Exchange Protocols: What are they and how are they made?

What are the characteristics of an Exchange Protocol?

I have created a short screencast highlighting some essential features:

- each Exchange Protocol is associated with a Lab Group

- each has a DOI

- the Procedure is a series of numbered steps in the active tense

- you can add a query for the author, or other comment

- you can add the protocol to a list of favourites

You can browse for other Exchange Protocols by clicking here.

How do you create an Exchange Protocol

The first time you come to share a protocol, this will be a two stage process, both of which are very easy to do.

Stage 1 is “Creating a labgroup”, and Stage 2 is “Creating the protocol”.

I have made two screen casts that show how these steps are achieved.

How to create a lab group starting from http://www.nature.com/protocolexchange/

How to create the protocol starting from http://www.nature.com/protocolexchange/protocols/new

Are there any needles in this haystack?

With increasing volumes of information being published we are becoming ever more reliant on good:

(1) Search engines, and

(2) Post-publication reviews (e.g. in the form of Featured articles, News and Views pieces, blog-posts, comments and ratings).

In this post, I would like to introduce you to the Protocols Browse function.

Google and PubMed are, I think, the best resources for finding information when you know (almost) exactly what you are looking for. There are times, though, when it is useful to browse through the literature to uncover things that might be interesting or useful. Nature Protocols and the Protocol Exchange share quite a powerful Browse function. Unfortunately it suffers slightly from not being an integral part of either home page and therefore I have these paranoid thoughts that users of our site are not even aware that it exists!

In a small attempt to address this, I have created a few very short screencasts to introduce people to Browsing Protocols.

The first shows an example of how to access the Browse function from the Nature Protocols homepage (http://www.natureprotocols.com/)

The second shows an example of how to browse community contributed protocols from the Protocol Exchange (http://www.nature.com/protocolexchange/protocols/)

Highlights from the Protocol Exchange

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.

http://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

Cognitive Ethology Lab, German Primate Center

Semyanov Lab, RIKEN Brain Science Institute

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I recently started a story on this which will contrinue to be updated.

Notes from the 3rd EMBO meeting, Vienna.

So I have finally finished collecting my thoughts from the 3rd EMBO meeting in Vienna, which I was fortunate enough to attend from the 10th-13th Sept.

Hosted in the Austria Centre Vienna

Austria Center Vienna

the meeting was attended by around 1300 people, and with over 600 posters and 21 concurrent sessions there was lots to keep participants busy! As my first conference experience for a good few years, it was a little overwhelming, but in a good way!

Vienna

I found Vienna to be a lovely city, as was the weather for the weekend, which helps with the laid back atmosphere…

MuseumsQuartier

The architecture is amazing, with beautiful buildings on every corner

Karlskirche

and although it was a little too cultural for my time-frame with many art galleries and museums that I didn’t manage to see, I did appreciate my visit to see the living art of the Spanish Riding School! Sadly we weren’t allowed to take pictures of the action, but here is one of the stars dozing in the sun

Lipizzaner

Back to business…

Anyway, on to the conference, which began with a series of plenary lectures on hosts & microbes, including a really interesting talk by Bonnie Bassler who explained their work investigating quorum sensing inhibitors as potential therapeutics to prevent pathogenesis. Although there is still some way to go before inhibitor compounds are made into drugs, this sounds like an exciting avenue of future research, especially given the multidrug resistance problems nowadays. I also really enjoyed the final talk in this session from Brett Finlay (despite the high content of toilet humour!) on the importance of our gut microbiota in our health and their role in resistance to allergic diseases such as asthma.

For the next 3 days, there was a great diversity of topics presented so I was too often spoilt for choice about which session to attend! Day two started with an excellent keynote lecture from Susan Lindquist discussing the role of protein folding in the inheritance of environmentally acquired traits via both Hsp90- and prion-mediated mechanisms. She explained how Hsp90 buffers the effects of genetic variation and acts as a potentiator of evolution, enabling previously hidden genetic variation to be revealed in times of stress. In the plenary session on genome evolution that followed, Paul Rainey presented evidence of the involvement of an epigenetic switch in bacterial genome evolution, reinforcing the theme that genome evolution is about so much more than just the underlying genetic variation.

