Thursday, July 28, 2011
E. coli genome crowd-sourcing consortium publishes their data: why choose a closed access magazine for an Open Source project?
Thursday, July 21, 2011
Today we published an article by Mellmann et al. entitled, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. The following is an opinion piece by Dr. Niyaz Ahmed, a section editor for PLoS ONE and the academic editor of this paper. He is an expert in the area of molecular epidemiology and genomics of bacterial pathogens at the University of Hyderabad, India.
When a monstrously virulent strain of never-before-seen E. coli suddenly appeared in Germany last month, the rush to decode became an immediate focus. Several groups became engaged simultaneously to crack the genome of the underlying bug and then followed a huge crowd-sourcing effort on the internet as soon as the genome sequences were made available. Given that reasonable data were made available by these authors within 60 hours of the outbreak, not much of the evolutionary history of the organism had been dissected and a great deal of the interpretation remained vague.
An informed, scientific treatise was needed to help health control authorities and policy makers launch a serious mitigation campaign; this work, in that sense, constitutes the first official report on the genomic footprint of the underlying E. coli strain. The authors report chronological (step-wise) recombination of the genome in the outbreak strains over a period of ten years. This reveals the extraordinary capability of certain pathogens to recombine so that a devastating phenotype finally emerges with a multi-dimensional fitness advantage. Further, the study of Mellmann et al. demonstrates the might of present-day sequencing technologies such as Ion Torrent in enabling genome-guided epidemiology, diagnostics, and interventions.
I have no hesitation to say that the study carried out by Mellmann et al. is truly a technical masterpiece, a first time proof-of-principle whereby next generation sequencing could be harnessed in real-time when certain 'gold standards' such as serotyping failed miserably. This report has an important bearing on the new proposed field of 'epidemic forecasting' in which the spread potentials of a pathogen could be predicted based on genomic fingerprints – in other words, predicting if the infection will assume pandemic proportions. The finding that the E. coli strains analyzed were enteroaggregative (EAEC) could explain this. EAECs could persist in recovered or subclinical cases and that they could be carried by the latter on travel routes worldwide.
One of the possible shortcomings of the study could be that it is silent on the mechanistic details of 'adornment' of these bacteria with several layers of fitness – multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one 'naturally' chimeric strain in just 10 years is extremely dramatic! The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori, an organism notorious for its speed of recombination, recasting its entire genome every forty years. We recently had an opportunity to sequence and look at H. pylori genomes hierarchically obtained across ten years. We did not find major insertion, deletion and substitution events.
Technology helped with the dissection of the E. coli epidemic in hours and days, but the editorial process also was seamless and prompt enough to enable rapid dissemination of results. Open and early access is very important for the dissemination of findings during epidemic times because much of the control and mitigation measures need planning in the light of latest research findings.
Sunday, July 10, 2011
The 2010 edition of Thomson Reuters' Journal Citation Reports, released on June 28th 2011, provides further evidence that open access journals are delivering not only high visibility but also high rates of citation and impact.
Altogether, 101 BioMed Central journals now have official impact factors. 21 journals recorded their first impact factors this year. Meanwhile, among the 80 journals which already had impact factors, 52 increased while only 28 declined. The average change in impact factor was an increase of 0.19 points.
