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Archive by date: October 2008

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The week on Nature Network: Friday 31 October

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Join Nature Networkers and other scientists on 7 November (2008) for a Nature Network Berlin dinner with Arianne Heinrichs, Chief Editor of Nature Reviews Molecular Cell Biology. Students are particularly welcome. Arianne will be in Berlin to give a lecture about scientific writing to students of the FMP (Leibnitz-Institut for Molekulare Pharmakologie in Forschungsverbund Berlin). See the Nature Network Berlin group for more details.

Two other upcoming events are on 18 November (2008) at the R&D society in London. Scott Keir highlights a seminar 'Facilitating Creativity and Innovation', which will cover how to optimize the relationship between R&D (research and development) and marketing – essential for successful commercialization of technology. Later in the day, Dr Allyson Reed, Director of Strategy and Communications of the UK Technology Strategy Board will speak on 'Connect and Catalyse' – how the Technology Strategy Board accelerates innovation. This will be followed by a discussion dinner with Allyson. (More details at Scott's post.) And here is an early 'heads-up' for the next Talk Science evening at the British Library in London, on 10 December (2008). The subject is 'Infectious disease: what can evolution do for us?' Please join the Nature Network group and make your own suggestions for topics to discuss in December.

'Inspired' by the hundreds of articles published weekly, particularly in large journals such as Journal of Biological Chemistry and PLOS One, Richard Grant asks whether anyone actually reads journals for research articles any more. Do people take each new issue of a journal (online or print) and read through the table of contents? Do people read tables of contents via email alerts or RSS feeds? Plenty of answers follow about how people read, and organize the articles they bookmark or accumulate.

Craig Rowell has an unusual take on search. "I believe that a key to improving literature searches is to know what question (not merely the hypothesis) the researcher thinks their work has answered. Knowing that an article feels it answers more of a “what” question rather than a “how” question could be of tremendous help when looking for relevant literature." He asks readers for feedback on his proposal of 'question inclusion' as a search field.

In a conversation about the recently awarded Nobel prize in chemistry, Heather Etchevers responds to the suggestion that as the gender distribution among active scientists becomes more even, a (slowly) growing number of women will be awarded future Nobels. She points out that a pertinent question in this regard is that of gender equity among the nominators. Anna Kushnir checked out the numbers: the committee on physiology has no women, chemistry has two of a total of seven, physics two of a total of eight, and economics one of a total of eight.

Stephen Curry was surprised to hear on the radio an interview with a scientist who claims to have "converted the electrical signal from a nerve cell into an audible sound and claimed that this revealed a kind of cellular intelligence. As far as I can tell, this ‘finding’ is not based on any kind of peer-reviewed research. It seemed to be pure supposition". The reliability of science as reported by the media is dissected in the comments that follow the post.

There is a fresh wind of hope for young italian scientists amidst the recent government restrictions to temporary employments, writes Poltronieri Palmiro at the Nature Network Italy forum. "It comes from a regional Institution, Regione Piemonte, an example to be followed by other counties in order to provide adequately to the innovation needs of industry and public research bodies. Recently, in a meeting with authorities of Puglia Region, I suggested that in addition to the salary, the regional authority should provide in the grants also a budget to cover research costs in autonomy from the bureacracy of the hosting Institute". Read on at the Italy forum.

Finally, if you ever wondered how your salary compares with a football coach, check out Mike Fowler's post When comics stop being funny. The subseqent discussion is perhaps aptly summed up by science writer Brian Clegg's comment: "If it’s any consolation, the bar for an average author’s income probably wouldn’t even be visible on the scale of that chart. AND they have even more insecure jobs than football coaches."

Previous Nature Network columns.

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Historical microbiology archive made free to all

In its November Editorial, Nature Reviews Microbiology (6, 794; 2008) reports that the archive of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) has been made available free online: a boon for scientists, historians and the public. The Society for General Microbiology publishes IJSEM on behalf of the International Committee on Systematics of Prokaryotes of the International Union of Microbiological Societies. The society has now provided funding for the entire back archive of the journal to be made freely available worldwide without a journal subscription. (The current content, or past two years, remains subject to access controls.)
From the Nature Reviews Microbiology Editorial: Systematics is the foundation for studies of all types of organisms, because it helps us to understand how one organism relates to another. The value of systematics is often underappreciated, however, for bacteria and viruses. For example, there is a huge imbalance between the 7,000 named bacterial species and the 1,000,000 named insect species. This is particularly important given that it is now well-known that bacteria and viruses are the most populous organisms on Earth, and furthermore, that more than 99% of bacteria have yet to be cultivated. Why should we be interested in naming and characterizing different species of bacteria? The advent of metagenomics has swelled the literature with ever-increasing estimates of numbers and types of bacteria and viruses in the biosphere. An important adjunct to genomics-based approaches is the detailed characterization of these myriad species and investigation of the relationships between them. The availability of the IJSEM archive will hopefully spur renewed interest in this area.
Jean Euzeby, the IJSEM list editor, maintains an incredibly useful web resource that details all those species that have been ratified — the List of Prokaryotic names with Standing in Nomenclature. Another useful site named Bacterial Nomenclature Up-to-Date has an up-to-date list of bacteria and is based on the work of Norbert Weiss, who maintained the database until his retirement in February 2003. The current database is maintained under the supervision of Manfred Kracht. Finally, a comprehensive taxonomy of the Bacteria and Archaea can be found in the Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7, which was last updated in 2007.
Other useful resources are described in the Editorial.