Next-generation sequencing

Another theme that spanned many sessions was the use of next-generation sequencing and the advances made possible in a variety of fields as a result of the development of these techniques. This was illustrated by Mike Stratton’s plenary lecture on the exome sequencing and analysis of cancer genomes. Hand-in-hand with such technological advances of course comes the need for methods to analyse the vast quantities of data produced. These ideas were further explored in the session on human genome variation & disease with a talk from Elaine Mardis covering whole genome sequencing approaches used to analyse cancer genomes, including their application to personal diagnosis and treatment.

Personal medicine

Continuing on the topic of personal medicine, Russ Altman from Stanford next introduced a pharmacogenomics database designed to allow the effect of human genetic variation on drug responses to be assessed. This became quite entertaining when he reported results from the analysis of the personal genome of his colleague, Steve Quake; he had obviously agreed to everyone at EMBO and beyond knowing how he is likely to respond to a variety of drugs as well as his genetic predisposition to various diseases, but it is quite wierd to feel like I know far more about his genome than about the man himself?!

Computer vision

As well as the increase in the throughput of sequencing methods, there is also now a need for computational methods to keep up with advances in imaging methods. This was explored in a stimulating session on computer vision of cellular function in which Andre Brown and Sean Megason (amongst others) described systems to image C. elegans behaviour and zebrafish embryo development, respectively, as well as outlining the software they designed to analyse the image data obtained. The real take home message from this session was that it’s no use having the means to obtain data on this scale if you don’t also have algorithms and software to enable efficient and accurate analysis of this data to extract the biological meaning. So I think this will be a big area for methods development going forwards.

TNTs

I also found a new area of molecular biology to me and was really interested to learn about the recent discovery of tunneling nanotubes (or TNTs). In a talk by Hans-Hermann Gerdes we heard how these nanotubes form and that they are used for long distance electrical coupling between cells, and as a method of cell-cell communication for the transfer of cytoplasmic molecules and organelles. Fascinating stuff!

And finally, the prize for the best talk goes to…

Florian Engert, for his virtual reality world for zebrafish larvae. Or as he put it, ‘The Matrix’ for fish! He presented work on adaptive motorlearning in zebrafish larvae and detailed the system he developed in which larvae are paralyzed and surrounded by a virtual reality environment, which allows the whole brain to be imaged at a single cell level in an awake animal as they respond to experimentally induced changes in the environment. This clearly provides an exciting system to study the neural circuitry underlying a range of visually-induced behaviours in zebrafish.

Featured protocols

I will finish with a reminder of a couple of Nature Protocols that I was really pleased to spot being put to good use in the work presented at EMBO.

Firstly, "CO-FISH ":http://www.nature.com/nprot/journal/v5/n7/full/nprot.2010.102.html (chromosome orientation fluorescent in situ hybridization) was being utilised by both Shahragim Tajbakhsh and Peter Lansdorp in their talks on the non-random segregation of chromosomes in mitosis.

nprot_2010_102-F1.jpg

And genomic SELEX formed the basis of the work presented in Renee Schroeder’s talk in the RNA & RNA mediated regulation session.

nprot_2006_372-F1.jpg

Update on inserting images into Exchange Protocols

A while ago, I wrote a post on how to insert images into the main text of Exchange Protocols.

I would like to write a quick update on this, because there is a slightly more elegant solution when trying to insert images that happen to be smaller or larger than the page-width.

1| Prepare your figure. In order for it to show as an image it has to be a jpeg, png or bitmap file. Unfortunately tif files will NOT show as images. The framed page is 560 pixels wide.

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2| Assuming that you are in the process of sharing a protocol, upload your figure by going to the “Images and Attachments” page. Notice that both the Name (e.g. Figure 1) and the Title (Overall heading) are required fields.

