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Category Archives: News and Updates
From PhD thesis to Protocol Exchange
In the last week, we have pushed nine new protocols live on the Protocol Exchange. They were all uploaded by Wei Zou and are based on work that he did towards a PhD in nutritional biochemistry1.
Conceptually, I think that extracting methods from the PhD thesis, converting to protocol format and publishing on-line is an excellent idea.
– The researcher is able to share the methods they have developed and optimised during the course of their PhD with a wider scientific community.
– If the appropriate references are prominently cited, this would likely increase traffic to related primary research articles.
There are added advantages of uploading them to a site like the Protocol Exchange, for example:
– The protocols would have a “home” that does not have to be maintained by the researcher or his/her institution (and would be “stationary” while the researchers may move from one laboratory to the next).
– The protocols are sorted by category and can be found using a search/browse faciltiy.
– Each protocol is indexed with CrossRef and assigned a DOI,and – in the case of Exchange Protocols – can found by searching via nature.com.
I acknowledge that there are some barriers to doing this. In the case of the Protocol Exchange, I think that the main ones are:
– Converting the text of the Procedure to the active tense (especially if the Procedure is quite long and/or is more discursive in nature).
– That it is not obvious how you would include in-text tables and figures (and equations) where these are necessary.
There are, however, some possibilities for making things easier:
You can, for example, upload a Word document or pdf so that the user can access a version including all (or parts) of the text so that it can be viewed or printed off with exactly the formatting that you would like2.
In conclusion:
I think that it would be great if more people uploaded the methods from their theses as Exchange Protocols!
I would be very interested in your views on this. You could share these by either filling in the fields in the survey, writing a comment below, or dropping an email.
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1 – Wei Zou is currently working at the California Department of Toxic Substances Control. The protocols mentioned above are based on work that he did towards a PhD in nutritional biochemistry (Carnitine and fatty acid metabolism, 2002) working with Sung Koo while both were at Kansas State University. These led to a primary article plus a patent. He then went on to do postdoctoral work on metabolomics under the supervision of Vladimir Tolstikov and group leader Professor Oliver Fiehn at UC Davis.
2 – In the case of Extraction of Fatty Acids for Capillary Gas Chromatography Analysis, the section describing the GC methods contained a lot of tabulated information, and it made most sense to upload this as a Word document and a link to this document was included in the Procedure section.
– Bull and co-workers went all the way, and uploaded each section of their protocol as individual pdfs, plus a pdf for the protocol in its entirety. Organotypic explant culture of adult rat retina for in vitro investigations of neurodegeneration, neuroprotection and cell transplantation.
Nature Protocols and Impact Factors
When we first launched "Nature Protocols ":https://www.nature.com/nprot I was keen to get our protocols indexed by all the big players. Whilst there was going to be a marketing campaign with ads in Nature and banner ads all over nature.com I knew we’d only get real users when people did their literature search and one of our protocols came top of the list. We wanted to be something researchers needed and found useful. However, alongside getting listed in the ISI Web of Knowledge came the news we’d also be eligible for an Impact Factor. It was clearly something scientists cared about. A lot of our early correspondence was about what our Impact Factor was. We had to be very apologetic and explain that we didn’t have one – first we’d need to publish some protocols, and then wait to see if they were cited. Personally I was relieved we didn’t have one because I wasn’t sure what an impact factor would mean for us, even if we did have one.
The Impact Factor comes into its own as a comparative factor. That’s why my colleagues upstairs at Nature are delighted with theirs, as at 36.101 it puts them ahead of their competitors. And also why journals with impact factors of 1 or 2 can also be delighted, as such an Impact Factor can be the highest in their specialist field. But when I looked into Impact Factors I realised that no protocols publications had them, so as a comparative factor, our impact factor would be rather meaningless. When and why would people cite protocols? We certainly wouldn’t be cited because we presented exciting new data and reported a major advance in scientific knowledge. I hoped that we’d be cited if we were used – and so lots of use would lead to a high impact factor. We’d obviously only get cited if the experiment worked, and so a higher impact factor would indicate good, reliable protocols. But, maybe we wouldn’t get cited, as citing the source of your protocol didn’t seem to be the ‘done thing’ at the time.
