Author Archives: Bronwen Dekker

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

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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 https://www.nature.com/protocolexchange/

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

Are there any needles in this haystack?

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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 (https://www.natureprotocols.com/)

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

Highlights from the Protocol Exchange

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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

Cognitive Ethology Lab, German Primate Center

Semyanov Lab, RIKEN Brain Science Institute

…………………….

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

Update on inserting images into Exchange Protocols

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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.

? TROUBLESHOOTING

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=" https://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="https://url/for/the/fullsize/image"> <img src="https://url/for/the/thumbnail/image" > </a>

For example:

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

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Recently I tweeted that https://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 https://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 https://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.

…………………

Word2Cleanhtml was written by Olly Cope.

…………………

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 https://word2cleanhtml.com/index.html

From PhD thesis to Protocol Exchange

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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.

…………………………………

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

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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_

Bronwen is off to Cambridge for a Synthesis in Organic Chemistry symposium

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Today, I am in a good mood, because I know that next week I am going to a conference! As much as I love looking at manuscripts and browsing through the literature for commissioning ideas, it will be good to be out of the office and listening to scientists talking about their work. Hopefully, I will get to meet and chat to a few as well! I will be staying in a little bed-and-breakfast in the evenings, and during the day I will attend talks by eminent chemists at the 22nd International Symposium: Synthesis in Organic Chemistry in Cambridge.

Is anyone else going to the meeting? If so leave a comment and I’ll make sure to look out for you. Or just come and say hello when you are there.

To highlight our chemistry content, the following protocols have been made open access until the end of July.

Protocols relating to metathesis:

Synthesis of N-heterocyclic carbene ligands and derived ruthenium olefin metathesis catalysts

Xavier Bantreil & Steven P Nolan

Synthesis of all-hydrocarbon stapled α-helical peptides by ring-closing olefin metathesis

Young-Woo Kim, Tom N Grossmann & Gregory L Verdine

Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach

Anupam Patgiri, Monica Z Menzenski, Andrew B Mahon & Paramjit S Arora

Olefin cross-metathesis-based approaches to furans: procedures for the preparation of di- and trisubstituted variants

Timothy J Donohoe, John F Bower & José A Basutto

Click chemistry

Alkyne-azide click reaction catalyzed by metallic copper under ultrasound

Pedro Cintas, Alessandro Barge, Silvia Tagliapietra, Luisa Boffa & Giancarlo Cravotto

More Click Chemistry protocols can be found here

Enzyme catalysed

Preparative scale Baeyer-Villiger biooxidation at high concentration using recombinant Escherichia coli and in situ substrate feeding and product removal process

Iris Hilker, Maria C Gutiérrez, Roland Furstoss, John Ward, Roland Wohlgemuth & Véronique Alphand

Other useful reactions

Pd-catalyzed Suzuki-Miyaura reactions of aryl halides using bulky biarylmonophosphine ligands

Ryan A Altman & Stephen L Buchwald

The partial reduction of electron-deficient pyrroles: procedures describing both Birch (Li/NH3) and ammonia-free (Li/DBB) conditions

Timothy J Donohoe & Rhian E Thomas

The use of the Ugi four-component condensation

Stefano Marcaccini & Tomás Torroba

Synthesis of specific reagents

A practical guide to the synthesis of dinitroindolinyl-caged neurotransmitters

Graham C R Ellis-Davies

A concise and scalable route to L-azidohomoalanine

Stefanie Roth, William C Drewe & Neil R Thomas

Analytical techniques

A method for concurrent diazomethane synthesis and substrate methylation in a 96-sample format

Lana S Barkawi & Jerry D Cohen

Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates

Sherif S Ebada, Ru Angelie Edrada, Wenhan Lin & Peter Proksch

Mosher ester analysis for the determination of absolute configuration of stereogenic (chiral) carbinol carbons Thomas R Hoye, Christopher S Jeffrey & Feng Shao

A Finer Point relating to Nature Protocols RSS feeds

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Following on from the previous post, I would like to show you what else you can do to customise your Nature Protocols RSS feeds.

If you have a look at the list of RSS feeds for the categories, you will notice that all of the links have “.rss” between “protocols” and the question mark.

For example:

Spectroscopy

https://www.nature.com/protocolexchange/protocols.rss?protocol_search%5Bfacets%5D%5Bcategory%5D=Spectroscopy

Structural Biology

https://www.nature.com/protocolexchange/protocols.rss?protocol_search%5Bfacets%5D%5Bcategory%5D=Structural+biology

Synthetic Chemistry

https://www.nature.com/protocolexchange/protocols.rss?protocol_search%5Bfacets%5D%5Bcategory%5D=Synthetic+chemistry

What is really cool, is that you can make an rss feed from any search term (or group of search terms) accessible from the Browse page.

For example, if you are very interested in NMR, you might search for this term within the Structural biology category, insert “.rss” into the webaddress and then copy the resulting link into your feedreader!

Webaddress for the search results:

https://www.nature.com/protocolexchange/protocols?commit=Go&protocol_search%5Bfacets%5D%5Bcategory%5D=Structural+biology&protocol_search%5Bq%5D=NMR

Webaddress for the RSS feed:

https://www.nature.com/protocolexchange/protocols.rss?commit=Go&protocol_search%5Bfacets%5D%5Bcategory%5D=Structural+biology&protocol_search%5Bq%5D=NMR

Another example application:

If you are collaborating with other research teams and want to be able to easily group protocols that “belong” to the collaboration, you could agree on a unique connecting word or phrase to add to the keywords when uploading your Exchange Protocols. You would be able to use this term to easily find the protocols, plus you could have an RSS feed to let you know when more protocols had been added.