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Neuropsychiatric diseases Insight free access for six months

Nature's Insight on neuropsychiatric diseases (Nature 455, 889-923; 2008) is free to access online for six months from the issue date (16 October 2008). Neuropsychiatric diseases, such as schizophrenia, depression and autism, are a huge burden on society, impairing the health of those affected, as well as their ability to learn and to work. Progress in defining the biological basis of these diseases is now being made. Technological advances in the areas of genomics and large-scale studies, as well as the development of new animal models, are improving our understanding of these diseases and are offering the prospect of fundamentally different options for treatment.
Nature editors I-han Chou and Tanguy Chouard write in their introduction to the Insight (Nature 455, 889; 2008):
Since the time of ancient Egypt, societies have struggled to understand mental illness and to care for those affected by it. But, over the millennia, the idea that mental illness might have a biological cause arose only intermittently, and treatments ranged from the benign (exercise, humour and music) to the barbaric (exorcism, imprisonment and lobotomy). By the mid-twentieth century, however, several breakthroughs had been made. Not only did health professionals understand mental illnesses to be diseases of the brain, but a set of systematic criteria for diagnosis had been developed, together with pharmaceutical and psychological therapies that are still central to modern psychiatry.
Today, despite decades of subsequent research, the prevalence of neuropsychiatric diseases has not decreased. Our understanding of the biological mechanisms of diseases such as mood disorders, schizophrenia and autism is frustratingly limited. And, although it has long been clear that most such diseases have a strong genetic component, the identities of the genes involved have proved elusive. There is also a lack of reliable biological markers for characterizing these diseases and, perhaps unsurprisingly, treatment options are far from optimal in terms of efficacy and specificity.
There is, however, some cause for optimism. Recent advances in genomic technology and large-scale studies are helping to identify genetic variants associated with diseases. In addition, new animal models of disorders such as depression and autism are providing ways to test hypotheses about the underlying neuropathology — at the molecular, neural-circuit and behavioural levels. This Insight highlights recent successes and new ideas in this crucial area of research. The hope is that developments such as these will lead to integrative approaches for designing better therapeutic strategies.

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'Next-generation' sequencing poster and podcast

A revolution in genomic science is underway. The reign of Sanger sequencing is coming to an end as a new generation of sequencing technologies allows vastly greater volumes of sequence information to be produced quickly and at an ever-decreasing cost. Nature Reviews Genetics and Nature Genetics present a free poster and a podcast on next-generation sequencing technologies, their myriad applications and challenges for the future.

From Nature Reviews Genetics (9, 811;2008): 'Next-generation' is a catch-all term for a range of approaches that differ in the way templates are prepared, the sequencing chemistry itself and the methods used to generate a sequence read-out. The poster, authored by Michael Metzker, enables readers to quickly grasp the methods that form the basis of the leading commercially available technologies and explains how they provide such high-throughput information so rapidly. Understanding how these technologies work is also key to appreciating which approach is best suited to which application.
The podcast brings to listeners insights from an international group of leading researchers in genetic and genomic research, exploring how next-generation sequencing technologies are being applied to fields as diverse as cancer research, small RNA biology and population genetics. Change is predicted to be rapid. According to one interviewee, sixty times more data than have so far been held in the world's nucleotide databases will be generated in just a year by one project alone. Highlighting the excitement surrounding these technologies, a Nature news story revealed one company's plans to sequence individual human genomes for $1,000 within a year.

The free poster and podcast are available here.

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Nanotechnology: when it pays to ask the public

When a research council in the UK consulted the public about different aspects of nanomedicine, the feedback was loud and clear, as Richard Jones reports for Nature Nanotechnology (3, 578 - 579; 2008). "Given the breadth, and the diffuseness, of nanotechnology as a field, and the wide range of potential impacts it might have, it has sometimes been difficult to maintain a focus and to find issues that people can get a purchase on, with the result that the recommendations can end up seeming, to some, disappointingly generic. In any case, the complex and decentralized nature of scientific decision-making sometimes makes it difficult to see how these deliberations actually make a concrete difference on policy. The results of a new public engagement exercise on the subject of nanotechnology for healthcare, carried out in the UK, directly address some of these criticisms and offer surprising and enlightening insights into potential public reactions to some of the predicted applications of nanotechnology in medicine".
But, asks Richard Jones, "what about broader worries concerning tensions between the involvement of the public in decision-making in science policy and the principle of the autonomy of the scientific enterprise? One answer, of course, is that it is right in principle that the public has a voice in the direction of an activity that involves considerable amounts of taxpayers' money, and that these exercises may help provide some public legitimacy for potentially controversial areas of science. The more provocative suggestion is that in an applied field like nanomedicine, taking the results of public engagement seriously may lead to significantly better decision-making. This is the proposition that now needs testing."

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The week on Nature Network: Friday 24 October

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Eva Amsen in the Ask the Nature editor forum asks whether there is a definitive resource for looking up the spelling and capitalization and hyphenation of scientific words."I used MESH to find the proper spelling of gene and protein names, but I’m now trying to find out if it’s “Western blot” or “western blot” or “Western Blot” and find that all three are in use. Southern was a name, but what is the rule for Northern and Western? Is there an OED of scientific language or something equally useful?"

In the Naturejobs careers forum, Paul Smaglik rounds-up news from the web related to scientific careers. Included in his post are links to the recent Times Higher Education Supplement ranking of the 'top 200' universities in the world and a report on US state biotechnology initiatives. On a similar theme, Matt Brown provides advice for how to get into science journalism, in a summary of Simon Franz's talk at the recent Source Event careers fair. Matt's post is the last of a series of four: previous entries can be accessed via this link.

Have you ever wondered about the differences and similarities between artists and scientists? Can we say that a successful scientist is also, per se a great artist? David Papapostolou is tackling these and related questions on a new blog about the interactions between art and science.

Frank Norman describes the Elucian Islands, a new site in Second Life that includes Nature Publsihing Group's Second Nature islands. "This new site provides space not just for scientific stuff but the whole range of knowledge and scholarship. It will be interesting to see how it develops", writes Frank. How long will it be, he muses, before Nature publishes its first paper that can only be fully appreciated in Second Life?

In the biomolecular NMR spectroscopy forum, Evgeny Fadeev introduces the Open NMR project, a NMR wiki (collaborative editing tool) that allows users to search and update the pulse sequence database, create pulse sequence images from wiki text, and to read and write about theory and practice of spectroscopy, software and anything else relevant to magnetic resonance.

