Method of the Year 2008: cast your vote!

Posted on 03 Sep 2008 by Maxine Clarke

When the Nature Methods editors sat down last year to select a Method of the Year for 2007, it was with the firm intention of initiating a yearly tradition. This year, the editors are are asking for your opinion, so please nominate candidate methods as well as vote and comment on posted suggestions.

From the editorial in the September issue of Nature Methods (5, 749; 2008):

The Method of the Year event is a celebration of methods development and innovation because we think that methods developers should have their share of the limelight. It is also a fun opportunity to assemble Commentaries, technical information and news items about a method we consider particularly important among the developments that we, as editors, continuously observe across a broad range of disciplines. But we also wanted to take the pulse at the bench and see what you, with firsthand experience, think of recent methods developments. This online one-click voting and nomination process is your opportunity to speak up.

We are interested in methods that have come into their own in 2008 and have had a proven impact, but also in your views on burgeoning methods which, while they are not quite ready for prime time, are worth watching.

Nature Methods focus on single-molecule techniques

Posted on 10 Jun 2008 by Maxine Clarke

In its June 2008 issue, Nature Methods presents a free-access focus on single-molecule techniques. Biologists are becoming increasingly interested in methodologies that can examine the mechanism of action of fundamental biological processes at the molecular level. The Nature Methods focus consists of four review articles that provide practical guidance for some of the techniques that are most integral to in vitro single-molecule experiments. These cover single-molecule fluorescence methods; microfluidic flow cells to manipulate experimental conditions during experiments; and force-spectroscopy techniques such as atomic force microscopy (AFM) and optical traps to manipulate individual molecules themselves.

From the focus’s Editorial: The ability to analyse biological systems at the single-molecule level opens avenues of investigation that are not possible using techniques that measure aggregate properties of molecular populations. This new vantage point can yield important insights. A textbook example is that of molecular motors. Although classical biological assays for motor function show that these molecules support constant-velocity movement, studies of individual molecules revealed that they take discrete individual steps. The technique that allowed these crucial biological observations came from the physics field in 1986—a momentous year that saw the first demonstration not only of the optical tweezers technique used in the subsequent molecular motor study but also of the atomic force microscope. Created by physicists, these force-spectroscopy methods form much of the backbone of the field of research now devoted to studying biological systems at the single-molecule level."

Please read on at the Nature Methods focus website. Comments from readers are welcome at Methagora, the Nature Methods blog.

Nature Biotechnology presents a bioentrepreneur round-table

Posted on 22 Apr 2008 by Maxine Clarke

Venture capital is a key part of growing a start-up company, but can be fraught with problems. Nature Biotechnology is gathering together a group of seasoned chief executives, venture capitalists and a venture lawyer at a one-day event ‘Bioentrepreneur beware: CEO war stories on investor nightmares’, to discuss what can go wrong during the financing process, including term-sheet negotiations that seriously dilute equity, rounds that fall through at the last second, investor activism and hostile takeover of board seats. Take the opportunity to participate in a lively panel discussion that will explore key issues when borrowing other people’s money and ways that you can ensure investor and management goals are compatible with your biotechnology business. The meeting will take place on 20 May 2008 at The Meritage Resort, Napa, California, and is free to attend. The speakers and programme, and more details, can be found here. For information and to register, please send full company name and contact details by email.

New features for Nature Precedings authors and readers

Posted on 12 Mar 2008 by Maxine Clarke

Via Hilary Spencer, Nature Precedings has just introduced some new features.

Comment notifications: authors can opt to receive notification when new comments are added to their Nature Precedings document by checking a box during the submission process. Commenters can also opt to receive notification of when someone responds to their comment.

Watermarks on PDFs: the DOI (or Handle) and date of posting are now embedded in all PDFs on Nature Precedings. By embedding the identifier in the document, readers can correctly reference or cite the document, even when they have received the document via email or accessed it via a “deep-link”.

Document thumbnails serve as a memory aid and preview; they can also be embedded in blogs and webpages.