- BMC Medicine (IF 5.75) saw a huge jump in its impact factor and is now in the top 10% of journals in the General Medicine category
- Retrovirology (IF 5.24), is now 4th of 32 in the Virology category, overtaking Journal of Virology
- Malaria Journal (IF 3.49) recorded its third successive increase and remains the 2nd most highly ranked journal in the Tropical Medicine category
- Journal of Cardiovascular Magnetic Resonance (IF 4.33), official journal of the Society for Cardiovascular Magnetic Resonance, almost doubled its previous impact factor of 2.28
- BMC Plant Biology (IF 4.09) increased from 3.77 to confirm its ranking in the top 10% of the Plant Science category
- BMC Veterinary Research (IF 2.37) makes an exceptionally strong start, ranking 8th of 145 in the Veterinary Sciences category
- Frontiers of Zoology (IF 2.42) debuts in the JCR in the top 10% of the Zoology category
- Particle and Fibre Toxicology (IF 4.91) ranks 4th of 83 in the Toxicology category
- Cell Division (IF 4.09) and Epigenetics & Chromatin (IF 4.73) also both make strong starts
Full list of 2010 impact factors for BioMed Central journals
(journals listed in bold have new or improved impact factors)
|Acta Veterinaria Scandinavica||1.20|
|Algorithms for Molecular Biology||2.80|
|Arthritis Research & Therapy||4.36|
|Behavioral Brain Functions||2.31|
|Biological Procedures Online||0.74|
|BioMedical Engineering OnLine||1.12|
|Biotechnology for Biofuels||4.15|
|BMC Cardiovascular Disorders||2.02||New|
|BMC Cell Biology||2.46|
|BMC Complementary and Alternative Medicine||2.20||New|
|BMC Developmental Biology||2.78|
|BMC Evolutionary Biology||3.70|
|BMC Family Practice||1.47|
|BMC Health Services Research||1.72|
|BMC Infectious Diseases||2.83|
|BMC Medical Education||1.20||New|
|BMC Medical Genetics||2.44|
|BMC Medical Genomics||3.77|
|BMC Medical Informatics and Decision Making||2.23|
|BMC Medical Research Methodology||2.15|
|BMC Molecular Biology||3.19|
|BMC Musculoskeletal Disorders||1.94|
|BMC Plant Biology||4.09|
|BMC Public Health||2.36|
|BMC Structural Biology||2.26|
|BMC Systems Biology||3.57|
|BMC Veterinary Research||2.37||New|
|Breast Cancer Research||5.79|
|Chemistry Central Journal*||1.12|
|Epigenetics & Chromatin||4.73||New|
|Frontiers in Zoology||2.52||New|
|Genetics Selection Evolution||1.48|
|Harm Reduction Journal||1.46||New|
|Human Resources for Health||1.38||New|
|Health and Quality of Life Outcomes||1.86|
|Hereditary Cancer in Clinical Practice||0.96|
|International Journal for Equity in Health||1.30||New|
|International Journal of Behavioral Nutrition and Physical Activity||3.17|
|International Journal of Health Geographics||2.34|
|Irish Veterinary Journal||0.33|
|Journal of Biomedical Science||1.96|
|Journal of Cardiothoracic Surgery||0.91|
|Journal of Cardiovascular Magnetic Resonance||4.33|
|Journal of Experimental & Clinical Cancer Research||1.92|
|Journal of Hematology & Oncology||2.93|
|Journal of Inflammation||2.02||New|
|Journal of Neurodevelopmental Disorders||1.27||New|
|Journal of NeuroEngineering and Rehabilitation||2.64|
|Journal of Neuroinflammation||5.79|
|Journal of the International Society for Sports Nutrition||2.68||New|
|Journal of Translational Medicine||3.51|
|Lipids in Health and Disease||2.24|
|Microbial Cell Factories||4.54|
|Nutrition & Metabolism||2.35|
|Orphanet Journal of Rare Diseases||5.93|
|Parasites and Vectors||2.13|
|Particle and Fibre Toxicology||4.91||New|
|Reproductive Biology and Endocrinology||1.70|
|Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine||2.18||New|
|Substance AbuseTreatment, Prevention, and Policy||1.58|
|Theoretical Biology and Medical Modelling||1.60||New|
|World Journal of Surgical Oncology||1.12||New|
* Based on Web of Science data, the impact factor listed for Chemistry Central Journal appears to be erroneously low and has been queried with Thomson Reuters.
For further information on impact factors and journal tracking, see BioMed Central's impact factor FAQ.
Posted by Matt Cockerill
Wednesday, July 6, 2011
a. This word has become a favourite of scientific people especially when they are answering questions. I am also guilty. Example as follows - Question: If the DNA is copied until the primer just falls off, how is it that all the pieces of DNA end up exactly the same length? Answer: Well, basically, you are almost correct however, only the first copy gives a random length. After that, basically, the primer in the next cycle has to start 637 base pairs from the start point of the first copy. So, basically, all except the first copy are the same length, basically 637.
