Posts

Reference Output from Mendeley using the custom citation style
, , ,

Formatting your references for The Canadian Entomologist using Mendeley

By Chris MacQuarrie, Natural Resources Canada Canadian Forest Service (Sault Ste. Marie, ON)

——————-

Opa Opa Citation Style! *

I recently switched over to the Mendeley citation manager after many years of being a loyal EndNote user. I’m liking Mendeley, but one thing I lost in the switch was the collection of custom citation styles I had put together during my MSc, PhD and Post-doc.

Mendeley Desktop

Mendeley Desktop

This wasn’t a problem until this week when I was preparing final edits on a manuscript for The Canadian Entomologist. Mendeley didn’t have a style for TCE, but what it does have is the ability to modify existing styles and create new ones.

I started with the existing style for the Canadian Journal of Fisheries and Aquatic Sciences because it’s an old stable-mate of TCE from the NRC press days and has a very similar citation style.

I used Mendeley’s Visual CSL Editor:

csl editor
to modify the CJFAS style to output what TCE requires in it’s reference section.The only ‘big’ difference I could find between is that TCE uses a comma after the journal name where CJFAS does not.

I also made a few changes. For instance, the CJFAS style didn’t have a output for theses so I created one for that reference class. I also modified a few of the settings to delete information that CJFAS needs but TCE doesn’t.

Reference Output from Mendeley using the custom citation style

Reference Output from Mendeley using the custom citation style

You can download the finished product from this link:

http://csl.mendeley.com/styles/18621721/TheCanadianEntomologist

Now, what’s neat, is that Mendeley’s citation styles are based on the open-source Citation Style Language so you can use this style in any citation management program that also uses CSL (e.g., Zotero and Papers).

A disclaimer. I hacked this together in a few hours and didn’t check all reference classes, so your milage may vary! As always, check your references section carefully before submission!

If you do spot an error or have a suggestion let me know here, on Twitter (@cmacquar) or at cjkmacquarrie@gmail.com.

*if you don’t get this reference, see here

,

Dear Buggy: a discussion on data

A belated Happy New Year to all!

Buggy is back for his first post of the year. This is also my first post in a while; put that down to a combination of conference season, project planning season and too much holiday cheer.

I recently had an exchange on Twitter exchange with a colleague (and yes, before you ask we are allowed to use social media at work) about where scientists could deposit their data on the web at the end of a study. I had a few suggestions (and, as usual, a few opinions) about how, where and why we should be depositing our data.

As science moves towards a more ‘open source’, philosophy making data available as part of the publication process is becoming more common. Of course the taxonomists, systematists and gene-jockies amongst us have been doing that for a while, using systems like NCBI’s GenBank. Where the revolution (if I could be so bold as to use that word) is coming is in the ecological sciences. Expectations amongst publishers and in the broader scientific community are changing twoards expecting that data will be made available online and in an accessible format. To accommodate this, a number of projects have been launched that are meant to be a place for us to publish data sets.

But why publish your data? In theory raw data was always available: you just needed to ask for it. In practice, people can refuse, move on or pass away; data can be lost, formats can change and software can go obsolete which makes the reuse of data difficult. Publishing your data solves this problem.

Publishing your data also makes your work reproducible. With access to your data and your analysis code, anyone can repeat your work – or better yet, extend your work and gain new insight. In fact, in a great many fields your paper will not be published until you deposit the data (see here, for instance). I’d also argue that if your research is publically funded you have an obligation to make your data available. Of course, that is, after you’re done with it!

So why don’t more of us share our data? Well the biggest fear, of course, is that you might get ‘scooped’. That’s reasonable, but I think it’s unfounded, and here’s why: we expect that if someone wants to use our ideas, they will cite us. Otherwise it’s plagiarism (or at least bad manners), and there are ways to deal with that. So, extending that logic,  It’s reasonable to expect that if someone wishes to use our data, they will cite us as well (and now you can even track those citations!)