Jean-Paul Boucher's job is to find and implement technology solutions that will directly impact the medical and scientific research mission of the US Natoinal Institutes of Health (NIH). Social tools like Nature Network "have the possibility to radically transform the way NIH does its business", he writes, "from direct expertise and material finding between labs (“has anyone used algae for X protocol before?”) to even cross-disciplinary research team collaboration." He asks Nature Network's NIH group members what kind of “collaboration” they want NIH to be able to do. Readers are invited to join the group and to give Jean-Paul their suggestions.

Previous Nature Network columns.

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Naturejobs podcasts for careers advice

The Naturejobs series of free audio shows features interviews and advice from experts in the field and highlights diverse career issues relevant to today's scientists. Naturejobs podcasts can be delivered directly to your desktop by subscribing to the free RSS feed. Simply click here and copy and paste the URL into your media player.

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Self-citation policy of Thomson Reuters explained

James Testa, of Thomson Reuters, explains the organization's policy on the abuse of excessive self-citation in a Correspondence (Nature 455, 729; 2008):

In reply to Tomá Opatrný's Correspondence 'Playing the system to give low-impact journals more clout' (Nature 455, 167; 2008), we would like to point out that the practice of journal self-citation is not new. Thomson Reuters is aware that some journals have used extensive reference to their prior content to influence their citation metrics. The contribution of so-called journal self-citation has been included in Journal Citation Reports since it first appeared in 1975. In recent years, these data have been made more prominent to inform our subscribers of the effects of journal self-citation.
Thomson Reuters also reviews self-citation data for journals in which an exceptionally high self-citation rate artificially influences the impact factor and therefore belies its contribution to the scientific literature. The role of a journal's impact factor as an objective and integral measure becomes questionable at this level of self-citation.
Nine journals received no listing in Journal Citation Reports last year because of exceptionally high self-citation counts; their titles are listed in the Notices file on the journal's website. Journal self-citations will be reviewed each year. Once the problem of excessive self-citation resolves and we can publish an accurate impact factor, the titles will again appear in the journal. Each title continues to be indexed in other Thomson Reuters products.
The cause of the increased 2007 impact factor of Folia Phoniatrica et Logopaedica will be examined as part of the routine review of journal self-citations, and a decision will be made regarding continued listing of the journal in 2008's Journal Citation Reports.

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Audible science journals needed

Science journals have been slow to make themselves audible, according to a Correspondence by Wouter M. J. Achten of the Katholieke Universiteit Leuven in Nature 455, 590 (2008). The Correspondence is reproduced here:

Podcasting has become very popular, mainly as a medium for entertainment. But it also holds huge potential for the visually impaired and others, such as dyslexics, who have reading difficulties. Simultaneously reading and listening to read-aloud news articles and scientific papers, for example, could increase readers' concentration and absorption of information. Such audio files would open a new world for the blind or partially sighted.
Software is available that translates text from digital files or directly from the Internet into a listener-friendly audio file, but it is expensive. Some freeware has built-in 'read out-loud' functions, but the quality is generally inferior.
Several newspapers and magazines already offer subscribers podcasts containing complete and navigable issues in read-aloud format. But the scientific press seems to be lagging behind. The Nature podcasts are a good start, but when shall we be able to listen to sections such as Research Highlights, News and Correspondence as downloadable audio?

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Metabolic syndrome: free web focus

Nature Publishing Group has created a web focus ‘Metabolic Syndrome 2008’ — showcasing a collection of original research articles from our academic and clinical practice journals that provide further insight into this global disease. Metabolic syndrome affects nearly 50 million Americans — almost one in four American adults. Approximately seven per cent of adults in their 20s and about 40 per cent of adults over the age of 40 meet the criteria for the syndrome. Metabolic syndrome is a cluster of conditions that occur together and increase the risk for heart disease, stroke and diabetes. Having just one of these conditions — increased blood pressure, elevated insulin levels, excess body fat around the waist or abnormal cholesterol levels — contributes to the risk of serious disease and in combination, the risk is even greater. There is no accepted or official definition of metabolic syndrome. Whether these risk factors actually can be referred to as a syndrome, they represent a growing medical condition involving multiple medical specialties. This free collection provides valuable insight into this emerging medical and public health epidemic.

‘Metabolic Syndrome 2008’ features content from the following journals:
American Journal of Hypertension
European Journal of Clinical Nutrition
The International Journal of Impotence Research: The Journal of Sexual Medicine
International Journal of Obesity
Journal of Human Hypertension
Nature Clinical Practice Cardiovascular Medicine
Nature Clinical Practice Endocrinology & Metabolism
Obesity

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Straight talking and the myth of 'independent' research

Nature Medicine (14, 1006 - 1007; 2008) features a question and answer session with Senator Charles Grassley. "What would a trim 75-year-old grain farmer have to say about drug safety and the payments given to medical researchers by drug companies? Lots, if he happens to be Charles Grassley, who has represented the state of Iowa in the US Senate since 1980. As the senior Republican on the Senate's finance and judiciary committees, he has carved out a role as a relentless watchdog who acts as a magnet for whistleblowers in government agencies ranging from the US Department of Defense to the FBI. In the last several years, Grassley has set his investigative sights on issues relating to medicine. A leading critic of the Food and Drug Administration since the surprise withdrawal from the market of Merck's painkiller Vioxx in 2004, Grassley is now focusing on university researchers funded by the National Institutes of Health who haven't been properly reporting income from drug companies. Meredith Wadman asked the senator what he hopes to achieve through his investigations." Read on, at Nature Medicine.

Sen Grassley's congressional investigation allegeing that some researchers have failed to report all the drug-company money that they have received — and that universities may have been too slow to police them is also subject of the leading Editorial in the current issue of Nature (Nature 455, 835; 16 October 2008, free to access online). A string of internal Emory University documents and e-mails made public last week after a hearing of the US Senate Committee on Finance, chaired by Sen Grassley, allege a web of consulting, lecturing and advisory-board relationships that Charles Nemeroff, chair of the psychiatry department at the University maintained with 16 pharmaceutical companies. According to Nature, Nemeroff is the seventh academic psychiatrist this year that Grassley has exposed as allegedly underreporting drug-company income. His office says that there are more revelations to come. Grassley has begun pressuring the NIH to mete out real punishment — as in pulling grants — to spur institutions to enforce proper reporting. Sen Grassley’s plan to make companies disclose in a publicly accessible database all payments of more than $500 that they make to physicians, and whether this would make it easier for universties to report such payments, is open for debate at the Nature Network Opinion forum.

