Dear Researcher

I hope that earlier this year you received an email from me. However I know that spam filters are sometimes overzealous, email accounts become dormant and atrophy, passwords are forgotten, or a hundred other reasons why emails don’t get read by their intended recipient.

I am writing to you because you have previously uploaded a protocol to the Protocols Network part of the Nature Protocols website. I wanted to let you know of some major changes to the site which have greatly increased its usefulness. I hope that you will find exciting.

The most important change is the name, which has now been changed to Protocol Exchange which we feel better reflects what the site actually achieves. We hope that the site can now become the attractive place for scientists to share their experimental knowledge that we always intended it to be. The most significant features are:

• The Protocols are laid out in a cleaner and more modular fashion more in line with the presentation of peer reviewed content in Nature research journals.
• Protocols are linked to the research papers that relate to them
• All the Protocols are now presented under a Creative Commons non-commercial licence which means that copyright remains with you as the authors but that anyone is free to read and use the protocols provided that they do not copy or reuse them for commercial purposes.

We have moved your Protocol into this new site and although we are fairly confident that no errors have been added during this transfer it would we very useful if you would look at your protocol and let us know if there any problems with it.

There is also a further feature which I want to tell you about. We have strengthened the concept of Lab Groups with respect to Protocols. In order to upload a Protocol to Protocol Exchange and author must be a member of a Lab Group. Anyone can set up a lab group and then either invite other people to join the group or adjust the settings of the group so other researchers can apply to join the group. Lab groups have a dedicated page on which are collected all the Protocols associated with that lab group. The owner of the group can also choose the upload a picture as a logo for the group and display the groups address and website address if they wish. There is also an RSS feed from each Lab Group page which will allow users to easily display the Protocol they have on the Protocol Exchange on their personal or departmental web pages. Finally all members of a lab group can read Protocols that are being drafted by members of the group

As you have a Protocol already uploaded to the Protocol Exchange we have also created a Lab Group for which you are the owner. You do not need to do anything with this lab group but we very much hope that you will log into Protocol Exchange and take control of your group. To do this please ‘log on’ at the Protocol Exchange site and, once you have done this, email me so that I can assign the Lab Group to you.

We hope that you will want to supply information about your lab including a photograph to act as the group logo and a URL to connect to your personal or departmental home pages. We also suggest that you invite the other members of your laboratory to join your Lab Group (which can be done by entering your colleagues’ email addresses). If you wish you can also change the preferences of the group to allow any users of the Protocol Exchange to request to join your group.

I really hope that you will come to Protocol Exchange and agree with us that this is an exceptionally effective way to share the experimental know-how of yourself and your colleagues. The resource is free to use both for authors and readers, and all Protocols receive a DOI allowing them to be cited in your research papers. All Protocols are also fully discoverable either by the Nature.com search engine or by a custom browse facility that covers the Protocols both in Protocol Exchange and in the peer reviewed journal Nature Protocols.

I hope that you will be as excited by Protocol Exchange as we are.

Thank you for your help in making Protocol Exchange a revolutionary resource to help speed scientific discovery.

Yours

Chris Surridge

Christopher Surridge, PhD

c.surridge [at] nature.com

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I, and many other people, have spent a lot of time over the last decade trying to figure out how to get scientists participate in online activity. Commenting on research papers would be nice for a start. Nature Protocols has had commenting on all its content from the start but the number of actual comments supplied is woefully low. Protocol Exchange also has commenting enabled and there this would act as a form of post publication peer-review as those Protocols are not reviewed before posting. Without this sort of activity whatever you find on the web needs to have a big ‘Caveat Emptor’ sign hanging over it.

I’m not going to thread my way through the various arguments about why researchers don’t comment online on research articles, or bemoan the fact that there can be tons of erudite discussion about a blog post about a piece of research, but not commenting on the research itself. I haven’t the strength (or caffeine levels) for that this morning. But there are two basic camps in all the discussions and brainstorms I’ve been involved with. First there is the cadre of glass-half-emptyites who look at past experiences and the arguments about why experts don’t comment and say that this is inevitable. We’ve tried and it hasn’t worked so there is no point expending more effort quixotically. The other group are the glass-half-fullers who think that if we could just understand exactly why the experts of the world don’t join in then we could provide systems and incentives to tempt them.

I’m definitely a glass-half-fuller and so is Daniel Mietchen. When he isn’t busy measuring brains at the University of Jena he’s involved in a whole lot of projects loosely under the umbrella of Open Science. At the moment one of these is a survey of people to understand why they do or don’t contribute to Wikipedia. Why is this great collaborative encyclopedia put together by interested amateurs while the experts whose contributions would be most valuable cheer (or sneer) from the sidelines? Is that characterization even correct?

This survey, Expert Barriers to Wikipedia, is being performed not by Daniel alone but by the Wikimedia Foundation Research Committee and I for one am going to be very interested in the results.

But before that please go and do what I did: take part.

