Introducing a new article type – the Protocol Update

Posted on 08 Nov 2012 by Katharine Barnes

Nature Protocols is coming to the end of its 7^th volume, and after publishing only one type of article for the past seven years, this month sees the introduction of a brand new article type: the Protocol Update.

At first glance our first Protocol Update¹ follows the same basic format as the hundreds of Protocols we’ve published so far. However it is an acknowledgement that over time protocols are improved upon. The major differences between Protocol Updates and Protocols are:

Protocol Updates have headers to say it is an update
Protocol Updates are always at the start of the issue
Protocol Updates contain a statement at the start to make it clear it is an update of a protocol we published previously (back in 2006² in this first example).
Protocol Updates include a discussion of how this new version compares to the original, explaining the rationale for the improvements as well as making it clear which parts remain the same.

You may be wondering why we have introduced this new article type. Whilst we have the functionality for authors and readers to comment on protocols, these comments are not peer reviewed and their presence at the end of a protocol means they can be missed by readers of the protocol. For the particular protocol we have updated, the authors, referees and editors agreed that there were sufficient improvements to the procedure presented back in 2006 to justify publishing a new version. The area covered – quality assurance for polychromatic flow cytometry – is basic but important to get right. It is needed to support a diverse range of methods with many biological applications, and this importance has driven various improvements. We decided we should acknowledge this and provide an updated protocol for its many users. However as it is not a new protocol – the authors are the same, the applications the same, and even some of the text – we are not labelling it as a new protocol. So you will see, if you compare the articles, that where there is new information, this is included, however where there is no change, but the information remains important for users of the protocol, it has been retained.

Given our large scope, and the many innovative new methods being developed, we don’t anticipate publishing many Protocol Update articles each year. There is just too much exciting research going on and it is important to focus on covering these new protocols, plus those we have still not managed to cover in the past seven years. The choice available to editors when commissioning new protocols can be overwhelming so we aim to continue to focus on commissioning topics we have not covered previously rather than revisiting what we have already published. However, we felt we needed the option, occasionally, to update an area we’ve covered before.

If you have any comments and suggestions we are, as always, keen for feedback.

¹Perfetto, S.P., Ambrozak, D., Nguyen, R., Chattopadhyay, P.K. and Roederer, M. Quality assurance for polychromatic flow cytometry using a suite of calibration beads. Nat. Protoc. 7 2067–2079 (2012)

² Perfetto, S.P., Ambrozak, D., Nguyen, R., Chattopadhyay, P. and Roederer, M. Quality assurance for polychromatic flow cytometry. Nat. Protoc. 1 1522-1530 (2006)

Antibodypedia on Facebook

Posted on 10 Sep 2012 by Christopher Surridge

Those readers who are avid, or even obsessive, followers of Nature’s various blogs will know that NPG is collaborating with a website called Antibodypedia since December of 2011. Well, last week we passed a significant milestone with the listing of its half-millionth antibody. And this week we are launching a Facebook page.

Antibodypedia attempts to pull together information about the performance of publicly available antibodies so that researchers can make informed decisions about which will work best in their experiments before they buy them. The data we aggregate are things like links to research papers in which the antibodies have been used, technical data from the antibody suppliers, and the results of experiments performed by independent scientists.

Antibodypedia is a great resource as it is, but the aggregation and presentation of information already available, albeit in diverse places, is only half of the story. We want it to also be a place where researchers can share their experiences with specific antibodies and discuss the problems that arise with immuno-based cell biology techniques.

We already have a mechanism in place for researchers to submit experiments showing the performance of antibodies, and an advisory board to help us peer-review those experiments to ensure their usefulness; it is a form of micro-publication. Now we are taking a further step in engaging with the research community with our Facebook page.

Why Facebook?

Well, it would have been perfectly possible to incorporate a message board, discussion forums and the other functionalities of a community site into Antibodypedia but the plain fact is the vast majority of researchers are already members of a global social networking site, so why ask them to join another one? Instead we are making things easy and carving out a small corner of Facebook for all things antibody(pedia). We will of course be posting a lot ourselves on the page—news, highlighting of research papers, running polls etc.— but we also hope that antibody-using researchers will start their own discussions, share their experiences and try to solve each other’s problems.

The page launches today so please come, take a look and ‘like’ us. Then come back regularly over the next few weeks to follow our posts, take part in the polls and, of course, leave a comment or two.