Researchers and their institutions need to dispel a myth about 'independent' research before the media does it for them, according to the latest Nature Biotechnology Editorial (26, 1051; 2008). The great unspoken reality is that relationships between companies and researchers are not only becoming the norm, but they are also essential for medicine to progress. Without the exchange of expertise and knowledge between industry and academia, much of medical progress would falter.
This truth remains unspoken because researchers and their institutions like to maintain an aura of lily-white independence from the commercial world. Researchers may feel, and they may be absolutely right, that allowing companies to contribute to payments for trials or research or publications does not threaten their independence of thought or action.
However, that is not how the general public or individual patients see 'independence'. For them, independence implies no financial ties, no associations, not a smidgeon of influence from commercial interests. This wholly unrealistic view of angelic independence is an impression that the academic world has fostered, if not actively, then at least through a persistent failure to counter it. And it is this view that the Sunshine Act and its database will blow wide open once and for all.
The way to prevent a public and media backlash is for physicians and researchers (and their institutions) to take immediate and active steps now to explain the interdependence of industrial and academic research. It must be the biomedical community that says "we have to talk to these companies" and "their money really helps push medicine forward." We need to make plain that there can be a win-win-win outcome for doctors, companies and patients alike. That will give patients a better view of the integrated worlds of research and commerce within healthcare and disarm a million trivial investigations based on nothing more than administrative discrepancies.

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Nature Photonics on raising science's public profile

Gaining the readers' interests should not come at the expense of veracity. Getting the facts correct when communicating science to the general public is essential, according to the latest editorial in Nature Photonics (2, 581; 2008). From the Editorial:

The challenge of delivering rigorous scientific information is greater in this new era of Internet and cable television, as readers are flooded with information. Hence catching the attention of the public is proving increasingly difficult. General media are often forced to look for angles of the story that favour popular interest. One of the ways of boosting public attention, is through making science personally relevant and accessible to non-traditional audiences. Nevertheless, a narrative that can cause a stir in the public's imagination can lead to oversimplification and misinterpretation of the scientific achievement.
Is it necessary to simplify science so that it is more appealing to the general public? Does winning the attention of the public guarantee a long-term relationship between science and society? What can be done to raise the profile of science at no expense of veracity? Certainly open and continuous discussions between both journalists and scientists would help to reach a balanced view on how to report scientific developments to the general public without losing scientific credibility.

Read the full Editorial here.

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Discuss Nature's Commentaries on innovation

Are you interested in innovation and how to promote and predict it? Check out Nature ’s series of commentaries on the subject and tell us what you think at a Nature Network forum for online discussion.
In June, Bill Destler, president of the Rochester Institute of Technology discussed his school’s plan to foster innovation through academic-industrial partnerships.
In July, Lan Xue director of the China Institute for Science and Technology Policy argues that pushes to globalize science must not threaten local innovations in developing countries.
In August, David Guston of Arizona State University discusses the inherrent contradictions in the idea of introducing innovation policies, and offers ways of anticipating change without predicting it.
In September, Fred Gault and Susanne Huttner discuss some of the ways the OECD is looking to apply metrics to measure the impacts of innovation policies.
Podcast Extra!
David Goldston talks with experts about policies to implement innovation in this run up to the US presidential election.
Do you think innovation can be directed? Can it be predicted? Encouraged? Measured? Join the discussion at Nature Network.
The Nature commentaries are collected in this web focus.

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The week on Nature Network: Friday 17 October

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

"Writer’s block can be an impediment to putting thoughts on paper but there are other obstacles as well – obstacles that can be overcome once they’re made explicit", writes Linda Cooper in the Good Paper Journal Club forum. "...many of the students I teach are ‘flummoxed’ because they have difficulty pinpointing their most important finding – they usually want to include – everything – in their articles – especially the technique they’ve struggled to develop. To help remedy this problem, students explain their research to a sympathetic group of their peers. Because this group is multidisciplinary, they can comfortably ask clarifying questions (questions that a specialist reader may not feel comfortable asking – you’re the expert after all!). This process helps researchers think critically about their work – a crucial step on the way to writing clearly about their important finding."

In a more light-hearted vein, Bob O'Hara points to a discussion from someone worried about whether papers are more cited if the author list contains "bigwigs". One study suggests it can do, if there aren’t too many authors. If it were true, does this reflect the actual contribution of the "name", or a tendency for other researchers to be drawn to the paper by the name they recognize?

Henry Gee continues a theme of how scientists communicate their work to the broader public. "Here is an example of what I mean by this authoritarian approach. Ten years ago, John Durant, then Professor of the Public Understanding of Science at Imperial College, used the release of the first X Files movie as an opportunity to attack pseudoscience (’Pseudo-science, complete fiction’, The Independent, p. 13, 21 August 1998). What Durant missed is that for all its content about aliens, paranormal phenomena and conspiracy theories, the X-Files is scientific in the sense that the two protagonists, FBI agents Mulder and Scully, approach their mysterious cases, each with their own hypotheses, which they argue about, and then seek to test, only to find, vwery often, that a definitive result remains just out of reach. The lab scientists among you will know just what I mean. Real science is often messy, argumentative – and inconclusive."

Craig Rowell has established a new Nature Network forum, 'Going to meetings', for people to list the meetings they plan to attend and what they are presenting. This will be an opportunity to educate everyone about different meetings, he notes, and to connect with other Nature Networkers at the conference.