3| Navigate to the section of the protocol where you would like to add the figure, and click on the link: “How do I enter formatted text, symbols, links and images?”, and expand the section: "URLS for files uploaded via the “Images and Attachments” page.

4| Copy the link for the image that you are interested in inserting including the exclamation marks, and paste it into, for example, the Introduction. (Use “Control-C” for copy, and “Control-V” for paste)

5| Save the changes, and preview your protocol. If the image is displaying perfectly, then your job is done!

? TROUBLESHOOTING

TROUBLESHOOTING

Step 1: My uploaded file is not showing up as an image

If you file is not one of the “image file types”, you can usually convert it to one.

For tiff files, my favoured method is to open the image in PAINT (Start > All programs > Accessories > Paint), and then “Save As” a png file.

For pdf files, I usually open the pdf and select the image using the snapshot tool. I then “paste” it into Paint and “Save As” a png file.

Step 5: The images is too wide for the screen or you think that it is too big

You can fix this by using the following bit of html:

<img src=" webaddress for the image " alt="Alternative text for your image" width="560" height="228" />

For example:

<img src=" http://www.nature.com/protocolexchange/system/uploads/1927/original/DSC_2524.JPG?1315930505 " alt="Alternative text for your image" width="426" height="285" />

Will result in:

Alternative text for your image

If you wanted to insert the thumbnail with a link to the main figure, then you could insert the following html into the text: <a href="http://url/for/the/fullsize/image"> <img src="http://url/for/the/thumbnail/image" > </a>

For example:

<a href="http://www.nature.com/protocolexchange/system/uploads/1927/original/DSC_2524.JPG?1315930505 "> <img src="http://www.nature.com/protocolexchange/system/uploads/1927/thumbnail/DSC_2524.png?1315930505 " > </a>

Will result in:

I am not going to go through the sums that you need to do to work out the numbers for the width and height of desired output, but there might be some value in mentioning ways of finding out the dimensions of your original image.

- If you are already in PAINT, then you can go to “Image > Attributes”.

- If have the full size image open in your browser, the you can right-click on the image. In Internet Explorer go to “Properties”, in firefox go to “Page info”, and in chrome go to “Inspect element”.

From Word document to clean html

Recently I tweeted that http://word2cleanhtml.com/ was the thing that had been missing from my life. I am not going to go into the reasons why it would be just that important to Me Personally, but I am excited enough to write a blogpost about it.

▲ Aside: Don’t forget to follow @NatureProtocols on http://www.twitter.com!!

♫ Here we go! Are you paying attention!

This Blogpost has been written in Word. The formatting has not been added using any of the weird stars and underscores that you normally find yourself using, and was achieved in six easy steps:

  1. Write the post with the desired formatting.
  2. Go to http://word2cleanhtml.com/index.html and paste in the text (Check the boxes “Remove empty paragraphs”, “Replace smart quotes with ascii equivalents”, “Indent with tabs, not spaces” and “Replace non-breaking spaces with ordinary spaces”).
  3. Copy the resulting clean html into a new Word document.
  4. Find and replace all paragraph marks with “nothing”.
  5. Find and replace all tabs with “nothing”.
  6. Paste the resulting text into the text field in movable type.

Can we even do a table??

Step Number

Problem

Solution

4

You can’t quite work out what to put in the “Find what” field.

Go to “More”, “Special” – the Paragraph Mark should be the top entry, and should be ^p.

6.

When you preview the document, the page layout is completely screwed up.

Every <p> needs to have a corresponding </p>. Similarly with <div> and </div>. Check that this is indeed thecase. A common “thing” is that you will not have copied and pasted the first “<” or the final “>”. If it just looks too complicated, it is worth either repeating the copy-and-paste steps OR just adding another </div> at the end of the text andhoping for the best.

And lastly: You could use this tool when uploading your protocols on the Protocol Exchange and (fingers crossed) your beautiful formatting will be preserved without anyone having to break a sweat.

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Word2Cleanhtml was written by Olly Cope.