2. I mean
a. This seems to be used as a spacer between sentences, where the speaker continually likes to embellish details and add ideas. I mean, just as one would normally give the listener person a chance to talk by leaving a short gap in the conversation, by using "I mean" the gap is stolen back so that the normal person might not get a word in edgeways. I mean, let's say that it was you being the listener, and you are a nice polite person; I mean, like Marj in the Simpsons. Then you never have a chance to speak because ...
3. Sort of
a. A vague term implying that the speaker has not put any thought into the discussion and is sort of making stuff up as he goes along. This seams to be common in presentations from young artists.
a. Australians have become adept at placing this word in the middle of sentences as some kind of emphasis. I think it is very common in interviews with surfers; yeah – .
a. Television personalities, especially on gardening shows, continually say absolutely. Then the show "Absolutely Fabulous" started up perhaps as a send up of this trend. Recently it has been used more and more by almost everyone. By adding this word, a very vague concept suddenly becomes absolutely correct and proven beyond all doubt. Also, other words can be added to it, especially "fabulous" to make something rather mundane and boring into something apparently exciting. Take the concept of picking up handfuls of animal poo. We don't have smellovision yet, and the warm temperature of a putrefying heap is hard to transmit to the gardening audience. But I can call it compost and say how this material is absolutely the best thing for your garden. How absolutely fabulous it is to feel the warmth as you thrust your hands into the pile in order to experience nature as the good bacteria convert biodegradeable organic material into absolutely perfect plant nutrients. Actually, it sounds rather attractive as I write this.
a. A non word, also used as a spacer to stop other people butting in. Luckily there is no need to use this on TV interviews because a smart editor will cut out all the wasted time anyway, so as to add more content, or another "non umming" person to the time allocated for the story.
a. This word is more often used by teenagers – or even myself actually – as emphasis in a story. But it is used rather informally, among friends, with alcohol on board usually, and often as a preamble to an acted out part of the story telling. I am having trouble explaining it but here goes. Just say that I am telling you about a scene from the movie Avatar. So the main actor Sam Worthington is just a dumb marine so he's like, "I need to walk again so I will do anything to pay for an operation"; but Sigourney weaver, she's like some kind of genius professor so she's like "don't break the machinery you dumbass!" etc.
8. You know
a. Everyone uses this Phrase, again a spacer to show that you probably don't know all the facts but what you say is probably about right. Of course, as the brainy listener, you probably have more information or already have heard this story, but if you do know it you would not be so rude as to correct the speaker or embellish his own story. You know.
I think it might be fun to add a few more of these and give funny examples. It would be good practice for a screen writer in a sitcom. My son reminded me of a program we used to have which converted normal speech to "Jive" which was a kind of black American street gang speech which most Australians would hardly ever hear but probably rappers and people from Los Angeles might be familiar with. Time is up – I can't spend my life just doing a blog. Back to real life.
Sunday, July 3, 2011
Because the concept of PLoS ONE was so simple, yet so revolutionary, its launch in December 2006 was met with equal parts excitement and skepticism. In the PLoS ONE model, editors and reviewers would not attempt to assess the potential importance of the work. Rather, as long as the research was determined to be solid, the author would pay a flat fee, and up it would go on the Web. Could something as simple as publishing articles just because they were "good science" really work?
"The idea was to decouple impact assessment and technical assessment," says Mark Patterson, director of publishing for the Public Library of Science, who was one of the staff involved with the journal from the beginning. "We were also trying to take the hassle out of publishing."
PLoS co-founders Pat Brown, Michael Eisen, and Harold Varmus were also the visionaries behind PLoS ONE, once again creating a new channel by viewing publishing through the lens of scientists. Their vision was to do away with the redundant process of submitting a paper to a journal, waiting for a rejection that was so often based on subjective qualities such as impact, and then resubmitting to a new title. Instead, research would be peer-reviewed against objective criteria and published after it was deemed worthy of joining the scientific literature—often with just one round of revisions. New technology would be leveraged so readers could add value to the content. Those comments would then help to indicate the importance of the work to the body of scientific knowledge.
When the concept was first introduced, it created a lot of chatter—especially in the blogosphere, says Patterson. And, as with any new journal, no one knew what the response would be. Even supporters of PLoS ONE wondered if the model would be seen as selective and prestigious in the scientific community. "I found it very exciting at the time," says Cameron Neylon, a biochemist at the Rutherford Appleton Laboratory in Didcot, England, and member of the PLoS ONE Academic Editor board. "But I was less than convinced it would take off."