Why aren’t scientists’ biographies in the bestseller list?, asks Nature's Books and Arts editor, Joanne Baker. She wonders whether our picture of science takes enough notice of the characters and life stories of individual scientists, noting an essay in the 16 Oct issue of Nature (p871), in which biographer Georgina Ferry* asks why the life stories of so few scientists make it into the bookshops or are in the "top 100" biographies on Amazon. What do you think? Join the discussion at the Nature Network Opinion forum, and add your favourite scientific biographies - so far including William Bateson and Alfred Wegener. (*Georgina Ferry is the author of very well-received biographies of Dorothy Hodgkin and Max Perutz.)

Previous Nature Network columns.

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Direct control of paralysed muscles by cortical neurons

The activation of a single neuron in the brain may be enough to help restore muscle activity in the arms of paralysed patients with spinal cord injuries. Chet T. Moritz, Steve I. Perlmutter and Eberhard E. Fetz report their research in Nature (doi:10.1038/nature07418) showing that a potential treatment for paralysis resulting from spinal cord injury is to route control signals from the brain around the injury by artificial connections. These results are the first demonstration that direct artificial connections between cortical cells and muscles can compensate for interrupted physiological pathways and restore volitional control of movement to paralysed limbs.
The implications of this research are covered by Nature News in a story that is free to access online. The authors discuss their work in this week's Nature Podcast.

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A tool for analysing and classifying the communication of genetics to the public

'Frame that gene: A tool for analysing and classifying the communication of genetics to the public' is the title of a commentary by Rebecca Carver, Ragnar Waldahl & Jarle Breivik of the University of Oslo in EMBO Reports ( 9, 943-947; 2008). They write:

Enabling the public to understand scientific concepts and advances, and the issues they raise, is an increasingly important challenge for scientists and politicians alike. Public opinion—received via polls and elections—can influence scientific policy-making, and hence affect the funding and even the nature or focus of research itself. The fierce dispute over genetically modified crops in Europe, and the sometimes bitter debates about research using human embryonic stem cells in both Europe and the USA, highlight the enormous importance of public opinion on scientific issues. A greater awareness of the ethical, technical and philosophical issues surrounding research, as well as a better understanding of the science itself, could lead to more rational debates and outcomes—at least, that is what many scientists hope. The media therefore has a central role in furthering or modifying the public understanding of, and engagement with, scientific issues: it is the main source of information for many people, even more so than politicians, educators or scientists.
The authors go on to outline their framing scheme, which "represents a transparent and easy way of classifying gene discourse. It can be applied to the analysis of any type of gene-related communication—including textbooks, classroom education, television programmes and government reports—and it forms a basis for quantitative analysis. One could use it to identify the 'gene profile' of a particular newspaper or author or to explore the effects of gene framing on the public understanding of life science in general. Framing of the gene concept has implications for important issues ranging from personal health—such as the risk of breast cancer or heart disease—to international politics—such as stem-cell research or the regulation of genetically modified crops. Assuming that this framing is largely an unconscious process, our study may act both as an eye-opener and as a helpful tool for journalists and scientists alike."

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Nature editorial on Zotero v Thomson Reuters

This is the text of an Editorial in Nature (455, 708; 9 October 2008), concluding that proprietary data formats may be legally defensible but open standards can be a better spur for innovation.

"A historian of science and computing, and a scholar whose PhD thesis was on "professionalization of cooking among domestic servants in eighteenth-century France", might seem unlikely characters to find at the centre of a multimillion-dollar lawsuit. But that is exactly what has happened in the suit brought against George Mason University (GMU) in Fairfax, Virginia, by Thomson Reuters, the company probably best known for its ISI science indicators.
Dan Cohen, director of GMU's Center for History and New Media, and Sean Takats, a GMU history professor, are also directors of Zotero: open-source software developed by the history centre that lets researchers organize and share their digital information iTunes style, whether it is in the form of citations, documents or web pages. Zotero is free and popular, and has attracted some 1 million downloads since its launch in October 2006.
Thomson makes the proprietary bibliography software EndNote, and claims that Zotero is causing its commercial business "irreparable harm" and is wilfully and intentionally destroying Thomson's customer base. In particular, Thomson is demanding that GMU stop distributing the newer beta-version of Zotero that allegedly allows EndNote's proprietary data format for storing journal citation styles to be converted into an open-standard format readable by Zotero and other software. Thomson claims that Zotero "reverse engineered or decompiled" not only the format, but also the EndNote software itself.
The company is seeking a minimum of US$10 million in damages annually until GMU halts distribution of Zotero's new feature. It also demands that GMU "terminate" the ability of each Zotero user to use or distribute any open-source files converted from EndNote's own data format. GMU seems ready to fight the suit; a spokesperson told Nature that the university believes it is "well within its rights", but declined to go into further detail given the ongoing litigation. Thomson was contacted but declined to comment, saying: "It is the policy of Thomson Reuters that we do not comment on pending litigation."

Continue reading "Nature editorial on Zotero v Thomson Reuters" »

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Nature web focus on frontiers in HIV/AIDS

Development of an effective HIV/AIDS vaccine and new drugs to treat established disease remain an urgent and pressing need. To conquer the enormous challenge demands a far better understanding of the biology of the virus, its interaction with infected cells, and the response of the immune system, than is currently at our disposal. A Nature web focus presents a selection of recent research papers in Nature that advance our knowledge in this regard. Click here to access selected content free online.

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Applying systems biology to benefit human health