Five years down the line – with a 2 year ISI Impact Factor of 8.362 – I am pleased to report that we are being cited. We have an Immediacy Index of 1.547 and "Article Influence Score ":https://en.wikipedia.org/wiki/Article_influence_score of 3.799. We’re all rather pleased, as we know our Impact Factor matters to some of our authors. We’re also curious – which articles have people been citing? Are they the methods people have been using? Have they been getting good results? How do these articles correlate with the articles that are most downloaded from our site?
Our most highly cited article according to ISI is Locating proteins in the cell using TargetP, SignalP and related tools by Emanuelsson et al. This is different from the most highly cited article according to Scopus – "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources ":https://dx.doi.org/10.1038/nprot.2008.211 – by Huang et al., although this comes in at second place. At third we have "Analyzing real-time PCR data by the comparative C-T method ":https://dx.doi.org/10.1038/nprot.2008.73 by Schmittgen et al. And in fourth, "In-gel digestion for mass spectrometric characterization of proteins and proteomes ":https://dx.doi.org/10.1038/nprot.2006.468 by Shevchenko _et al. _and in fifth, Protein structure prediction on the Web: a case study using the Phyre server. Interestingly there are lots of bioinformatics protocols in this list.
Of course, our 2010 2 year Impact Factor is only based on articles published in 2008 and 2009, so only two of those protocols, those in second and third place, will have been included. And also, only the cites in 2010. I was – and remain – curious about our five year impact factor. Whilst methods are developing all the time, protocols do tend to have a long life. A tweak here and there (hopefully highlighted as a comment to the protocol), but we hope our more useful protocols will still be in use, and cited, 5 years on. I guess we’ll have to wait and see
Happy Birthday Nature Protocols – 5 today!
Five years ago today we launched Nature Protocols. It was the culmination of 6 months of hard work for the editorial team. Dot Clyde and myself had both started work at NPG at the start of January with a long list of things to sort out. First we had to decide on our scope, answering questions such as do physicists use protocols? Next we had to decide on a format. Although we had a rough guide from our colleagues on Nature Methods who had published some protocols, we had much more freedom. No page budgets and an online format. Dot had just left the lab, as had the rest of the editorial team we recruited (Bronwen, Alex, Andy, Baldo and Hannah), so there was much discussion of what scientists REALLY wanted to know about. Next there was peer reviewing – what would we ask the peer reviewers to do? Ideally we’d have liked them to repeat the procedure, but clearly that was not practical (although on occasion we have had peer reviewers do just that!) And then there was presentation – sorting out exactly how we would present all that information we gathered. Plus who was going to copy edit it all. Then of course, last, but most certainly not least, who would we invite to write? And would they agree to write for this new type of publication?
Thankfully many of the authors we approached were as enthusiastic about the concept of Nature Protocols as we were. We quickly received plenty of manuscripts to send out to peer review (helped by the fact that the protocols were already written and much tried-and-tested in our authors labs). Many of the peer reviewers we approached were pleased to help, and on 12th May we put our first example protocols on our web page. It was great to finally have some actual content, alongside the information about what we were doing.
Then on June 30th 2006 we published our first batch of content – a whopping 87 Nature Protocols protocols. Over the following months we published many more so by 29th December we’d published 322. By January 2008 we had over 1000 protocols on our site, including almost 800 Nature Protocols protocols.
In addition, we’d also worked on our system for researchers to post protocols-in-progress onto the site. Then called the Protocols Network, this launched with 14 protocols, all contributed by authors of recent papers published in other Nature publications. Today that system is bigger and better than ever before, and was recently relaunched as the Protocol Exchange, including lots of added featured we didn’t quite get round to including in 2006.
So, 5 years on, where is Nature Protocols now? The editors are all a little older (here we all are back in 2006):
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On the roof terrace in the summer of 2006. Back row, from left: Andy, Alex, Dot, Baldo. Front row, from left: Katharine, Hannah, Naomi (our first editorial assistant), Bronwen.
