development. Nevertheless, recent advances in both these areas provide some cautious hope for the future—at least in the case of genotype 1 infection [13,14]. Key to successful vaccine development will be the generation of effective, sustained, and broad anti-HCV immune responses. However, the immune responses to non–genotype 1 viruses are very poorly described, and recent data suggest that there is relatively little overlap between immune responses to genotypes 1 and 3. Thus, at present it is unclear whether HCV vaccines against specific genotypes will provide any cross-protection against other genotypes [15]. The situation with drugs may be even more complex, with pre-existing diversity even within genotype 1 already providing some level of drug resistance [16].

Future studies of the diverse HCV genotypes that exist globally—hopefully facilitated by the recently published methods—will, therefore, help us understand the overall clinical impact of HCV in affected populations and will determine our potential to intervene. Since HCV emerged from the shadows 20 years ago, it has shown itself to be “smarter than the average virus.” Thus, it may take longer than 20 years for us to put it back into the shadows, and it will probably take all our efforts to do so.

References
1. World Hepatitis Alliance (2009) World Hepatitis Day. Available: http://www.worldhepatitisday.org/. Accessed 11 May 2009.
2. Klenerman P, Kim A (2007) HCV–HIV coinfection: Simple messages from a complex disease. PLoS Med 4: e240. doi:10.1371/journal.pmed.0040240
3. Houghton M (2009) Discovery of the hepatitis C virus. Liver Int 29 (Suppl 1): 82- 88.
4. Wakita T, Pietschmann T, Kato T, Date T, Miyamoto M, et al. (2005) Production of infectious hepatitis C virus in tissue culture from a cloned viral genome.
Nat Med 11: 791-796.
5. Simmonds P (2004) Genetic diversity and evolution of hepatitis C virus—15 years on. J Gen Virol 85: 3173-3188.
6. Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, et al. (2001) The epidemic behavior of the hepatitis C virus. Science 292: 2323-2325.
7. Kuiken C, Simmonds P (2009) Nomenclature and numbering of the hepatitis C virus. Methods Mol Biol 510: 33-53.
8. Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, et al. (2009) Genetic history of hepatitis C virus in East Asia. J Virol 83: 1071-1082.
9. Zeuzem S, Berg T, Moeller B, Hinrichsen H, Mauss S, et al. (2009) Expert opinion on the treatment of patients with chronic hepatitis C. J Viral Hepat 16: 75-90.
10. Torres-Puente M, Cuevas JM, Jimenez-Hernandez N, Bracho MA, Garcia-Robles I, et al. (2008) Genetic variability in hepatitis C virus and its role in antiviral
treatment response. J Viral Hepat 15: 188-199.
11. Drexler JF, Kupfer B, Petersen N, Grotto RMT, Rodrigues SMC, et al. (2009) A novel diagnostic target in the hepatitis C virus genome. PLoS Med 6: e1000031. doi:10.1371/journal.pmed.1000031
12. Nagamine K, Hase T, Notomi T (2002) Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes 16: 223-229.
13. Thompson AJ, McHutchison JG (2009) Review article: Investigational agents for chronic hepatitis C. Aliment Pharmacol Ther 29: 689-705.
14. Thimme R, Neumann-Haefelin C, Boettler T, Blum HE (2008) Adaptive immune responses to hepatitis C virus: From viral immunobiology to a vaccine. Biol Chem 389: 457-467.
15. Schulze Zur Wiesch J, Lauer GM, Timm J, Kuntzen T, Neukamm M, et al. (2007) Immunologic evidence for lack of heterologous protection following resolution of HCV in patients with non-genotype 1 infection. Blood 110: 1559-1569.
16. Gaudieri S, Rauch A, Pfafferott K, Barnes E, Cheng W, et al. (2009) Hepatitis C virus drug resistance and immune-driven adaptations: Relevance to new antiviral therapy. Hepatology 49: 1069-1082.
17. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, et al. (2008) The influenza virus resource at the National Center for Biotechnology Information. J Virol 82: 596-601.
18. Combet C, Penin F, Geourjon C, Deleage G (2004) HCVDB: Hepatitis C virus sequences database. Appl Bioinformatics 3: 237-240.
19. Division of AIDS, National Institute of Allergy and Infectious Diseases (2009) HIV databases. Available: http://www.hiv.lanl.gov/. Accessed 11 May 2009.

Figure 1 Legend

Complete genome trees of the hepatitis C virus, HIV-1 (M-group), and the hemagglutinin region of influenza A. Nucleotide sequences were randomly selected from their respective databases representing each of the major subtypes from each virus [17–19]. Only non-recombinant genomes were included. Maximum likelihood trees were built using GARLI (Genetic Algorithm for Rapid Likelihood Inference, available at http://www.nescent.org/). Trees have been drawn to the same scale.

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Inaugural Meeting of the Concept Web Alliance

Richard Cave — Mon, 18 May 2009 10:54:53 -0700

On May 7 - 8th, I attended the inaugural meeting of the Concept Web Alliance. CWA wants to enable interoperability between large triple stores like the Large Knowledge Collider (LarKC) and provide an Open Access mechanism for accessing the triple stores. This is great for the projects in life sciences as the semantic triple stores are becoming the de facto way to store data for gene expression and sequencing, biobanks, etc.

The CWA mission statement is:

”To enable an open collaborative environment to jointly address the challenges associated with high volume scholarly and professional data production, storage, interoperability and analyses for knowledge discovery.”

You can read the entire CWA declaration.