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This post has been edited since it was originally published; the whole things works even better if you tick the “Indent with tabs, not spaces” box in http://word2cleanhtml.com/index.html

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.

Themes from the 22nd International Symposium: Synthesis in Organic Chemistry

Having left my meticulously drawn maps and notes on the dining room table, I boldly set off to Cambridge for the Synthesis in Organic Chemistry Symposium. I was immediately confronted by three Universal Laws:

1. If a bed-and-breakfast is within a 100 m radius of a person’s home, said person is unlikely to know of its existence.

2. People driving swish cars seldom know the directions to the nearest train station (or anything else regarding public transport).

3. Turning right instead of left can have consequences significantly exceeding the ease with which the mistake can be made.

Despite these obstacles, I found Vine Farm, and later the train station, the important bus stops, and Churchill College itself.

After a moderately sunny weekend, the days of the conference were cold, overcast and windy: perfect weather to take shelter in a lecture theatre and escape into the wonderful world of organic synthesis. I was pleasantly surprised to find that I understood enough of the chemistry to follow most of the talks and found myself wishing that I could be in the lab again.

Themes that emerged, at least in my own mind, were:

1. Flow Chemistry and Automated Synthesis.

Steven Ley has developed many flow chemistry methods, and talked about using these systems for reactions where the method has already been optimised and where a compound needs to be prepared in bulk, to allow the valuable minds and skills of PhD students and post-docs to concentrate on new reactions. Vapourtec had a stand to demonstrate their instruments plus an impressive list of publications where their machines had been used many of which had Steve Ley’s name in the author list.

The ReactIR Flow Cell was also mentioned in Helma Wennemers talk in the context of looking at reaction mechanisms.

Peter Seeberger also talked about automated synthesis, this time for the synthesis of oligosaccharides in an approach analogous to that of automated peptide synthesis. His protocol Continuous-flow reactor-based synthesis of carbohydrate and dihydrolipoic acid-capped quantum dots is being published on our site this week.

2. Emergence of kits to perform catalytic reactions.

Prof. Buchwald spoke about the palladium-catalyzed cross coupling reactions that his group has developed and studied, revealed how the ligand names were derived (named after labmembers (e.g. BrettPhos after Brett Fors) and his cats (e.g. RuPhos after Rufus)) and that he was working with Aldrich and STREM to provide the catalyst reagents in kit form.

Both STREM and another company, Johnson Matthey Catalysts had stands at the conference. Johnson Matthey Catalysts provide kits for performing a range of reactions, including those catalysed by enzymes.

3. The pervasive use of SciFinder.

SciFinder was in fact mentioned in the very first talk by Larry Overman, and quite often in conversation during the course of the conference. It is affiliated with the American Chemical Society and I gather that it was a database containing metadata for chemistry-related articles – similar in a way to PubMed, but with more functionality (including the ability to search by chemical structure) and a price-tag. I was relieved to find that Nature Protocols was present in the database!

4. The Holy Grail of 100 % ee

Unsurprisingly, almost all of the compounds-of-interest were chiral, and their successful synthesis required developing enantioselective reactions. Helma Wennemers, for example, talked about her work on developing catalysts that are based on the chemistry of the active sites of enzymes.

And Finally

While all of the talks were excellent, the one that was most memorable was Eiichi Nakamura’s “Imaging of Single Organic Molecules in Motion”. I am not sure how I managed to miss the publication of the original papers, but watching the electron microscopy videos of molecules wiggling through or on top of nanotubes was very pleasing indeed (see also this JACS image challenge).

Alkenyl fullerene in a carbon nanotube

And the most entertaining talk – which included various magic tricks! – was that given by David Leigh on “Making the tiniest machines”. The machines he described were based on catenanes and rotaxanes, which are both examples of interlocked molecules. Again, I am not sure what rock I was trapped under not to notice the original publications, but these images might whet your appetitie if you also somehow managed to miss them.

from A synthetic small molecule that can walk down a track_

from A molecular information ratchet_