A key part of the current effort is to convene scholarly metrics thought leaders to help spearhead the widespread adoption of ALM. By engaging leading authorities in metrics, and bringing them together in a working group, PLoS can better coordinate the development of ALM. The following experts serve on the ALM Technical Working Group in an advisory role to help steer the direction of PLoS ALM implementation:

• Pedro Beltrao, University of California San Francisco
• Phil Bourne, University of California Santa Cruz
• Bjoern Brembs, Freie Universität Berlin
• Martin Fenner, PLoS
• Duncan Hull, European Bioinformatics Institute
• Cameron Neylon, Science and Technology Facilities Council Oxford
• Heather Piwowar, NESCent, Duke University
• Jason Priem, University of North Carolina at Chapel Hill
• Dario Taraborelli, Wikimedia Foundation
• Jevin West, University of Washington
• Johan Bollen, Indiana University

Starting May 16, 2012, Martin Fenner will join PLoS as the ALM Technical Lead. Martin announced the news on his PLoS blog Goobledygook last month. Martin has been a leading advocate of scholarly metrics and has worked on several article usage applications. As ALM Technical Lead, he will not only help with the development of the PLoS ALM application, he will also lead developer outreach for the project.

Further information on all these developments are available on a new ALM website launched today, please take a moment to check it out. We also encourage you to visit our journals and to view ALM by clicking on an article metrics tab.

We are also pleased to announce that Kristen Ratan has been appointed head of a united Publications and Products group. Kristen brings a wealth of experience in both scientific publishing and product development, and has quickly made significant contributions to PLoS. Kristen’s passion for innovation, people, and publishing will be a tremendous asset for us as we continue our leadership in Open Access publishing.  With the extensive experience of Ginny Barbour and Theo Bloom, both recently promoted to Editorial Directors, PLoS has strong editorial leadership in place that complements Kristen’s product and platform development experience. The Open Access movement is increasing in momentum and we appreciate the support of the community as we continue our effort to accelerate progress in science and medicine by leading a transformation in research communication.

PLoS Computational Biology Meets Wikipedia | Topic Pages

Guest post by Daniel Mietchen, the PLoS Computational Biology technical editor for Topic Pages. As Wikimedian in Residence on Open Science, he helped to define the workflow for Topic Page article submission and peer review.

On Tuesday morning, the English Wikipedia’s main page contained a short statement informing visitors “that the protein Concanavalin A (pictured) cuts itself in two and then reassembles in a circularly permuted order” when cut in half, with the bolded link inviting clicks from those wishing to find out more.

Two proteins that are related by a circular permutation. (Image from Bliven S, Prlić A (2012) Circular Permutation in Proteins. PLoS Comput Biol 8(3): e1002445. doi:10.1371/journal.pcbi.1002445)

The clicks led to Circular permutation in proteins, an article that describes circular permutation in proteins as

“a type of relationship between proteins, whereby the proteins have a changed order of amino acids in their protein sequence, such that the sequence of the first portion of one protein (adjacent to the N-terminus) is related to that of the second portion of the other protein (near its C-terminus), and vice versa.”

Subjecting the quote to a Google search reveals that there is an article in PLoS Computational Biology that is also entitled Circular Permutation in Proteins, in which the concept is defined in exactly the same way.

Rather than a bug, this striking similarity between the Wikipedia and journal articles is a feature, reflecting the new manuscript track of Topic Pages at PLoS Computational Biology. As explained in an accompanying editorial (whose title has been circularly permuted to yield the title of this blog post), “Topic Pages are the version of record of a page to be posted to (the English version of) Wikipedia.”

In other words, Topic Pages expand on earlier attempts to add a dynamic component to scholarly publishing. They provide the English Wikipedia with expert-written and expert-reviewed content, and allow authors to get credit for their work.

Like the phrase quoted above, the paper contains direct links to Wikipedia pages for background, which dramatically reduces the need to rehash what is already known, while still allowing for a minimum of context.

The reviews that have been produced as a result of the journal’s peer review process have since been posted to the talk page of the Wikipedia entry (along with some further procedural explanations) and as comments to the paper itself.

While the workflow for the initial Topic Page at PLoS Computational Biology was a work-in-progress (as described by both authors), we anticipate considerable streamlining of the workflows for future ones.