Please join the Nature Precedings group on Nature Network to receive updates and make suggestions about the site, as well as to join the conversations between Hilary, Timo Hannay and Nature Precedings users and authors.

Production tracking system for Nature journals

Posted on 18 Feb 2008 by Maxine Clarke

Nature has introduced a web-based production tracking system for research manuscripts that have been accepted for publication, which we hope will bring many benefits for authors. In the first phase at Nature, authors are able to access a website to download the journal’s edited version of the text of their accepted manuscript, so they can make their corrections and upload the revised version back into the system. Very soon afterwards, the typeset PDF, laid out and complete with figures and/or tables, can also be uploaded and checked by the authors.

According to a survey of authors who have been testing the system in the past few weeks, a substantial majority strongly agreed that the new process is easy to operate and, for those who had published in Nature before, 100 per cent found the new system easier. One author wrote: “If it will always remain this efficient and user friendly, it is an easy, professional way of taking a manuscript through the production process.” Another said: “I found the responses by the Nature staff to email queries were very impressive, being both very rapid and very helpful.”

The system is being further developed, already being in use in several of the Nature monthly journals. We will keep authors informed as we introduce new components.

Targeting lipid signalling in disease

Posted on 07 Feb 2008 by Maxine Clarke

A free poster, by Matthias P. Wymann, Thomas Rückle, Christian Rommel, Matthias Schwarz and Roger Schneiterfrom, is published this month (February) by Nature Reviews Molecular Cell Biology . The poster provides an overview of the protein—lipid signalling network, and how this network can be exploited pharmacologically in the study of proliferative, inflammatory and metabolic diseases. It accompanies a review article by Matthias P. Wymann and Roger Schneiter in Nature Reviews Molecular and Cell Biology (9, 162-176; 2008), which also contains a Web Focus on Lipids.

View the poster as a high-resolution PDF.

Nature Physics seeks views on online communication tools

Posted on 06 Feb 2008 by Maxine Clarke

The Nature Physics editors (Nature Physics 4, 81; 2008) want to hear from physicists what kind of tools would help in managing the ever-growing tide of information from, and the exciting possibilities of, the internet. One hundred years ago, communication was relatively slow, and scientists attended conferences to find out what was going on outside their own place of work; now, we live in an environment in which there is an over-abundance of data-rich information that is a challenge to assimilate. What tools do scientists most need to communicate, share and organize information in the most meaningful, or “filtered”, way? Nature Publishing Group has already created several such tools, for example Connotea, a reference management system, and Nature Network, a social website for various kinds of specialist discussion forums. The editors would like to hear from readers about the tools they would like to see developed. Please send them an email if you have suggestions you’d like to make, or drop a comment to this post.

Nature Physics February 2008 Editorial: A tangled web we weave.

What’s in a Jane?

Posted on 31 Jan 2008 by Maxine Clarke

Martijn J. Schuemie and Jan A. Kors (Bioinformatics doi:10.1093/bioinformatics/btn006 ) have created a freely available web-based application that, on the basis of a sample text, can suggest “journals and experts who have published similar articles”. Their aim is to help scientists to determine which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work. The application is called Jane (for journal/author name estimator).

I inputted some sample text to Jane, and was told that the Saudi Medical Journal was my top choice. No disrespect to that journal, but I know (because I am a person and not a computer) that this journal would be inappropriate for my test sample in at least two ways.

I would not primarily recommend an automatic selector to authors trying to decide where to submit their articles. When someone is ready to submit a paper, she or he will have given talks about the work and circulated drafts for comments from others in the field. That is a good time to ask for suggestions and advice about journals in which to publish. The scientist is then well-advised to read the author guidance on a few journals’ websites, to find out about editorial scope, impact factor and so on.

I think it is possibly counter-productive to use this kind of text-based comparison system on its own for making decisions about journal submission. At Nature, for example, we are looking for novel results, not something similar to what we have just published. Other journals are the same – most of them are looking for distinctive articles, not incremental repeats.