The feedback we’ve had from authors and users has been fantastic and largely positive, which is the best reward an editor can have. Our most cited article on Scopus – "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources by Huang, Sherman and Lempicki ":https://dx.doi.org/10.1038/nprot.2008.211 – published in December 2008 has been cited 847 times. We’ve published old favourites, such as the single step method of RNA isolation by acid guanidinium thiocyanate-phenol-choroform by Piotr Chomczynski & Nicoletta Sacchi and the latest protocols published in Nature, such as "Kazutoshi Takahashi, Keisuke Okita, Masato Nakagawa & Shinya Yamanakas’ protocol for the induction of pluripotent stem cells from fibroblast cultures ":https://dx.doi.org/10.1038/nprot.2007.418. We’ve followed dramatic progress in certain fields – for example, the new protocols available using next generation sequencing have revolutionised research progress. It’s now possible to rapidly sequence single cells, as demonstrated by Fuchou Tang, Catalin Barbacioru, Ellen Nordman, Bin Li, Nanlan Xu, Vladimir I Bashkirov, Kaiqin Lao & M Azim Surani who used RNA-Seq analysis to capture the transcriptome landscape of a single cell. We continue to enjoy following the progress of stem cell research, which, as well as making dramatic progress actually generating stem cells, has produced improved protocols for researchers in other areas, such as the ability to generate gene knockout rats, described by Chang Tong, Guanyi Huang, Charles Ashton, Ping Li & Qi-Long Ying.
And the future? Well, I’ve taken a step back now and so that’s a question for our current Chief Editor, Chris Surridge, but I am sure we will continue to concentrate on our core aim back from 2006 of “publishing the protocols being used to answer outstanding biological and biomedical science research questions, including methods grounded in physics and chemistry that have a practical application to the study of biological problems”. All that’s left for me to do now is give a final thanks to all who have contributed to the success of Nature Protocols so far and say, heres to the next 5 years!
Focusing on stem cells
Since Nature Protocols launched we’ve been having a shall-we-shan’t-we discussion about the relative merits of article series. On one hand they seem such a great idea – bringing together lots of protocols in a specific area to make life easier for researchers in that area. On the other hand we worry they’ll alienate researchers working on other things – why do the mass spectrometrists get special treatment and not us? And how do you decide what to include on such a page – anything vaguely connected or just the hard core of a particular topic? Then finally, as an Editor I just find myself wondering why I am making more work for myself…
But back in 2009 we took the plunge and launched our Stem Cell Series page. At the time stem cells were all the rage – if you watched the TV news at night you’d think all diseases were on the verge of being cured by these fantastic new cells. Unless you lived in the US, where they were not viewed so kindly by some.
Recently the page has slipped a bit in priorities – launching the Protocol Exchange was quite a job. But we feel it’s now time to revitalise it. Stem cells remain a hot research topic, and the optimism about their potential remains. Each week more and more possible applications are being devised. I’m pleased to see that our recently published stem cell protocols are reflecting this increased variety. Currently featured, in addition to our typical protocols showing how to get your stem cells initially, or how to go from stem cells to your cells of choice, there are some intriguing ways to look at your stem cells. Some of these methods can be applied to cells other than stem cells so do check it out even if your favourite cell is not a stem cell.
The juries still out on whether series pages are a useful addition to our site. So, if you’ve not checked for a while, or if you’ve not looked at all, we do suggest you take a peek. And do let us know what you think – should we run series or not? And if so, what topics should we cover?
The arrival of guidelines for reporting experiments
Are you conducting experiments using animals or developing protocols in this area of research? If so, you may be interested to take a look at the ARRIVE (Animal Research: Reporting In Vivo Experiments) guidelines when reporting your results and writing up those experimental procedures. These guidelines were published in June 2010 to improve the reporting of research using animals and can be found here. The guidelines themselves are presented in Table 2 of this paper, and consist of twenty items that can be used as a checklist for authors preparing a manuscript on this topic. Of course they are useful for peer-reviewers and journal editors too!
The ARRIVE guidelines provide recommendations about the content of all the standard sections of a manuscript, covering many points you would expect such as ethics statements and description of the experimental procedures and animals used. In addition, they suggest how to report the statistical analysis of results, as well as providing information about the study design, which is particularly relevant when writing up a protocol. To apply these guidelines to the preparation of a protocol for Nature Protocols, an Experimental Design section in the Introduction can be a good place to include further information on study design and the housing and husbandry of experimental animals, while the Procedure and Anticipated Results sections obviously allow detailed description of the methods used to obtain and analyse the results.