It didn't take long before PLoS ONE began emphatically to answer the skeptics.
In 2007, the journal received about 2,500 submissions and published 1,200 articles. In 2010, PLoS ONE received nearly 13,560 articles and published 6,800—with about 60 being published daily. It is now the single largest journal being published today.
The PLoS ONE business model is scalable. Its publishing costs have always been fully covered by the publication fees and it became a financial success. In 2010, due in part to this meteoric rise, PLoS became self-sustaining. The innovative concept and its capacity for rapid growth have caught the attention of other publishers. In a clear nod to the success of PLoS ONE, "clones" are popping up —from SAGE Open, to BMJ Open to Scientific Reports by Nature.
For its groundbreaking model of open-access publishing success, SPARC (the Scholarly Publishing and Academic Resources Coalition), has named PLoS ONE as its July 2011 Innovator.
"PLoS ONE is a game-changer," said Heather Joseph, SPARC's Executive Director. "It breaks through the preconception that authors— and readers—require a journal to determine the significance of scientific research, and demonstrates that the community is ready and willing to take on that role."
PLoS ONE has made a powerful—and quick—change in scientific publishing, which is a conventional industry, says Peter Jerram, chief executive officer of PLoS. "It's a testament to the idea," he says. "If you only look at how rigorous the science is and whether the conclusions are supported by the data, then a lot of great science gets out there more quickly, including some that wouldn't otherwise see the light of day."
The model represents something completely new and has attracted staff from more traditional publishers, such as Peter Binfield. In early 2008, Binfield succeeded Chris Surridge as managing editor of PLoS ONE. Binfield had been a career publisher who had always worked with the traditional subscription model. While he was one of the initial PLoS ONE skeptics, he felt Open Access was a better way to accelerate advancement in science and he very quickly became a fan of the journal.
"It seemed self-evident to me that this was the future of academic publishing," says Binfield.
It was groundbreaking to establish a journal that would publish first and only then figure out impact. With PLoS ONE, the author didn't get kudos or a badge of honor for being accepted to the journal. Rather, in this model the reader would make the judgment call as to how important the research was, from their unique vantage point.
The PLoS ONE process is more efficient and transparent than the traditional, subjective journal peer review process. "Not asking the impact question makes it a cleaner and more objective review," says Binfield.
And, contrary to early concerns that anything could make its way onto PLoS ONE, significant filters were established. On average, two external reviewers read every paper, and most are sent back to the author for revision. The journal applies stringent policies dealing with items such as disclosure requirements, data deposition standards, and ethical concerns. In addition, every paper has to pass a detailed technical checklist of over 40 items before even entering the peer review process. About 65-70 percent of submissions end up being published, says Binfield. Online tools are then used to evaluate, sort, and filter content after publication, not before.
There are approximately 10,000 publishers today, producing 25,000 journals with about 1.5 million articles per year. In an industry that has been slow to change, PLoS ONE is proving that new business models that don't charge subscription fees can survive—and thrive, says Binfield. In four years, this one journal has become the largest peer-reviewed journal in existence. On its current trajectory, PLoS ONE could be responsible for publishing fully 3 percent of the biomedical literature in 2012.
Looking ahead, Binfield sees the potential that, rather than having thousands of smaller journals, the vast majority of the world's literature could eventually be in as few as 100 journals, all with a similar profile to PLoS ONE. "It's moving very rapidly. It feels like a tipping point in the industry," he says.
Surveys of PLoS ONE authors help shed light on the journal's phenomenal success. The number one reason scientists submit is because it is open-access. They want their work to be freely accessible and widely available. The second draw is speed. Rather than waiting months or years to get a paper accepted in a traditional journal, PLoS ONE gets researchers' work out quickly. Finally, the quality of the PLoS brand is an important factor and the objective peer review is also appreciated, says Binfield.
Gary Ward, professor of microbiology and molecular genetics at the University of Vermont, who became Chair of the PLoS board of directors in January, just had his first paper accepted to PLoS ONE.