Protocols relating to the Structure and Composition of Plant Cell Walls

Posted on 24 Aug 2012 by Bronwen Dekker

People have already exploited the physical properties of plant cell walls in, for example, the production of paper, textiles and building materials. In the future it may be possible to engineer plants to produce other environmentally friendly / biocompatible materials with different performance characteristics.

In addition, plant cell walls are potentially a very large source of carbohydrates for biofuels, and methods to better understand the ultrastructural and chemical barriers to their digestibility, as well as to monitor responses to different experimental treatments, would be very valuable in this research.

Over the past month, we have published five protocols that relate to plant cell walls: their structure and composition, and the biochemistry underlying their development. I have created a webpage where these, and any future protocols that we might publish on this subject, can be collated.

Protocols relating to Plant Cell Walls

In a sense this series on plant cell walls is a return home. The department in which I did the Cell Biology part of my undergraduate degree was very much focussed on plant biology, and TEM of recalcitrant seeds was part of the course. There was, therefore, a time when the walls of my room were littered with little printouts showing images of cells walls and sections of endoplasmic reticulum that had patterns that somehow pleased me. I had a hand-wavey “understanding” of how cell walls formed, and some sort of feeling for the fact that this was not a trivial process.

Admittedly all of this was rather a long time ago, and I suppose is only interesting if you happen to think of me solely as a chemistry-type!

It does, however, give me the small amount of credibility to enable me to say that almost everything that I learnt at University in this subject area is now out of date. In fact, it is almost completely pointless for me to mentally refer back to my undergraduate biology courses as a source of information or inspiration. This is not really because the information that that I was taught was wrong, but that the mental conclusions I made were based on an incomplete picture. This can be exemplified by the fact that there were two things about the title of the following article by Nottburger Gierlinger and Manfred Schwanninger –

Chemical Imaging of Poplar Wood Cell Walls by Confocal Raman Microscopy

– that somehow surprised me:

– There is something about the chemistry of plant cell walls that people are finding very interesting
– Raman spectroscopy has made the transition to being a microscopy technique

If people are looking at plant cell walls using confocal Raman microscopy (which is surely on the super-cool end of the techniques spectrum), they must be looking at it using other more familiar techniques as well.

Further investigation convinced me it would be a good idea to commission a collection of protocols covering a variety of approaches that can be taken to gain a better understanding of plant cells walls. I got in touch in Professor Geoffrey Fincher, and I am very grateful for his help in shepherding the preparation of four additional protocols. I would also very much like to thank the authors for all their hard work and patience; I am very pleased with these protocols and hope that they will be interesting and useful to other researchers.

These are the five protocols that resulted from this process:

Whole Plant Cell Wall Characterization using Solution-state 2D-NMR
Shawn D. Mansfield, Hoon Kim, Fachuang Lu, and John Ralph
https://www.nature.com/nprot/journal/v7/n9/full/nprot.2012.064.html

Determining the polysaccharide composition of plant cell walls
Filomena A Pettolino, Cherie Walsh, Geoffrey B Fincher & Antony Bacic
https://www.nature.com/nprot/journal/v7/n9/full/nprot.2012.081.html

Radiometric and spectrophotometric in vitro assays of glycosyltransferases involved in plant cell wall carbohydrate biosynthesis
Christian Brown, Felicia Leijon & Vincent Bulone
https://www.nature.com/nprot/journal/v7/n9/full/nprot.2012.089.html

Preparation of plant cells for transmission electron microscopy to optimize immunogold labeling of carbohydrate and protein epitopes
Sarah M Wilson & Antony Bacic
https://www.nature.com/nprot/journal/v7/n9/full/nprot.2012.096.html

Imaging of plant cell walls by confocal Raman microscopy
Notburga Gierlinger, Tobias Keplinger & Michael Harrington
https://www.nature.com/nprot/journal/v7/n9/full/nprot.2012.092.html

The Season of the Impact Factor

Posted on 29 Jun 2012 by Christopher Surridge

It is that time of year again! A bit like Christmas, now is the time when journal editors wait expectantly to open their presents; or in this case present singular. I’m talking about the annual release of Impact Factors from ISI. I’m not going to go through all the reasons why Impact Factors may not be the best way to judge scientific research. Katharine made some comments about that last year and I haven’t changed my opinion much since I railed against their tyranny at another journal. But Impact Factors and the other citation metrics probably say something about a journal so I thought I’d give you the numbers for Nature Protocols and say what I’m taking from them.

My favourite cover image from 2011.