I’m really pleased with the way that the Browse function that we have implemented for Protocols is working. I keep finding different ways to use it. As anyone who has been following our Twitter feed, and you really should be, will have seen we have used the browse to assemble lists of Protocols relating to quite specific subject areas. We have done: Stable isotope labelling for mass spectrometry, X-ray crystallography and Synthetic Chemistry.

There are plenty more possibilities for such lists and even more when we introduce user tagging of Protocols later in the year.

Another facet of the browse is identifying Protocols based on the Journals in which related research papers have been published. We have called this the Associated Publications facet (a name which took much sweat and revision to settle on if you can believe it). You can access this feature, like all the other facets of the browse, through the left hand column but you can also create direct links. So if you want to see protocols associated with Nature papers you can see them all here. You will find 96 protocols there, which got me thinking about how the other Nature journals were doing. Here is the list.

Close behind Nature are:

Nature Medicine (48 protocols)

Nature Immunology (45 protocols)

And

Nature Methods (35 protocols)

In the 20s:

Nature Structural & Molecular Biology (https://bit.ly/i2mUfP)

Nature Neuroscience (https://bit.ly/gJfbrz)

Nature Genetics (20 protocols)

Then:

Nature Cell Biology (17 protocols)

Nature Biotechnology (12 protocols)

Nature Communications (5 protocols)

Nature Chemical Biology (1 protocol)

Nature Physics (1 protocol)

So that is where we stand.

But then I thought it might be good to use this as an incentive to my fellow editors to tell their authors about the awesome power of Nature Protocols and Protocol Exchange. So I’m going to give a bottle of champagne to whichever journal increases their number of associated Protocols by the most over the next 6 months (so that is numbers on the 15th August); probably as a percentage of the number of research papers they publish to make things a little fairer. So if you want to support your favourite Nature journal to the bubbly come to Protocol Exchange, set up a Lab Group and upload your Protocols.

Now you might legitimately complain that I’ve only mentioned Nature journals. Well this feature works equally well for non-Nature titles. The best of those at the moment is Nucleic Acids Research with 3 associated Protocols. There might well be champagne available to any other journals that substantially increases its number of associated Protocols. I’m not promising that as I can’t think what the appropriate rules of such a competition might be but we could always see how things go.

So let the games commence!

p.s. You are quite right, that Nature Physics hit was a bug which I’ve now rectified. But it made you check didn’t it! And it made Nature Physics editor Alison Wright start calculating her odds for winning the champagne. I reckon on about 10:1 but would love to be proved wrong.

I often come across methodologies that are just so cool that I need to tell someone about them. More than that I wanted to be doing the experiments themselves. One of these has just been published in PLoS ONE

Céline Frère and colleagues from the University of Queensland, Australia and Georgetown University, USA have worked out a way to collect and sequence the genomic and mitochondrial DNA from dolphins and, hopefully, other cetaceans¹. They trained six bottlenose dolphins at the National Aquarium in Baltimore, Maryland to blow on demand into a sample tube.

But I’m not talking about exhaling through their mouths. Nope, they blew through their blow holes, the characteristic structure on the top of the heads of dolphins, whales and porpoises through which they so dramatically vent when at the water’s surface. The researchers looked for both nuclear and mitochondrial DNA in this cetacean snot and showed that the sequences produced were identical to the sequences obtained from blood samples from each individual dolphin. With this successful proof of principle under their belts the researchers are now trying to apply this to a population of wild dolphins in Shark Bay, Western Australia.

Being able to collect DNA samples in a non-invasive way is hugely preferable to the current standard procedure, dart biopsy.

“Dart biopsying is considered inappropriate for very young animals and the technique requires considerable skill to avoid injuring the animals,” says Janet Mann, one of the authors and a professor of biology and psychology at Georgetown. “Thus identifying alternative genetic collection techniques for cetaceans remains a priority, especially for internationally protected species.”

The technique isn’t yet perfect.

Both biopsy and blow-sampling require close proximity of the boat, but blow-sampling can be achieved when dolphins voluntarily bow-ride and involves no harmful contact. While we recognise the important role played by dart-biopsying, we provide evidence that blow-sampling is a viable alternative and less invasive mode of DNA collection.

Perhaps they should team up with Katarina Acevedo-Whitehouse and colleagues, who last year showed how to sample blow from free-swimming, wild whales using a remote controlled toy helicopter².

Now there’s an experiment I’d love to try myself.

¹ Frère, C.H., et al. Thar She Blows! A Novel Method for DNA Collection from Cetacean Blow. PLoS ONE 5, e12299 (2010). doi: 10.1371/journal.pone.0012299

² Acevedo-Whitehouse, K., Rocha-Gosselin, A. & Gendron, D. A novel noninvasive tool for disease surveillance of free-ranging whales and its relevance to conservation programs. Anim. Cons. 13, 217-225 (2009). doi: 10.1111/j.1469-1795.2009.00326.x