Other journals wishing to experiment with wiki contributions are invited to use the dedicated Topic Pages wiki for preparing articles in their respective manuscript track. To further stimulate such experiments, Wikimedia Germany has approved funds to help other journals integrate their workflows with those of Wikimedia projects.

We hope that such a shared experimental environment and code base can provide fertile ground for publishers to develop best practices and standards on the way towards more dynamic modes of publishing. We acknowledge the help and support we have received from several WikiProjects, most notably those on Computational Biology, Molecular and Cellular Biology, and Open Access.

This innovative, online publication channel for the rapid communication of new scientific research and ideas aims to minimize delays between the generation and publication of new research. All content published is peer-reviewed, citable, publicly archived in PubMed, and indexed by Scopus.

PLoS Currents removes barriers to communication and exchange through:

• A single, integrated solution for writing and publishing
• Flexible article format for increased ease of submission
• Streamlined peer-review process that establishes the legitimacy of the work
• Individual sections tailored to a specific research community

Its six sections include:

• PLoS Currents: Disasters
• PLoS Currents: Muscular Dystrophy (Produced with support from Parent Project Muscular Dystrophy)
• PLoS Currents: Huntington Disease (Produced with support from CHDI Foundation)
• PLoS Currents: Tree of Life
• PLoS Currents: Evidence on Genomic Tests
• PLoS Currents: Influenza

For this redesign, we partnered with Solvitor LLC* to implement Annotum (the name of this new publishing platform). Carl Leubsdorf, Jr., founder of Solvitor LLC, describes Annotum as “an open-source, open-access, open-process authoring and publishing system based on WordPress.”

We welcome you to browse articles and submit your research to one of the PLoS Currents sections today. Contact us at currents@plos.org.

*Annotum is a product of Solvitor LLC with heavy lifting by Crowd Favorite, and with special thanks to Google, PLoS, NIH/NLM/NCBI, and Automattic.

Today, there are ever more pressing needs for up-to-date information to be quickly available and easily accessible. This has never been more true than in the field of disasters, where slowness in sharing knowledge can be the difference between life or death for thousands of people, or the avoidance or mitigation of catastrophic outcomes for an ecosystem.

Despite the breadth of technological possibilities available, publishers and scientific journals have not provided adequate solutions for publication during fast moving emergencies. One study, published in 2009 showed that the majority of the epidemiological articles on the SARS epidemic of 2003 were submitted after the epidemic had ended, many several years after – and this for an emergency that lasted just a few months. The UNIDSR has identified that, “the sharing of research findings, lessons learned and best practices” are a priority in its Hyogo Framework for Action 2005-2015.

PLoS is proud therefore to announce the launch of PLoS Currents: Disasters, a new, innovative open-access publication for the rapid communication of new research results and operational analyses derived from the study or management of all types of disasters. All research is citable and permanently archived in PubMed Central as well as indexed in Scopus and PubMed.

Our primary aim is rapid dissemination to make essential, and in many cases otherwise hard to publish, findings as widely available as possible as quickly as possible, so they can be used and built upon. We have implemented an integrated authoring, editorial, and peer-review system called Annotum, a new publishing platform, which we believe can cut the publishing time down to a few weeks, or even days. Authors directly compose or insert their manuscript in the web-based application and peer review occurs within it. All of the content is published under a Creative Commons Attribution License (CCBY), which means that articles are immediately free to read but more importantly can then be reused in any way, provided that the authors and original sources are attributed correctly.

PLoS Currents is a flexible publishing channel, which responds to the particular needs of the community of disasters-related researchers and practitioners. In addition to the decreased publishing time through a streamlined review and production process, it offers:

• Flexibility: open article formats to reflect the diverse types of disasters-related research
• Revisions: updated versions of articles that document the latest results or analyses.

The most recent article, from 16 international experts in the fields of research, education, ethics and operational aspects of disaster medical management, highlights a critical issue in disaster management and describes a template for uniform data reporting of acute medical response in disasters.

PLoS Currents: Disasters is supported by an international group of researchers, practitioners, who serve on its editorial and review board.