So the 2011 Impact Factor for Nature Protocols is 9.924 which I’m really happy about. It would be a presentable number for a journal publishing primary research, and we don’t publish primary research. I would expect protocols to be formally cited less often. Also it is up 1.562 points from the 2010 value so Nature Protocols is probably being cited more than 12 months ago and hopefully that is an indication that our articles are being used more than 12 months ago. If our articles are being used more than they were then that’s good news.

Impact Factors are quite good for making comparisons between similar journals, but sadly none of the other main publishers of protocols is indexed by ISI and so don’t get given Impact Factors. I analysed the citation of those journals a few months ago and I’ll let you draw your own conclusions about what thier IF might be if they were given one. What ISI does do is put Nature Protocols in a group of journals publishing “Biochemical Research Methods”. Our colleagues at Nature Methods top that list with an IF of 19.276. However it is a bit like comparing chalk and cheese as other journals in this group are things like Acta Crystallographica Section D: Biological Crystallography (IF 12.619), Current Opinion in Biotechnology (IF 7.711) and even PLoS Computational Biology (IF 5.215). Still in the group we rank third, up from fourth last year, so again pleasing.

The numbers that please me are those that suggest that Nature Protocols articles have some longevity. If you calculate IF over 5 years instead of 2 it rises to 10.201 suggesting that Protocols are relevant well beyond their initial publication. Many journals, possibly even most (I’m eyeballing rather than having done a proper analysis) have a lower 5-year IF than their standard 2-year IF.

For a slightly more sophisticated measure there is the Eigen Factor score. This is calculated in a similar way to Google’s page rank algorithm in that not all links are of equal value and self citations aren’t counted at all. For 2011 ours is 0.10716. I’m not completely clear how to interpret that but it is more than for 2010 so that must be good!

Last up the Article Influence Score. This is derived from the Eigen Factor and then normalised for the size of the journal so that the ‘average’ journal will have an Influence of 1.000. Ours for 2011 is 4.422 which is again more than it was last year and shows, to misquote the immortal Yogi, that we are “smarter than the average journal (Boo-Boo)”.

So it’s all good (for as much as Impact Factors and similar measures can tell you anything about a journal). But at Nature Protocols we don’t really care about the value of our IF. In the next 12 months we will try to commission and publish even better protocols so that more scientists will be helped in their research. If someone can quantify that then I’d like to hear about it.

Bidirectional linking between Nature articles and Exchange Protocols

Posted on 20 May 2012 by Bronwen Dekker

Last week, the Kipnis Lab, University of Virginia uploaded two Exchange Protocols associated with their recent Nature paper.

FACS of acutely isolated mouse microglia

Assay of phagocytic function in primary murine microglia

While I am always pretty excited when people submit new protocols to the Protocol Exchange, the very latest protocols were especially pleasing for two important reasons:

(1) The authors had made special effort with their labgroup page including a photograph of their research team as the logo, and a list of key primary papers that they had published.

(2) It was the first time that we noticed that there were links from the Nature paper to the two Exchange Protocols!

If you go to the paper (Wild-type microglia arrest pathology in a mouse model of Rett syndrome), navigate to the Methods sections, and scroll down you will – as if by magic – see the two titles!

We quickly checked through other recent Exchange Protocols, and found that the links had been added retrospectively for some other Nature articles. Hopefully we will see links from other NPG titles very soon!

PS: You will probably have noticed that Exchange Protocols contain links to the relevant primary papers where they have been used.

The first few months of Antibodypedia

Posted on 17 Apr 2012 by Christopher Surridge

This is a guest blog post from Victoria Newman, the Antibodypedia curator.

Late last December I wrote a blog post for Stepwise announcing the launch of the new NPG resource Antibodypedia | nature (www.antibodypedia.com), an open-access platform to search for antibody data and commentary. I’ll talk more about what we’re trying to do below; however, as a quick status update, since our launch we’ve been steadily adding antibodies and making improvements here and there and have had lots of positive feedback from users. Most impressively, since the New Year we’ve been accessed from 136 countries, with repeat visitors from 113 countries in the last four weeks. Yay for open-access! But we know there is always room for change and we value your comments. Send us your feedback or, if you’re planning on attending the FASEB Experimental Biology (ASBMB) meeting next week in San Diego, stop by the NPG booth and let me know what you think in person: I’ll be there from 12-3 on the afternoon of Monday the 23^rd.