Rather than relying on computer searches to choose where to submit, I highly recommend looking at our free Author and Reviewers’ website for writing and submission advice. From there one can go straight to a great set of articles written by professional journal editors about how, where and why to submit and publish at the free science-information website SciDev.Net.

In addition, scientists can upload a draft manuscript into a community preprint server, where others in the field can comment and suggest. (Nature Precedings is one such, which provides meta-features such as alerting people in the field when new preprints have been uploaded, but many others. ArXiv is another, for the physical sciences.)

I think it will be a sad day when science journals publish “articles selected for us by computer”.

(I first read about Jane at Nature Network in a post by Graham Steel.)

Ask the Nature editor about all kinds of subjects

Posted on 30 Jan 2008 by Maxine Clarke

One of the longest, and longest-lasting, Nature Network discussions in which I have participated is called “”https://network.nature.com/forums/askthenatureeditor/595?“>High Impact made by famous ones”, started in October 2007 by a graduate student known as “”https://network.nature.com/profile/irna">Universal research" as part of the “”https://network.nature.com/group/askthenatureeditor">Ask the Nature editor" forum.

The forum, incidentally, is hosted by the editors of Nature Network, and is for scientists who want to learn more about getting their work published in Nature and the Nature journals, and about careers in scientific editing, straight from the editors of these journals. You are welcome to join the group and post your questions.

Returning to the discussion thread about those “famous ones”. The Nature and Nature journal editors who regularly handle manuscript submissions provide their answers to a wide range of questions, including whether being well-known or having a stellar track-record is more likely to get your mansucript sent for peer-review or published (answer: no); blinding of the peer-review process (double-blinding gets an airing, but Nature journal editors explain why they feel the system of single-blinding is best for scientists); duplicate publication (or “salami slicing” as it is often known); and independence of editors from those whose work is being considered.

This thread may not be the longest or the oldest that I have ever seen, but it is certainly among the most focused and useful for authors, and I highly recommend you read it for a unique insight into the editors’ thought-processes. If you are at the start of your publishing career as a scientist, you are likely to find this forum very helpful. We welcome you there.

NSMB tribute to Arthur Kornberg

Posted on 14 Jan 2008 by Maxine Clarke

“Arthur Kornberg was one of the greatest biochemists of the twentieth century. His career spanned more than 60 years, and such has been the impact of his work on modern biomedical science that his influence will endure for decades.” So opens Nature‘s obituary of Arthur Kornberg, by Tania Baker, at Nature 450, 809; 2007.

Boyana Konforti, Chief Editor of Nature Structural and Molecular Biology, has asked close colleagues to contribute their thoughts and recollections about Kornberg, who died last October. These reminiscences have now been compiled and published together, along with photos, as a permanent record and tribute in the pages of Nature Structural & Molecular Biology. Boyana writes: "In writing these remembrances of Arthur, we have all tried to capture a bit of what he was like, and what working with him meant to us, in the hope that those who knew him will have even richer memories to share and—more importantly—those who didn’t know him will get a glimpse of him through our memories. To my mind it is these personal stories (and many more like them) that will be his longest-lasting legacy". The tributes can be seen here: A Tribute to Arthur Kornberg 1918-2007 (Nature Structural & Molecular Biology 15, 2 – 17; 2008). Contributors are Robert S. Fuller, Robert A. Bambara, Tania Baker, Barbara Funnell, Elmar Wahle, Michael O’Donnell, Dale Kaiser, Kirsten Skarstad, Boyana Konforti, Satoko Maki, Tsutomu Katayama, Kazuhisa Sekimizu, Joel H. Weiner, Ronald W. Davis, Lee Rowen, Myron F. Goodman, James Spudich, Suzanne Pfeffer, Charles C. Richardson, Piotr Polaczek, RIch Calendar, Richard Kolodner, Jack Griffith, Bruce Stillman, Paul Modrich, Charles Brenner and Charley Yanofsky.

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