The hype that greeted the development of systems biology was followed by inevitable disappointment. But in reality, much groundwork has been done and tangible progress is expected. In a Nature Commentary (Nature 455, 730-731; 9 October 2008), Adriano Henney and Giulio Superti-Furga broaden a debate that began at a recent workshop in Portofino, Italy, on the application of systems biology to drug discovery by inviting readers to contribute their ideas. Delegates at Portofino drew up ‘roadmaps’ for three areas: metabolic disorders; cancer; and inflammation and infectious diseases — and are developing them as live documents to monitor progress. To comment on the article and related documents, visit the Nature Network forum 'Applying systems biology to benefit human health'.
At the Nature Network forum, Superti-Furga writes about the group's frustration about the scepticism within institutions, biopharmaceutical companies and funding agencies regarding the usefulness of systems approaches to medicine and in particular in drug discovery. Mindful of the danger of encouraging a climate of unrealistic expectations and delusions, "with genomics-like anticlimactic conservatism as consequence", Superti-Furga and colleagues have initiated a community-wide research roadmap proposal. "The purpose is to define the areas worth focusing on to obtain the facts that are needed as proof of concept for the entire community. In a careful process, we have engaged some of you first in interviews, then with on-line questionnaires and finally with a meeting restricted to 25 people that occurred in May (in Portofino, Italy). The outcome of the meeting is summarized in a Commentary that just appeared in Nature (enclosed). So far it has not been practical to engage all of you directly but we now need your help as we are preparing a white paper that covers much more ground of the Portofino discussions and following that measures for implementation."
"We got this rolling and would like to know if the community is willing to participate in the autodiscipline needed to achieve the goals of the recommendations. Moreover, we are looking for further focus and detail on the proposed ideas and on what could be additional ideas that the group may have overseen." The group will post on the following topics:
-Setting data standards
-Optimizing the application of existing tools
-Predictive toxicology
-Therapeutic area focus
-Communication and outreach
Please join the discussion at Nature Network by providing your feedback and proposals.
Applying systems biology to benefit human health forum at Nature Network.

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Nature Neuroscience on philanthropic support for science

The October editorial in Nature Neuroscience (11, 1117; 2008) describes how the contribution of private philanthropy to research has been growing. Although these large infusions of money can galvanize research, private and public funds now increasingly seem to support similar projects. Caution is warranted to prevent funding for specific topics from skewing research to the detriment of other fields.
"University College London (UCL) recently won £140 million ($245 million) of private funding for a new initiative to study neural circuits and behavior, fighting off tough competition from Oxford and Cambridge. With reduced government grants and increasingly expensive technology, funding from private sources is crucial to continuing advancement in science. However, whereas private funding once aimed to fund risky projects and fill in gaps in public funding, public and private sources now increasingly seem to funnel money toward similar projects. It is essential that funding for specific topics does not skew research to the detriment of important areas that might be temporarily less fashionable.
Although foundations have always been a part of the research funding landscape, the contribution of private philanthropy to biomedical research has been steadily increasing. The Germany-based Hertie Foundation has spent more than $122 million on neuroscience since 2000, a threefold increase compared to what it spent in the previous quarter-century. In the UK, funding from the Wellcome Trust is almost comparable to the funds available from the government's Medical Research Council. In the US, philanthropic funding for the biomedical sciences is reported to be about $5 billion a year, roughly one-sixth that of the total amount granted by the National Institutes of Health. Such a trend certainly seems like welcome news to the scientific community."
Read the rest of this Editorial here.
A Connotea library of background material is available here.


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Eric Hand blogging at the American Astronomical Society meeting

Eric Hand is currently blogging at In The Field from the Division of Planetary Sciences fall meeting of the American Astronomical Society at Cornell University in Ithaca, New York - a "gorges" place. His posts from the meeting can be viewed here. (For orientation, the introductory post is here.)

Here's Eric's report of Sho Sakada's talk: "the far side of the moon is full of gravitational lows. Scientists have long thought that the near side cooled more slowly, and that the moon's warm mantle and core were tugged closer to the Earth. This dense rock is much closer to the surface on the near side, as evidenced by the mare basalt flows in all of the basins. The far side has a much thicker crust."

Check out Eric's reports for space music, tigers and sharks, and more, over at In the Field (the Nature news reporters' blog from conferences and events).


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The week on Nature Network: Friday 10 October

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

In praise of the scientific amateur, Richard Grant writes: "the ‘cult of the amateur’ if you like, is tightly linked to our engagement with the wider public. There are a lot of very smart people out there who are not doing science as a day job. They may not have scientific training, and might in fact have some wrong-headed notions, but that does not mean they’re stupid. They may, in fact, have a lot to contribute. What, in effect, could we spool out to enthusiastic and capable amateurs in our own fields? Would it be useful? And as these people get involved, and talk to their friends and families, would it eventually serve to increase scientific literacy?"

Frank Gannon's recent EMBO Reports editorial on bullying in science is discussed in some detail. Heather Etchevers refers to a HHMI booklet Making the Right Moves: a practical guide to scientific management for postdocs and new faculty, available free either as a download or by mail, which she and others have found helpful.

The Italian government is intending to interrupt the temporary employment in the public administration which will affect all the “precari” in the public research institutions in the country. The amendment, known as “Brunetta” after the minister of public administration and innovation, is supposedly aimed at cutting the cost of the temporary employment, increasing the efficiency and promoting the stabilization with competitive examination. Its practical effect, however, is that thousands of temporary employee will lose their job 30 days after the promulgation of the decree. Piero Visconti asks those in the Nature Network Italy forum: will you be affected by the amendment? Do you agree with the protest? What do you think is the most effective way to change the political agenda in terms of funding research and promoting job security for Italian researchers?

Anna Kushnir asks whether there "are aspects of a grad student’s personality which can serve as predictors for whether or not they remain in science, whether or not they love it or hate it by the end. I also wish to figure out how much of the decision is dictated by external factors, such as the quantity and quality of a student’s interaction with their advisor, or the success of abject failure of their thesis project(s). I guess I am asking if there are people who are pre-destined, programmed and fit to continue on in science. Who are those people? What are they like?" Provide your answers on an online postcard at Nature Network.

Previous Nature Network columns.

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Focus on symbiosis at Nature Reviews Microbiology

This month (October 2008) Nature Reviews Microbiology publishes a Focus on Symbiosis . Microbial symbioses include beneficial, harmful and neutral relationships and are important in animal and plant health, immunity and disease, as well as in ecology and the environment. The special Focus issue of Nature Reviews Microbiology highlights exciting advances in understanding of partnerships between organisms and their environments.
Topics covered include manipulation of insects by endosymbiotic bacteria, marine chemosynthetic symbioses, the ancient arbuscular mycorrhiza, model symbiosis systems, the highly distinctive features of gut microbiotas and how they have evolved, and a glimpse of how experimental approaches will shape the future of this fascinating field. These Reviews and Perspectives highlight this emerging and important field. The accompanying library collates the most recent relevant original Research articles, News & Views and Reviews from across Nature Publishing Group.