So what does Antibodypedia do? We think of it as a microjournal, publishing bite-sized bits of data rather than full-length manuscripts. The data are specific to assays involving antibodies, since we believe that there’s huge scope for improvement with regard to their annotation—the process of buying them can be intensely chaotic, sometimes with very little information available to suggest that one reagent works better than another in the experiment you’re trying to plan. Our aim is to provide data from the antibody user community (including published references citing reagents) and antibody vendors or distributors to give users as well-rounded as possible a grasp of how a product works for different techniques. Because we feel strongly that your data (the control experiments in your lab notebook that may make it into supplementary data or may never see the light of day again) are the best way to convince other users that reagents do or don’t work, we’ve arranged to assign a DOI to each data submission so they can be cited onward. They don’t have to look lovely, especially if you think they’re evidence that something isn’t working, but we feel that they should be made public to help you troubleshoot your blank western blot. So send us your data—help users to answer the eternal question ‘Did I forget to induce my cultures again?’.

Advanced Search

Because we want to provide researchers with the capacity to identify antibodies proven to work in specific techniques, Antibodypedia is structured slightly differently from many of the antibody search engines you might find out there: its organization is gene-centric, so each antibody directed against a single protein target can be retrieved by a search for that antigen. ‘Advanced search’ lets you find antibodies that are recommended or validated for one or more types of experiment, sold by a particular provider, and linked to reference citations, among other things. The ‘Advanced search’ menu is always undergoing development, so please let us know if it’s missing something you’d find useful.

After you’ve defined and run your search, your results will be displayed as a table, with each row representing a single antibody.

Search Results

Clicking on a reagent will take you to antibody pages, which host or link to both user- and provider-sourced data as well as protocols and published references using those reagents.

Antibody Details

You can also choose some of the antibodies retrieved by your search for side-by-side comparison to decide more easily which one(s) you’d like to test. Our antibody pages link directly out to vendor pages as well so you can find pricing and ordering information.

We think Antibodypedia will simplify selecting an antibody for a particular experiment by making quality control data both accessible to bench scientists and easy to interpret. But in order to maximize our utility, we need your help. Tell us which antibody providers you’d like to see listed in Antibodypedia so we can contact them and which techniques you use that aren’t currently searchable so we can start gathering data for them. And most importantly: submit to us so that we can populate antibody entries with your results! Remember that we’re not asking for publication-quality images, just something that can be interpreted as positive or negative proof that something’s working along with some notes on how you set up your experiment. Help us create an efficient means to search for good antibodies so you and your colleagues can plan your assays with less waste of time and money.

Blowing our own trumpet

Posted on 28 Mar 2012 by Christopher Surridge

As the sharp eyed among you might have noticed, Nature Protocols is running an ad campaign at the moment. If you haven’t here is one of our banners:

With this campaign we are offering anyone the opportunity of a month’s access to Nature Protocols. There are no catches other than that we want to know who you are, that we will send you an email after your month is up (which you can cheerfully ignore if you wish) to ask what you thought of the journal and prompting you to recommend us to your institution’s library, and that you will need to create an account for yourself on nature.com (which is also free). For that you can spend a month happily exploring the entire archive of Nature Protocols content.

Anyway, in the ads we are making a very specific claim: that nature Protocols is the most referenced source for protocols. A bold claim which I think I should justify here.

Normally when journals want to talk about their citations they turn to the Impact Factors calculated by ISI. That’s fine in the main, if you treat that number with some caution and only use it to compare very similar journals covering similar topics. Nature Protocols had an IF of 8.4 for 2010 (the most recent number) which we are very happy with although we hope that the number for 2011 (released in June 2012) will be a little higher.

However, laboratory protocols are useful long past the two year window from the year of publication that IFs consider. We could look at a 5-year impact factor (also 8.4 although higher if you believe in accuracy to more decimal places, which I don’t) which would be better, but the fact is that ISI don’t index or calculate IFs for the other publishers of research protocols: Current Protocols, Cold Spring Harbor Protocols, or Springer’s Methods In … series; and those are the people we would like to compare ourselves against.