There were a number of representatives from the STM publishing world (Abel Packer from Bireme is a founding CWA member, Nature, Springer, SEED, The Scientist, Thomson Reuters) and I had some good conversations about the vision of the CWA in relation to STM publishers. All agree that the CWA is a much needed initiative but there are questions on how it can feed back into a revenue model. Most STM publishers don’t have triple stores that can be offered to the CWA endeavor. They publish the final result - research articles based on the triple stores.

But I see a few ways that publishers can benefit from working with the CWA:

1. The CWA can provide tools that link the data stores directly to the content of the research article. Search, data mining, and visualization tools can be created for publishers which would give their users new ways of interacting with the research article. Users can find the research articles that they really want and can dig into the underlying data even if the data is a massive data store. For the publisher, this can increase revenue by bringing more traffic, focused advertising campaigns, etc. CWA can provide these tools for a fee which would be used to sustain and further the CWA mission.

2. The CWA can provide tools to automate semantic encoding of the research article. As an example, David Shotten has shown how this can be used by publishers by encoding a PLoS NTD article - see Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article and has another paper titled ““Semantic Publishing: the coming revolution in scientific journal publishing” - preprint available here. Knewco also has some great technology in this space – check out their Concept Web.

3. Publishers can provide Open Data back to the CWA. Publishers could provide access to content tagged with RDFa for easier auto-machine discovery, allow access to the data from the supplemental information in the research article or provide triples generated from the content of the research article itself. PLoS is a bit ahead of the publishing curve as all of the PLoS journals run on the Ambra/Topaz platform which stores the content of the research articles as triples. We’re looking at ways to provide access to a subset of these triples (we would need to remove user information) through a SPARQL endpoint or other means of access. This would allow for direct access to the triples that could then be given back to the CWA.

What other ways can publishers interact with the CWA? The CWA wants to know how your organization can participate.

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PLoS Biology Migration to Ambra/Topaz

Richard Cave — Wed, 13 May 2009 12:38:35 -0700

Yesterday, we migrated PLoS Biology to the Ambra/Topaz platform. This completed a two year, 5 journal, ~9000 article migration involving many of the PLoS staff. Now all of the PLoS journals have the same feature set including notes, comments, ratings, article impact metrics, etc. Migrating all of the PLoS journals to a single platform is a major milestone for PLoS and will allow us to finally create cross-journal features such as cross-journal search.

We released a snapshot version of Ambra to production just before the PLoS Biology migration that fixed a number of bugs that were uncovered with the PLoS Medicine migration in March. These bug fixes will likely be unnoticed by most users.

We also standardized our environments for performance testing of the Ambra/Topaz platform in Amazon EC2. The development team created scripts to automate the launch of the Ambra/Topaz platform in the Amazon “cloud” with a snapshot of our production data. We will continue working on these scripts so that others to easily launch Ambra/Topaz instances and test the platform (stay tuned for more info).

Liz has provided a bit more information on migration at the everyONE blog.

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Living through the Swine Flu epidemic - a perspective from Mexico

Liz Allen — Thu, 30 Apr 2009 09:30:59 -0700

PLoS production and editorial staff are in close contact with our soon to be published authors around the world and they often get to know them quite well during the to and fro of correspondence. A scientist from Mexico, who has a book review article that has been accepted for publication and will shortly be published in PLoS Biology, told us what it is like to live and work there at the current time, and we thought that we would share that with you.

"Although it is said that Darwin was a bit of a hypochondriac, microbes are conspicuously absent in his writings and in those of his circle of close friends and colleagues. Caught in the middle of the celebrations of Darwin’s bicentenary, the inhabitants of Mexico are now painfully aware that the unexpected emergence and rapid spread of the swine flu epidemic demonstrate that we live in the midst of an evolving microbial world and that our individual health and collective well-being depend on it. I have been in Mexico City since the beginning of the crisis, and thanks to my friends who are physicians, I quickly became aware of the risks, but nothing had prepared me for the impact of seeing the streets, parks and gardens empty, the schools, cinemas, restaurants and churches closed, and increasing numbers of people with the mouth covered and a look of disbelief and uncertainty in their faces.

Mexicans do not shy away from physical contact: we express our affections by embracing, kissing, shaking hands and holding relatives, friends and specially children closely. The knowledge that the spread of the swine flu virus can be limited by avoiding close physical contact is changing quickly the way we relate, but two days ago the press agencies distributed a photograph of a young Mexican couple kissing tenderly with their protective masks on.

We always find ways to overcome hard times. Let us hope we continue to do so".

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PLoS Computational Biology editors win awards

Evie Browne — Tue, 28 Apr 2009 04:00:27 -0700

PLoS Computational Biology is pleased to acknowledge two of our editors, Philip E. Bourne and Lars Jensen, who have won prestigious awards in recent weeks.

Philip E. Bourne, PLoS Computational Biology Editor-in-Chief, was honoured with the Benjamin Franklin Award, given by the Bioinformatics Organization at the 2009 Bio-IT World Conference & Expo in Boston. We are particularly pleased to note that this award is given for Open Access in the Life Sciences and is in part due to Phil’s work with PLoS, along with his involvement and leadership roles in such innovative projects as the Protein Data Bank and Scivee.tv. Professor Bourne is a founding editor of PLoS Computational Biology, and his leadership has been a driving force for Open Access in this field and throughout the sciences. Read more about the presentation here.

A PLoS Computational Biology Associate Editor, Lars Jensen, is part of the team which won the Elsevier Grand Challenge, a competition to “describe and prototype a tool to improve the interpretation and identification of meaning in (online) journals and text databases relating to the life sciences.” Dr Jensen’s team from the European Molecular Biology Laboratory have developed Reflect, a program which can tag gene, protein, or small molecule names on any website. The competition itself has stimulated developments in science and science publishing, and we look forward to seeing new ways to improve, use and re-use journal content.

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