Professor Virginia Murray, an Editor for PLoS Currents: Disasters, and the Head of Extreme Events and Health Protection at the Health Protection Agency, said “evidence based advice is essential for providing relevant up-to-date evidence based information to support the development of planning for extreme events – PLoS Currents: Disasters is a valuable publication resource to help to build the information that is so vitally needed for this purpose.”

Professor Mike Clarke, also an Editor for PLoS Currents: Disasters, and the current Chair of the MRC Network of Hubs for Trials Methodology Research and one of the founders of Evidence Aid, said “We are increasingly aware of the problems caused by research not being published in a timely and accessible way, and the damage this does to decision making and, consequently, to health care and health. The arrival of PLoS Currents: Disasters will help ensure that we learn from those lessons, by improving access to the knowledge needed in disasters. Evidence Aid is trying to make it easier for people to use systematic reviews of relevant information, and this new resource is a landmark step in making this information available.”

Fabrice Renaud, Head of the Environmental Vulnerability and Ecosystems Services Section, United Nations University Institute for Environment and Human Security, Bonn, Germany and an Editor of PLoS Currents: Disasters said: “PLoS Currents: Disasters will enable scientists and practitioners who directly work on the many facets of disaster prevention, disaster management and disaster response to rapidly share their on the ground expertise, observations and research results with a wide range of stakeholders.

Professor David Sanderson, Director, Centre for Development and Emergency Practice (CENDEP) and an Editor of PLoS Currents: Disasters said: “PLoS Currents: Disasters aims to fill an important gap – that of getting good evidence-based research out fast to those working in disasters.”

PLoS Currents started with its first section, Influenza, in 2009. Today, we continue the spirit of innovation with the launch of our sixth and newest member, PLoS Currents: Disasters, which we will be developing over the next few months. Contact us at disasters@plos.org with any questions, comments, or suggestions on further developments or leave a comment below.

PLoS Currents: Disasters welcomes your submissions.

In early July 2012, Cameron Neylon will join PLoS as Director of Advocacy.

In his new position, Cameron will promote advocacy of Open Access and develop strategies to drive the broader reinvention of research communication, both within the existing PLoS journals and beyond. He will work with other Open Access advocates, funders, publishers and scholarly societies to raise awareness and promote the adoption of research communication systems that support the public’s access and contribution to research. Cameron’s passion and dedication to Open Access are manifest in his speaking engagements and leadership in online media. His knowledge of policy and the scientific community in the EU and Asia/Pacific region will be a great asset to PLoS. He is among the most effective, articulate and balanced advocates of open and collaborative science, and of quality, speed and sustainability in research communication. Please join us in welcoming Cameron and congratulating him on his new role.

To find out more about these article enhancements, you can watch a short (<2 minute) video and browse these screen shots.

Article-Level Metrics now displayed on the article itself

New data source: article views from PMC

New visual display of data sources

This is the first in a series of forthcoming developments to ALM that we expect to roll out in the next 12 months – you can expect to see the addition of Twitter as a data source in the next few weeks and a number of tools will be added to make use of ALM data in the journals this year – so watch this blog for tagged posts.

Talking to various participants at the excellent Science Online 2012 event in North Carolina earlier this month it became clear that while some are ALM experts there are many who haven’t heard that PLoS provides performance data for every article including the following data from the sources noted:

• Article usage – PLoS:  page views, PDF and XML downloads. NEW: PubMedCentral:  page views, PDF downloads
• Citations–CrossRef, PubMed Central, Scopus, ISI Web of Science
• PLoS reader evaluation –Comments, Notes, Star rating
• Blog coverage – Research Blogging, Nature Blogs
• Social tools –CiteULike and Connotea. NEW: Mendeley and  Facebook.

Additionally, PLoS provides context for the performance of each article by providing journal and topic averages so researchers can see how their research compares with that of others.

The best way to get familiar with ALM’s is to click on the metrics tab at the top of your article – then you can understand more about the impact of your research and the discussions that it inspired!

Diseases transmitted by insects form a huge burden on human and animal populations. Insect control has historically been one of many strategies for control of diseases such as dengue, malaria, and sleeping sickness. The debate on whether GM insects could be used for disease control began as soon as transgenic insects were first produced in the 1980s. Since then, several experimental releases of GM insects have taken place. These trials show promise for limiting the spread of many vector-borne diseases (most notably Dengue fever). Articles in this collection showcase different aspects of this new technology including development, environmental impact, and regulation. Public discussion of the science and application of GM insects is necessary as new developments bring potential wide releases closer to a reality.