So I had to do the calculating myself using the Scopus database of citations maintained by Elsevier. Using that I looked at all the papers published by Nature Protocols and our big three rivals from 2006, when Nature Protocols launched, to the present (well January this year when I did the number crunching anyway). I looked at every citation to any paper classified as ‘Article’ or ‘Review’. I also restricted the “Methods In …” series to research in the biological and biomedical subject areas. These are the data I got:

Published since 2006	Nature Protocols	Current Protocols	Cold Spring Harbor	Methods in …
Total Number	1,474	1,859	1,090	1,0791
Total Cited	1,351	793	742	5,672
Total Citations	34,586	2,687	2,154	23,246
Average Citation Per Article	23.46	1.45	1.98	2.15
Average Citation per Cited Article	25.60	3.39	2.90	4.10
Highest citation	1,311	71	14	309
No in top 100 cited	91	1	0	8

As you can imagine that is very pleasing. Even if you mistrust simple means for a distribution that is far from Normal, Nature Protocols as a whole has been cited more than any of our competitors, and that despite publishing a much lesser number of Protocols than “Methods in…”. (I would say we are more selective but I feel I’m already crowing too much). And this isn’t due to one or two exceptionally highly cited protocols. It is true that one protocol* has been cited over 1300 times—1,533 times as of today—but of the 100 best cited protocols in this period from these sources 91 of them were published in Nature Protocols.

So there is the justification. Nature Protocols protocols are cited more often, and so presumably used more often, than any others.

—

* Da Wei Huang, Brad T Sherman & Richard A Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44-57 (2009) doi:10.1038/nprot.2008.211

Antibodypedia is up and running!

Posted on 23 Dec 2011 by Christopher Surridge

This is a guest post from Victoria Newman

Hello, I’m Victoria.

I’m the curator of Antibodypedia, an open-access database of antibody validation data and user commentary initially founded as part of the Human Antibody Initiative/Human Protein Atlas. In addition to running Nature Protocols, Chris is in charge of the collaboration that has started between Nature Publishing Group and Antibodypedia which is my excuse for posting on this blog. I was hired as curator last June and am psyched to say that we finally launched the new Antibodypedia site on December 4 at the ASCB’s annual meeting.

The problem facing anyone who uses antibodies in their research is that for any given target there are a lot of antibodies available so how can you tell which one will work for you. What is needed is somewhere researchers can go which has a comprehensive list of antibodies available with information about how they perform in the various applications for which antibodies are employed. That is exactly what Antibodypedia is attempting to create.

There are quite a few antibody comparison forums out there if you search the web, so what makes Antibodypedia special?

First, we’re gene-centric: search for any antigen (human now, but expanding into other model systems in 2012) and you’ll pull up a whole list of antibodies directed against that target. You can sort and refine the results in a number of ways: by the antibody’s host, the types of experiments in which it’ll work, or whether or not it’s been used in research publications, among other things.

Secondly, you can submit your own data to us (with experimental protocols, please). We are of course making available the data that the providers of antibodies have but I’m sure you will agree that the most valuable information is that from researchers doing the same kind of experiments as yourselves. We hope this will do a number of things: showing whether and how to use a particular antibody for a specific experiment; helping decide the working concentration or dilution that are appropriate for an assay; identifying whether the antibody works as described by the vendor or in more (or fewer) assays.

This is all valuable information and yet all too often the data about the performance of antibodies languishes in researchers notebooks. The control experiments that had to be done before the ‘real’ experiments, those that will see publication in a research paper, could be started. Rather than forcing scientists in different labs to pointlessly duplicate these experiments we would like to see them made available to everyone, and see the researchers getting some credit for their experimentation. We are looking at these data as a ‘micro-publication’ and will be giving them DOIs to make them easily citable.

We want to encourage best practice for different experimental categories, so we’ve put together submission guidelines with suggested controls that will make your blank western blot immediately interpretable by everyone.

One more thing—you can also find additional resources, including links to useful sites and online tools, at Antibodypedia, and we’ve assembled a list of hundreds of Nature Protocols and Protocol Exchange protocols using antibody based techniques.

Stop by www.antibodypedia.com to browse, search or submit data. And tell us what you think either by commenting here or emailing contact@antibodypedia.com.

Episode IV – A New Hope

Posted on 21 Dec 2011 by Christopher Surridge

Let’s start with a welcome: Welcome to Stepwise.

I know that Nature Protocols has had a blog for quite a while now but over the last few months we have let things slide a bit, chiefly because we knew the change in our blogging platform would give us an opportunity to do more things. Also we had the chance to give it a proper name; “Nature Protocols Blog” being no-one’s favourite.