I’d go further and state that the benefits to publishing data outweighs the pitfalls. From an ‘economic’ perspective we can gain professional currency in the form of citations (see here and here), which have value in application, tenure and promotion packages.

Professionally, publishing data can help you attract new collaborators and new research opportunities. Publishing your data is just one more way people can become aware of you and your work and that awareness is important.  There is the old saying that data without context is just noise. If your data can be applied elsewhere, only you as the collector can provide that additional insight into the specifics of your system. That insight can help to explain new results, but it can also lead to new hypotheses and collaborations with people you may never have otherwise interacted with (or who would have never read your paper).

Personally, I think that the potential for greater insight resulting from others ‘playing around’ with your data can only result in a deeper understanding of your own system. And really, isn’t that something we’re all after?

Below is a list of some places where you can publish your data. Do you have any other suggestions, or want to share your experiences with publishing data? Let me know in the comments.

Buggy.

(With thanks to Simon Bridge of Natural Resources Canada Canadian Forest Service for suggesting I write this up.)

_____________________

Dryad 

From their about page: “Dryad is both an international repository of data underlying peer-reviewed articles in the basic and applied biosciences, and a membership organization, governed by journals, publishers, scientific societies, and other stakeholders. Dryad welcomes data submissions related to published, or accepted, scholarly publications.”

The Ecological Society of America’s Data Registry  

A data repository for articles published in the ESA’s journals)

treebase

A repository for phylogentic trees and data

Or find a journal where you can publish the data as a digital appendix like I did here.

, ,

Dear Buggy: Writing your first manuscript

Dear Buggy is the the alter-ego of Dr. Chris MacQuarrie, a research entomologist with the Canadian Forest Service. You can ask Buggy questions of your own on Twitter @CMacQuar.

—————————-

Hello all,

Writing your first manuscript can be difficult. I remember spending a ridiculous amount of time preparing the first draft of my first paper. I thought I had produced something pretty good. So imagine my surprise when the file came back from my supervisor dripping in red ink (digital red ink, that is).

I had two big problems. First, like many new students, I didn’t make a particularly convincing argument in my introduction, my methods were confusing, the results were a mess and the discussion was meandering. My second problem confounded the first. I wasn’t a good writer.

Solving the first problem was easy. I had two very patient supervisors who taught me how to write a scientific paper. Solving the second problem is taking a little longer, because the only way to become a better writer is to practice. That is, you need to write. I write as much as I can, but I still have a lot of work to do. I’m lucky that I’ve had the good fortune to work with good writers and good editors from whom I’ve managed to learn some good habits (and break some bad ones).

The rest of my education has come from books. I thought I’d share some of these with you.

Books about writing in science:

How to write and publish a scientific paper 6th ed. by RA Day and B. Gastel

This is an excellent primer on how to write a scientific paper and should be on the bookshelf of every grad student.The 6th edition is a bit pricey, but you might be able to pick up a copy of the 4th or 5th edition at a good used bookstore. I own the 4th edition, it’s a bit dated but more than adequate for everyday use.

Writing Papers in the Biological Sciences 5th ed. by V McMillan

I was introduced to this book during my undergrad where it was on the required reading list (in part, I think because the author is also an alumni of the University of Saskatchewan’s biology department) I’ve carried it with me ever since. McMillan focuses on writing term papers and lab reports with less attention paid to writing journal articles, so this might be a better choice for undergrads. That said, there are good sections on formatting and citing that also apply to graduate level work. The current edition also covers the formatting of posters.

Writing to Learn Biology by R Moore

A Short Guide to Writing about Biology 7th ed. by J Pechenik

These two were recommended to me by Cedric Gillot, editor of the Bulletin (Cedric is one of those good editors I mentioned earlier. He’s been editing my work, on and off, for over 15 years).

Moore’s book looks to be out of print but many copies are available from online used book stores (as are most of the books in this post).  Pechenik’s book is well reviewed on Amazon. I’ll track down a copy and report back. If you’ve read this book let me know what you thought.