He and other researchers welcome the relief that PLoS ONE provides from the "treadmill" of submitting and resubmitting to traditional journals, says Ward.
"I love the concept of eliminating this huge waste of time by simply removing subjective evaluations of importance from the review process," says Ward. "If the paper is well-written and the conclusions don't overreach, then let the community decide the impact."
Ward calls the PLoS ONE approach the ultimate in "crowd sourcing" that also contains rigorous review—just a different kind of peer review.
PLoS ONE features original research from all disciplines within science and medicine (although most submissions are in life and health sciences). By providing an interdisciplinary platform, the hope is to facilitate discovery of connections between papers and subject areas. "The fact that you can read around the edges of a field is a big deal," says Binfield. "PLoS ONE forms a home for any article; it no longer has to have a journal of its own."
Behind the success
The concept of publishing without having to battle the system was the big driver behind the explosive growth of PLoS ONE. The trust of the PLoS brand also helped, says Patterson. Of course, there is the human capital that has had to expand to keep up with the rapidly growing journal.
Handling 2,000 submissions a month and publishing 60 articles daily takes a substantial group of people. The paid staff on the journal, which handles the checks and balances of the system, has increased to handle the growing number of submissions. There are about 35 full-time equivalents, with some positions contracted out. Then there are 1,700 academic editors on the journal, individually handling each paper and finding peer reviewers so that every paper is appropriately reviewed.
"We have been up to the challenge; we've kept pace," says Patterson.
CEO Jerram says he is amazed at the dedication of the people who work for PLoS ONE and that has made a palpable difference in the journal's success. "There is a real passion and commitment there," he says.
Binfield says while the staff works hard and the work can be stressful, it is a mission-driven organization, and they are energized by what they are doing. "We feel like we are doing the right thing for the right reasons," he says.
The process has worked because the model scales with the volume of submissions: Every article adds more work, but also adds revenue. The publication fee for each published paper is $1,350, which is usually covered by grant money. Unlike a traditional journal, PLoS ONE allows researchers to publish papers of unlimited length, with full color throughout and containing any amount of supplemental material such as spreadsheets or videos. Occasionally authors take fee waivers, but about 90 percent of authors pay the full amount.
The goal of making PLoS self-sustaining was met last year. The organization was originally established with the help of foundations and outsider support, but as the suite of publications has grown to make PLoS self-sustaining, they have been able to develop additional innovations such as article-level metrics, PLoS Currents and PLoS Hubs.
The followers and the future
"The model is working beautifully. It's financially sustainable and there is increasing rapid growth. This is something science is really embracing," says Ward. "The competition is crazy not to go this way," says Ward. The mission of PLoS is to make as much of the literature open-access as possible, and to show how Open Access can transform the literature into a more powerful resource for education and research.
While PLoS ONE pioneered coverage of the whole of science, many who have adapted the model are using it for single subject areas, says Binfield. "We are encouraged and excited to see these clones launched," he says. "It validates that this model is here to stay … We can see the future path and the launch of these clones just cements it."
Will PLoS adopt the PLoS ONE model for its other journals?
Chairman of the Board Ward says that the history of PLoS, (which is based in San Francisco and Cambridge, England and is the world's largest not-for-profit open-access journal publisher) has always been one of an organization pushing the envelope. "We are constantly looking at the editorial structure, the business model," he says. However, once a journal is established, it is harder to make wholesales changes. Ward says PLoS will continue to consider what works best for all of its titles and the organization is committed to being innovative. "We want to keep PLoS on the cutting edge," says Ward.
A goal of PLoS is to help publishers move into Open Access and PLoS ONE is indeed a new model for publishing, says Jerram. In the future, he says there may be better ways to communicate science than through journals. The real power and promise of Open Access is to make scientific information and data not only able to be read, but also re-used. "Open Access is the enabler that makes other things possible," says Jerram.
Binfield envisions more and more journals following PLoS ONE's lead and he says that it is very exciting to see the transformations that are underway. "I come into work every day with the knowledge that I am helping to advance science by accelerating and improving the process of disseminating scientific results," he says. "It's an important thing to have the knowledge that what we are doing is making a big difference in the world."
by Caralee Adams