The no-one’s in question-in other words the authors of this blog-are: Chris Surridge (that’s me), Katharine Barnes, Dot Clyde, Hannah Clarke and Bronwen Dekker. Collectively the editors of Nature Protocols and the guardians of the Protocol Exchange. We tend to blog about different things and hopefully you will pick up on our various interests with time. The thing to bear in mind is that Katharine, Dot, Hannah and Bronwen know stuff, while I just pontificate.

Why Stepwise?

The very first blog post for the Nature Protocols blog was in May 2010, and asked the very important question: “What should we call our blog?”. While we all agreed that out blog should have an outstanding name, we were not able to get terribly much further than “Nature Protocols Blog” until Dot looked up from her computer in a commissioning meeting and said: Stepwise! Well protocols are made up from procedural steps and we try very hard to be wise about them. I hope that isn’t too much of a cryptic crossword clue justification.

What we will do here is continue to share news, helpful hints on how to use our nature Protocols and Protocol Exchange, comments about our protocols, or give updates from conferences.
These are handily organised into the following categories:

We might blog about things that just catch our eyes as well.If you are new in these parts here are some example posts that highlight what we are all about:

We try to maintain an active twitter account for news about published protocols, and other things we happen to find interesting.
Follow us at: @NatureProtocolsIf you would like to contact us you can also email: protocols@nature.comOr just comment ion this blog. We’ll do our best to answer your questions. What do you want to know?

Highlights from the Protocol Exchange

Posted on 07 Oct 2011 by Bronwen Dekker

Yesterday we published a really nice Exchange Protocol entitled A highly-sensitive and rapid Surface Plasmon Resonance immunoassay procedure based on the covalent-orientated immobilization of antibodies. It is a variation on a recent Nature Protocol (Multisubstrate-compatible ELISA procedures for rapid and high-sensitivity immunoassays), where detection is via SPR rather than ELISA. And it is pleasing to me that we were able to accomodate both methods by using both Nature Protocols and the Protocol Exchange.

The Protocol Exchange is an open-access resource where scientists can share their protocols, and browse those that others have added. Exchange Protocols are accessed from a Browse page (which also includes entries from Nature Protocols), and can be either Community or Supplier Contributed.

A full list of Community Contributed protocols

A full list of Supplier Contributed protocols

My five favourite Exchange Protocols

Protocols on the Protocol Exchange are not peer-reviewed or edited, therefore the protocols highlighted are ones that are nice examples of using our format (i.e. ones that I happen to somehow please me!). If there are ones that you think should be included on this Top-Five list, then please let us know which are your favourites!

♫ Neural Stem Cell Culture: Neurosphere generation, microscopical analysis and cryopreservation

♫ Seeing is believing: in vivo functional real-time imaging of transplanted islets using positron emission tomography

♫ Development of QSAR models using C-QSAR program: a regression program that has dual databases of over 21,000 QSAR models

♫ Probing RNA structure genome-wide using high throughput sequencing

♫ A method for labeling polyacrylamide gels

Exchange Protocols that have interesting comments

One of the really nice features of both Nature Protocols and the Protocol Exchange is that it is possible to comment on protocols. While this resource is under-utilised, there are a few protocols that have very interesting discussions associated with them, and I have highlighted these below.

☺ Production of neuron-preferential lentiviral vectors

☺ High-throughput cloning and expression in Lactococcus lactis

☺ Calcium flux: Indo-1 loading and sample staining procedure for simultaneous measurement of intracellular Ca2+

☺ Assessment of cry1Ab transgene cassette in commercial Bt corn MON810: gene, event, construct and GMO specific concurrent characterization

A complete list of Exchange Protocols with comments can be found here.

https://www.delicious.com/BronwenAnn/exchange-comments

Labgroups that have contributed loads of protocols.

It would be really great if research laboratories used the Protocol Exchange as a way to archive and share their methods within their group, with collaborators and with the wider community.

This has not really happened yet, but there are a few people who have uploaded collections of protocols either all relating to a single research paper or, in the case of Wei Zou, to a PhD thesis.

▲ Yokoyama Lab (RIKEN BRC), Nagata Lab

(a series of protocols relating to a Nature Structural and Molecular Biology paper)

▲ Wolf Frommer lab (a series of protocols relating to a Nature paper)

▲ Jeak Ling DING’s lab (a series of protocols relating to a Nature Immunology paper)

▲ Ben Davis Lab (a series of protocols – including a Nature Protocol – relating to a Nature paper).

Labgroups that have pretty logos

When you create a labgroup, you can add an image, or logo, to go with it. There are a few really pretty ones which I have listed below.

Ren Lab, Oregon Health & Science University