Books on writing in general:

These three books are not about writing in science, but are all excellent guides on how to write well.

How to Speak and Write Correctly by J Devlin.

Perhaps the granddaddy of all grammar guides. While it’s a bit dated (Devlin goes into detail on the proper use of ‘shall’ and ‘thou’), writers should still find it relevant. In particular, those, like me, that were never taught the rules of english grammarl. One other plus, since it was published in 1910, the copyright has expired and it can be had for free!
The Elements of Style 4th ed. by W Stunk and E.B. White.

The classic guide to writing in english. Buy this. Read it. Then put it on your bookshelf and read it again every year for the rest of your life. The best $12 you can invest towards becoming a better writer.

On writing well by W Zinsser

Zinsser focuses on guiding the writer to telling a compelling story. A great resource if you fancy becoming a writer about science (in addition to a writer of science). Regardless, science is about telling stories and the advice in this book about constructing a narrative can be applied to writing in the peer-reviewed literature.
And two for the road…

These last two books are on the art and craft of writing. Both are fun reads and worth checking out.

On Writing by S King.

Yes, that ‘S King’. King has much good advice to offer to all writers. If you ever wondered how King could be such a prolific writer, consider this: he writes at least 1000 words a day, six days a week. Anyone who has spent that much of their life writing should have good advice to offer. Set any doubts that you may have about King as a fiction writer and read this book. Probably one of his best.

When you catch an adjective. Kill it. by B. Yagoda

cover photo [ http://covers.openlibrary.org/w/id/528568-M.jpg ]

A fun little book about exercising verbosity from your writing. Clearly, I need to read it again.

I’d also love to hear your recommendations. What books influenced you as a writer?

Cover images in this post are from the Open Library project. Links are to Amazon.ca, but you should be able to find many of these in your local used bookstore, university bookstore or library.

, , ,

Dear Buggy: Where Do Research Ideas Come From?

Dear Buggy is the the alter-ego of Dr. Chris MacQuarrie, a research entomologist with the Canadian Forest Service. You can ask Buggy questions of your own on Twitter @CMacQuar.

—————————-

Hello!

Dear Buggy has lept out of the pages of the ESC Bulletin and landed in the new and exciting wilderness of the ESC blog. My loyal readers shouldn’t worry, I’ll still be writing my column, but between editions of the Bulletin I’ll be posting here.

I’m very excited to be contributing to the ESC blog, but I’ll admit I am a tad nervous. When Crystal and Morgan invited me to contribute I was worried that it would be hard to come up with interesting topics. Thankfully the ideas began to flow after a glass of good scotch and I think I’ve come up with a few ideas that should keep me busy. After that? Well I’m always open to suggestions.

While thinking about this first blog post for ‘Dear Buggy’ I recalled how I felt when I first signed on to write Dear Buggy for the Bulletin. Where was I going to get these ideas!? Fortunately, a lot of the suggestions for my early columns come from the then-editor, Kevin Floate. Kevin had the original idea for Dear Buggy and shared with me his collection of questions and ideas. Later on, the ideas began to flow and inspiration came from others around me. Although, when I’m stuck for an topic I still go back to the original list that Kevin gave me. Good ideas can be hard to come by when you’ve got writer’s block and a deadline is fast approaching

As I planned this blog post I began to muse over the source of all my ideas, in particular “Where do I get my research ideas?”.

For example, when I was a new MSc student many of my research questions were influenced by the ideas of my supervisors. This isn’t all that unusual.  I suspect that when most of us started in research we were given, or at the least influenced, by ideas of others. As we mature scientifically we eventually start to come up with our own ideas. In fact, a good part of becoming a successful, independent researcher is tied to coming up with good ideas (which we might also call hypotheses). So where do these ideas come from? And perhaps more importantly, what do we do with these ideas once we have them?