In an Editorial, Michael J Lehane (Liverpool School of Tropical Medicine) and Serap Aksoy (Yale School of Public Health) state that GM insects “may provide great promise for new means of controlling diseases with a devastating impact on people’s lives. If so, then public acceptance is likely to be a key issue in their implementation.” With many countries considering open field trials of GM insects, a Viewpoint by Guy Reeves et al. examines the regulation process of the first 3 countries that have had field trials of GM insects. Commentary by John Mumford highlights that both national and international regulations are required due to factors regarding each country’s individual environmental risk to GM insects.  In a Commentary from an industry perspective, Luke Alphey and Camilla Beech argue that “the agencies tasked to regulate GM insects have appropriately taken a cautious, thorough approach that allows progress towards realisation of the substantial benefits GM insect technology could potentially provide, while rigorously protecting the public and environment.”

The articles in this collection highlight many different points of view surrounding the research into GM insects. As the recent history of GM insect development demonstrates, public discussion is necessary as scientists continue to research GM insect technologies to control some of the world’s most devastating diseases.

This blog post was written by Renata Santillan (Publications Assistant of PLoS Neglected Tropical Diseases). Image Credit: James Gathany, Centers for Disease Control and Prevention.

A highlight of the event was the publications workshop. A panel of editors from a variety of journals fielded questions about the ins and outs of the publication process. Our own PLoS Pathogens editors Kami Kim, Dominique Soldati-Favre, and Artur Scherf contributed to the panel along with Silvia Moreno who represented for PLoS ONE.

PLoS Pathogens was pleased to sponsor two prizes for outstanding presentations at the meeting. Congratulations to Christina Mueller (University of Geneva) and Sebastian Lourido (Washington University School of Medicine) who impressed the judges to become the recipient of these awards.

Christina’s presentation described the essential role of Toxoplasma gondii armadillo repeats containing protein (TgARO) in the biogenesis of rhoptry organelles. Rhoptries, together with micronemes are specialized secretory organelles that crucially assist Apicomplexans in host cell invasion. In the absence of TgARO, T. gondii parasites show a severe and selective defect in invasion. This dramatic impairment is caused by a defect in rhoptry organelle biogenesis. Electron microscopy revealed that rhoptry organelles are absent and in addition, single rhoptry-like structures appear at unusual sites within TgARO depleted parasites.

Sebastian’s work also investigated the biology of the parasite Toxoplasma gondii in this case exploring the roles of calcium-dependent protein kinases (CDPKs). One of these kinases, CDPK1, is responsible for regulating the secretion of specialized organelles that mediate motility and host cell invasion by the parasite. Unique among parasite kinases, CDPK1 has a large ATP-binding pocket that can accommodate bulky ATP analogues, which can allow for the tracking of its direct targets in the context of a cell lysate. Combining this with other genetic approaches, Sebastian’s group is in the process of identifying the targets that contribute to regulated secretion, with the hopes of understanding the cellular pathways regulating this central process in the parasite life-cycle.

The full abstracts for these and other presentations are available now online.

This blog post was written by Elizabeth Flavall (Senior Publications Assistant of PLoS Pathogens).

This new environment is scalable to support the future growth of the journals, flexible in that it can store any type of data/content, built to minimize downtime, much easier for developing new features and best of all, it makes the journal websites perform much faster.

The migration to New Hope occurred over a 3 day period in November and New Hope officially went into production on November 14. This migration was the culmination of months of development and testing. The migration was completely seamless and users experienced no downtime!

Three weeks after the migration to New Hope, we can show that the new platform really did enhance our journal’s performance. For example:

• Average load time of this PLoS ONE article went from 4 seconds to 0.8 seconds.
• Nightly indexing of article data from Mulgara to Solr used to take 3-6 hours. From MySQL to Solr, the indexing now takes 24 minutes.

Warmest congratulations to the New Hope development team (and our intrepid Linux systems administrator) for building a streamlined new home for the PLoS Journals!