Although we do not publish primary research at Nature Protocols, but instead focus on tried-and-tested methods that have been previously published, we do find that these guidelines provide a useful resource and we encourage our authors to comply with the ARRIVE reporting guidelines when documenting protocols that involve animal studies.
An Exchange of Views
It’s the first of December so let’s open the first window of the protocols advent calendar. And behind it we find a very pleasant surprise. All shiny and new, a free and open web resource for the sharing of protocols across the scientific community. And the name of this wonder is:
I confess this isn’t so much of a surprise to those of us who have been working on the project for a year or more. It’s serendipitous that it is live today but we knew that it was coming. Strictly speaking it isn’t even a new idea either. Nature Protocols has been allowing authors to upload their protocols onto a section of the website called Protocols Network. However that site was a little low on functionality, so we now bring you a gleaming new site, explicitly for the exchange of methodological know-how.
Why is this important?
Science doesn’t progress by results alone. Essentially the same experiments are employed again and again by different researchers to explore similar but different questions. More than that no result in science can be trusted unless it can be reproduced, and for someone else to repeat an experiment they need to know exactly what was done. In research papers there are methods sections but they are often less detailed than one would wish. As helpful as a restaurant review when you are trying to cook a romantic meal. What you really need is a tried and tested recipe. Of course that is what Nature Protocols brings you but no journal can publish how every experiment is done in every lab in the world. Nature Protocols tries to bring you the gold standard procedures, peer reviewed and professionally presented. But there is a wealth of experimental know-how that is locked up in the personal manuals of laboratories only accessible to people working in those labs. In these hyper-connected times we must be able to do better; unlock that knowledge to make setting up new experiments easier and research as a whole more reproducible. That is where Protocol Exchange comes in.
There is a great deal to tell you about Protocol Exchange perhaps enough to take up all the windows on our advent calendar, or at least enough for a Twelve days of ProtEx-mas (other winter festivals are available). For now let’s start with the basics.
What can you find in Protocol Exchange?
Well protocols obviously. Researchers can upload their protocols to Protocol Exchange through a simple and intuitive series of pages. There are fields for introduction, materials, anticipated results, figures, tables, in fact most of the things that go into the Nature Protocols format. Most of them aren’t obligatory but if you do take the time to fill them in the result is a beautifully styled protocol, easy to read and navigate. Sharing a protocol on Protocol Exchange costs nothing. Reading a protocol costs nothing. Indeed all the protocols are presented under a Creative Commons Attribution-Noncommercial licence which allows for unrestricted copying and reuse of the protocol as long as the source if properly credited and the reuse is not for commercial purposes.
Connected to protocols are the research papers in which they are used. Protocol Exchange captures that information too. When sharing a protocol the authors can identify any research papers in which the protocol has been used or which is in some other way related to the protocol. All we need is the DOI of those papers and Protocol Exchange will create a page with citation and other information about the paper under which is a list of all the protocols that we have related to those papers. And of course a direct link to the research paper wherever it is published.
Three legged stools are the most stable and Protocol Exchange third leg is the people who create the protocols. Not individual authors so much as the Lab Groups in which the protocol was developed. Every protocol in Protocol Exchange has an associated Lab Group. Anybody can create a Lab Group and then invite other researchers to join. Or the Group can accept applications for membership. Or the Group can be set open so that anyone can join straight away. A little bit of social networking the reflect the way that scientists collaborate to invent and evolve ways of doing science.
We expect that Lab Groups will be used as the name suggests. A researcher will set up a group and invite all the other people in their lab. Then all the Protocols from that lab, whoever actually writes them, can be collected together. Lab Groups have their own personal page which lists all the Protocols from that group. A picture can be uploaded to be the logo of the Group, a link to the personal or departmental website can be added and other information about the Group if desired. All members of a Lab Group can see any of the Protocols being drafted by other members of the Group before they are officially shared, giving them the opportunity to offer constructive advice to their colleagues. There is much more to be said about Lab Groups as I think there are some subtle and powerful ways that they can be used, but that is for another day.
Come and have a look at Protocol Exchange. I really believe that this could be a major tool for scientists striving for reproducibility. As we have moved all the protocols from the old Protocols Network into Protocol Exchange there is already plenty to look at.
Best practice isn’t something that can be achieved in isolation, Nature Protocols and Protocol Exchange are where best practice can be spread around.
Next time: Two Turtle Doves!