I find inspiration hits at the oddest times and in the oddest places . I think Jorge Cham at PhD comics captured it best in this series of comics. Like most, I’ve been inspired in the ‘usual’ places: reading papers, attending seminars, talking with colleagues, etc… But inspiration can happen in other places as well. My mind tends to wander on my bike-ride home, when I’m pushing my daughter in her stroller, and quite often when I’m sharing a glass of scotch with my wife (who, lucky for me, is also an entomologist). As it turns out, this ‘mind wandering’ actually helps you have those ‘eureka’ moments, especially if you have been banging your head against the wall for awhile. I wrote recently about figuring out when you are best at writing. I think that advice can be extended to figuring out when and where you are inspired and to make sure you go there often.

But what about capturing ideas? My mind is like the proverbial sieve, but with one annoying quirk. I often can remember that I had an idea, I just can’t remember what it was.

To combat this selective memory I try to capture my ideas in my work journal as soon as possible. I’m a bit old fashioned so my journal is still kept in a notebook. Since my journal is also where I keep track my current projects, I make sure I highlight any new ideas so they are easy to find later on. There are many, many web-tools out there that can do the same job. The trick, though is to find something that works for you and to use it. My wife, for example,  is also an artist and long-ago got in the habit of carrying a sketchbook with her. That sketchbook now contains just as many ideas for research projects as it does ideas for art projects.

Finally, I must make a confession. Most of my ideas are bad. Some are half baked, others were thought of by someone else and rejected 30 years ago, a lot are impractical, infeasible, or near-impossible to execute or fit into the research that I’m doing. These over time get filtered out. Those that survive this process of natural selection, I keep. I then draw from this storehouse when the right moment comes along. Not all of these ideas will pan out of course, but by hanging on to the good ones I always have the right idea at hand when opportunity presents itself.

I’d be curious to hear about where you find your inspiration and how you track your ideas. Leave them in the comments section and I’ll summarize the best ones in a later post.

Cheers and see you next month,

Buggy.

, ,

Dear Buggy: How do I manage my time?

“Dear Buggy” is an advice column featured in the ESC Bulletin, written by Dr. Chris MacQuarrie.  “Buggy” will also be offering his great tips, tricks and hints every other month here at the ESC blog. In the meantime, enjoy this teaser from the June 2012 edition of the Bulletin!

_____________________________

Dear Buggy,

I’ve got too many things on the go and I can’t seem to keep on track. My field season starts next week, but I haven’t even started planning for it yet. I’ve missed two due dates in the last month, plus I think I may have stood up my boyfriend last night. I would call him to apologize, but I forgot to pay my phone bill last month and they cut me off. Help me! How do I manage my time?

Signed,

‘Short on Time in Terrace’

Thanks for the ‘timely’ question. Hopefully you will have managed to contact your boyfriend before this is published! Teaching yourself how to manage your time is an important skill to develop while you’re young. Speaking from experience, I can assure you that things only get worse as you progress through your career. Your time is precious.

Our tasks, and the time it takes to do them, can be organized on different temporal scales. Since entomologists are already pretty good at thinking about the world at different scales, it should be a logical step for you to think about your time in this way. For example, you have to finish your thesis in the next 5 years; you have to prepare and pass your qualification exams next year, your field season starts in a month, your project proposal is due next week, you are teaching tomorrow, and you have a dental appointment in an hour. Obviously, how you manage these different commitments varies depending on their immediacy. To be efficient, you must manage your time over all temporal scales. That way, things won’t sneak up on you.

Click here to read the rest of this great column in the Bulletin!

_______________________________

Chris MacQuarrie is a research scientist with the Canadian Forest Service in Sault Ste. Marie where he studies the management of native and invasive insects. Currently, he’s beginning to realize that all time management tactics go out the window when you have a toddler in the house. “Dear Buggy” is always looking for suggestions or guest contributors. Have an idea or a question? Send it to: cjkmacquarrie@gmail.com or post it in the Facebook student group.