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To show or not to show data

'Data not shown' is an outdated caveat that obscures the transparency of a scientific report and weakens the peer review process, according to Nature Chemical Biology (4, 575; 2008).
"Technology and competition perpetually raise the bar for the quality and quantity of experimental data that authors must include to publish a high-impact manuscript. Almost uniformly, journals have amended their formats to accommodate the increased volume of data while maintaining page restrictions by providing the supplementary information option online for authors and readers. Despite these changes, many authors still rely on the caveat of 'data not shown'. At Nature Chemical Biology, we discourage the use of this phrase and the omission of important data for two major reasons. First, the exclusion of essential data undermines the peer review process, and second, readers need access to data to form independent opinions about and to replicate the results of published papers. Thus, we suggest that the time for 'data not shown' has passed."
Read the rest of this Editorial here.
For additional details on presenting and consolidating methods, see the journal's Guide to Authors.
See the NPG authors' and referees' website for more details on our data sharing and database deposition policies.

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Nature debate: Enhancing The Brain

The first in a series of Nature debates, Enhancing the Brain, takes place at King's Place in London on Monday 13 October. Experts in science, science policy and science ethics selected by Nature, the leading weekly international journal of science, will discuss the risks, benefits and extent of how far research can extend our mental and physical abilities. The first of two panel events focuses on research underway that is extending the human brain: from intelligence and emotional tolerance, to sleep needs, memory power and more. What are the risks and benefits to the individual and to society of these developments? Would you boost your brain power? Why, when and why not? Should doctors, scientists, students, teachers or soldiers use such aids? Come along and take part in this mind-stretching evening. Tickets are £11.50.
Chair: Ehsan Masood, acting Chief Commissioning Editor of Nature.
Panel:
• Prof Barbara Sahakian, Professor of Clinical Neuropsychology at Addenbrooke’s Hospital, Cambridge.
• Prof John Harris, Lord Alliance Professor of Bioethics at the University of Manchester.
• Prof Nick Bostrom, Director of the Oxford University Future of Humanity Institute.
Booking enquiries can be made by email. To check ticket availability please use the King's Place online booking service.

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Nature Geoscience calls for outreach

Life in the twenty-first century requires an understanding of science and technology (see Nature Geoscience 1, 635; 2008) Students, educators and scientists will be celebrating the eleventh annual Earth Science Week from 12 to 18 October, with the theme 'No child left inside'. The event, organized by the American Geological Institute, aims to bring to life the relevance and importance of the science of the Earth and engender a lifelong interest in the topic.
According to Nature Geoscience, "the goal of this event is to engage students and their families in the geosciences, which are all too often relegated to early school years or removed from elementary and secondary school curricula entirely. The lack of exposure to the Earth sciences in school may be partly to blame for shrinking numbers of graduates with concentrations in geology, and it is probably compounded by the increasing tendency to rely on PowerPoint lectures and mail-order mineral kits instead of field experiences.
But the need for outreach goes much further than convincing the best students to take up a career in the geosciences. Earth science issues ranging from climate change to earthquake risks and from ocean acidification to sinking coastal cities confront politicians and voters alike. The science underlying these questions is complex, the impacts are potentially devastating and there are no quick fix solutions. It is impossible to make rational decisions on any of these issues without at least a basic understanding of the science behind the problems.
Unfortunately, the 2006 Program for International Student Assessment (PISA) suggests that many young people advancing through the educational systems of their countries are essentially scientifically illiterate. The report shows that almost 20% of 15-year-old students, distributed equally across industrialized and developing nations, do not understand the most basic science."
.....
"In addition to the occasional open days offered by more and more universities and research institutions, much can be done by individual scientists. Local and national programmes such as TRIO and Upward Bound are looking for volunteer scientists to host secondary level students in their lab for a few weeks during summer. Meanwhile, programmes like ScienceQuest need scientists and graduate students to be interviewed, or to provide materials and guidance for projects and experiments. Secondary and elementary school teachers are often pleased if researchers bring experiments into their classrooms or offer to guide field-trips for a day. Your child's teacher is a great place to start. You could also volunteer to give a presentation at a museum or a school's career day, or spend an afternoon with a scouting troop earning their geology badges."

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Bullying as a pervasive problem in science research

Frank Gannon, in his October editorial for EMBO Reports (9, 937; 2008) identifies bullying as a pervasive problem in academic research, which scientists seem to accept "without further comment or disapproval as though it were a normal part of life." From bullying of junior scientists (PhD students) or of peers, to defending accusations of dishonesty, Gannon provides a host of situations in which he believes this behaviour is rampant. He writes: "the reaction of some scientists when their grant application or submission is rejected can be downright disgraceful. If they know that they are dealing with more junior people, they will emphasize that they are the expert and that the decision should not rest with 'some ignorant editor' who is not a 'real scientist' anyway. They will ridicule the referees who critically analysed their work; they will persist, bully and coerce until they get beyond the initial rejection."...
..."I might be exaggerating the extent and seriousness of bullying in academic science, but its existence is undeniable. Science certainly needs a degree of competition and is genuinely driven by the incentive to be the first to discover; we are a competitive species after all. Nonetheless, we should consider the damage we inflict on one another and on research itself if we tolerate bullying. Academic science needs all types of characters; not only the dominant and aggressive ones, but also the pensive and quiet workers. More importantly, scientific research flourishes best in an environment characterized by mutual respect, tolerance and support, and where bullying has no place."

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The week on Nature Network: Friday 3 October

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Catherine Mavriplis of the US National Science Foundation is part of a group researching the situation of women in career breaks (voluntary or not), and which aims to provide resources for these highly trained scientists to re-enter research. She is looking for women to interview to gather data and trends that will serve for a larger survey later this year. If you would like to contribute your own experiences, please visit the Mind the Gap website, where there is more information about the project as well as contact details.

At the Nature Jobs careers forum, Paul Smaglik has been watching an NIH Powerpoint presentation (link in the forum post) which asks for “best practices for predoc and postdoc training.” Paul writes: "As far as I know (and according to the extramural NIH officials I interviewed for the policy piece) this has not yet formally happened. So, I am wondering what readers think should be “best practices”? Please share! Meanwhile, I will search PDA recommendations nationwide, and throw in my own 2 cents (tuppence, in England) about what SHOULD constitute best practices. Also, please let us know if universities with ‘best practices’ practice what they preach."

Nature has just published a special issue on the US elections (free to access until the election date). News Editor Alex Witze draws attention to the question asked by Nature's book review editor, Joanne Baker, to several leading thinkers to recommend the single science book the next president should read. Check out their suggestions here. What book would you recommend? Let us know at the Nature Network forum.

With Nobel prize season upon us (the first prize, in physiology or medicine, is announced on Monday), Anna Kushnir suggests that Nature Network and other science bloggers all write related posts. Topics she suggests inlclude choosing a scientist who you think deserves the award; predictions of winners; or descriptions of how the work of Nobel prize winners affected your own work and influenced you. If you'd like to participate, start today! Posts on the topic during the next week from today should be tagged "Nobel prize" for aggregation purposes. Simon Frantz , who runs the Nobelprize.org site, draws attention to the Nobel organization's Q&A each prize announcement, in which people can submit questions to each prize-awarding committee, and to newly awarded Nobel laureates. Anna is collecting questions from Nature Network users, who can then vote on which to submit to the committee after the award announcements are made. Please visit this forum link to submit your question(s).

Nature Network users discuss David Crotty's post ‘Digital intimacy’ at his blog Bench Marks, on topics such as reporting (blogging) at conferences and 'scooping' via internet posting. The post also discusses the benefits and disadvantages to scientists of online forums such as Nature Network and FriendFeed. From the discussion at Bench Marks, David comments "open networks should currently be viewed somewhat skeptically–do they represent the mainstream of science? Or are they instead skewed toward certain personality types, or people with their own agendas (such as personal promotion and/or promotion of a cause) and those with a fondness for new technologies?" Plenty to discuss.

Martin Fenner provides a very useful round-up post 'New ways to look at your presentation', including various tips and advice about using PowerPoint, and describing some newer ways to present your results. Well worth a read, and there are plenty of useful references in the post for those who want further details and interactive examples.
In a separate post, Martin interviews Alexander Griekspoor about Papers, a Mac-based solution to the problem of storing and organizing your PDF article collection. Alexander's description of what Papers does: it "provides a complete workflow for finding new articles using built-in search engines, browsing the publisher’s website using the built-in Safari web browser, downloading, archiving and renaming the PDF files, and organising and indexing these articles. Finally, it allows you to easily read the papers and share them with colleagues."

Previous Nature Network columns.

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UK physics gets a health check

In a Commentary exclusive to Nature (Nature 455, 592; 2 October 2008), Professor Bill Wakeham, Vice Chancellor of the University of Southampton, discusses the findings of his long-awaited review on the state of physics in the United Kingdom. The field is healthy, he says, but scientists need to reclaim the intellectual ownership of research at the margins of the discipline such as medical or atmospheric physics. Read the article free online for two weeks from today, and check out next week’s issue on 9 October for more news and audio. (Nature's website is here.)
There is a Nature Network forum for discussion of Wakeham's key messages that physicists will need to take ownership over their field and capture new funding streams. All are cordially invited to participate.
See also a related Nature news story by Geoff Brumfiel. (Nature 1 October 2008. doi:10.1038/news.2008.1145)


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Do longer papers gather more citations?

A longer paper gathers more citations : Nature News
From Nature 455, 274-275 (2008):
Researchers could garner more citations simply by making their papers longer, a study seems to imply (K. Z. Stanek, Preprint at http://arxiv.org/abs/0809.0692; 2008).
In an analysis of 30,027 peer-reviewed papers published between 2000 and 2004 in top astronomy journals, astronomer Krzysztof Stanek of Ohio State University in Columbus found that the median number of citations increases with the length of the paper — from just 6 for papers of 2–3 pages to about 50 for 50-page papers.
There is, however, a limit to the benefits of size: citations start to tail off when papers reach lengths of 80 pages or so, perhaps because fewer people have the stamina to read them.
It is unexpected, says astronomer Jörg Dietrich of the European Southern Observatory headquarters in Germany, who recently conducted a similar analysis and found the same results but didn't publish them. "I expected that shorter papers would be cited more than longer ones," he says. "I assumed that people don't have the time to read long papers."
Papers of about 4 pages — the length of Letters in Astrophysical Journal and Astronomy and Astrophysics, which report brief summaries of work that is usually published in more detail later — fare better than papers 5–10 pages long. But brevity offers no such benefit for papers in the other two journals considered, Astronomical Journal and Monthly Notices of the Royal Astronomical Society, which do not have Letters.

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European Commission survey on Internet resources for research

Via e-mail from Arnaud Berghmans of Deloitte Belgium on behalf of Augusto Burgueño of the Research Directorate-General of the European Commission:
Deloitte is conducting, on behalf of the European Commission, a survey on Internet-based services in support of the research process. So far, responses have been received from more than 3,500 EU researchers. As a benchmark, Deloitte would like to get the opinion of researchers already using the Internet for research and is asking readers of this website for their help by taking the survey.
About the survey
With this survey, the European Commission would like to find out which Internet-based resources (such as websites, wikis, social networks, mailing lists, bulleting boards, chat rooms, etc) the research community at large currently uses when carrying out research, and which ones it would be willing to use in the future.
The survey has six sections corresponding to the following phases of a research project: (1) Generate, elaborate and refine ideas; (2) Find partners; (3) Set up the research project; (4) Seek funding; (5) Run the research project; and (6) Exploit results. Each section has 3 questions.
The results of this survey will help the European Commission better understand what Internet-based services could in the future facilitate the participation of the research community in the European research and innovation programmes.
The questionnaire is anonymous and responses are aggregated for analysis. It takes ten minutes to complete.
Upon request, the survey results can be shared.
Link to the survey is here