Endnote
February 10, 2018
Nobody who is younger than me in the scientific generation sense should ever be manually entering references in manuscripts or grant applications.
Ever.
DrugMonkey
biomedical research, just another job…
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biomedical research, just another job…
Nobody who is younger than me in the scientific generation sense should ever be manually entering references in manuscripts or grant applications.
Ever.
DrugMonkey 
February 11, 2018 at 5:01 am
On the other hand they shouldn’t be using some crappy proprietary software like Endnote either. Ideally, they should be using open source tools like LaTeX/BibTex which people in the mathematical sciences have been using for years, which make beautiful typeset manuscripts that journals can print directly (which is why things like arXiv took off earlier in those fields), but if people really want to cling to Microsoft Word, there are open source bibliographic management tools like Zotero that can work with Word as Endnote does.
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February 11, 2018 at 7:24 am
I agree that using open source tools (provided that they are not bug ridden) is good.
But I don’t see the necessity of using tools like LaTeX for those in the biomedical sciences.
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February 11, 2018 at 11:31 am
My PI, who I suspect is younger than you, writes them manually. My PI apparently started because they were co-first authors on manuscripts and most reference software do not reflect co-first authorships. I seriously doubt manually writing them is more accurate (I mean, how often do you check for co-first authors? It wasn’t easy on Pubmed), but what do I know? I’m of that lazy younger generation… I would be happy if we could use DOIs (although that’s hard to do with older papers).
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February 11, 2018 at 12:28 pm
I met another postdoc who had never used Endnote before, I had to stop and check to see if they also mouth pipette. And for all the LaTeX or Zotero evangelists, I’m not chasing from Endnote, it has too much traction and works quite fine for me and others.
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February 11, 2018 at 3:55 pm
Jonathan, I have no need to spend time teaching students how to write with LaTeX so that they can compile their documents and beautifully typeset the equations that their documents don’t have. It’s bad enough to spend time helping them learn to write. If they can use Word, I’ll go with that.
For those who need it, LaTeX is great. For the rest, let us be at peace. It’s fundamentalists, like you, who make things more difficult for everyone.
I have used many flavors of LaTeX and related reference management systems. Overall, it’s not any better, or worse, than Word + EndNote.
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February 11, 2018 at 10:21 pm
Mendeley is pretty good (way better than EndNote) and free.
Or you can use colwiz (also free and way better than EndNote).
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February 12, 2018 at 12:52 am
The advantage of LaTeX isn’t just the vastly better support for equations, though. It’s that it separates content from format. You can literally take a manuscript and apply a format of a different journal and you’ll get a manuscript formatted to that journal’s requirements. If people agree that manually entering references is stupid, why accept manually reformatting manuscripts?
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February 12, 2018 at 9:24 am
Good point, Jonathan. The question then is: is it worth spending the time to learn LaTeX to have that quicker reformatting advantage? (ignoring other possible advantages, for now)
My papers are readily accepted by all publishers the first time around, so I don’t even know what reformatting is. /s
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February 12, 2018 at 10:58 am
How does lAtEx do at the reformat down to 4,000 words from 5,000 words JB? And in reformatting the author declarations / acknowledgements from one blurb to three subsections to separate docs? Unstructured to structured Abstract?
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February 12, 2018 at 11:45 am
I was given a copy of Reference Manager (possibly illegally I see in retrospect) from a professor in undergrad for writing my senior thesis. It was clunky, late 90s era Windows software, but it quickly made clear the value in creating a reference database. When I began working in a lab as a grad student my PI had a disc for Endnote that circulated around. I mostly recall everyone finding it terribly unstable, and no one wanted to pay for newer versions.
This led me to discovering Zotero, which at the time existed only as a plugin for Firefox. Its long since become a standalone program with nice plugin support. I don’t mind the storage limitations as I’ve never found much value in storing PDFs online. My database automatically syncs between devices, which is all I really want in being able to work from any computer. My uni purchases a license for RefWorks for any student or faculty to use free of charge. Even with free options (Zotero, Mendeley) and the provided license I still have encountered a student manually formatting references.
Very little experience with LaTeX outside formatting equations in my thesis, and I agree with others that its a tough sell in biomedical sciences.
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February 12, 2018 at 1:44 pm
For people worried about the learning curve with LaTeX, try Overleaf. It has a WYSIWYG editor that can toggle to the code, so you can slowly start checking out the syntax without freaking out about manuscript “deadlines.” It also has easy version control if you’re scared of git. It’s also free, and I don’t work for them.
The biomedical sciences are headed for LaTeX. I’m editing a special issue of a fancy biomed journal, and some of our authors (bless their hearts, and I mean it) are forcing the journal to accept their manuscripts as pdf (rather than docx), because the authors do all their work in LaTeX. And they should, because it is the sensible approach when you have a lot of equations–and I hope equations become more common. In theory it also allows you to recompile figures and the paper automatically as new data come in, but I rarely do this.
I tried co-authoring a paper a while ago that was entirely in markdown with Paperpile. That was inelegant. Also inelegant is using reveal.js with Mathjax instead of Keynote, Beamer, or Powerpoint, but if I need something so pretty that it garners compliments, it works like a charm.
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February 12, 2018 at 4:25 pm
I teach my students about reference format. The fact that the biomedical sciences don’t have just one format (like APA, or MLA) causes constant mass confusion. Then I teach my students about End Note, Refworks (free through our library), Zotero, and Mendeley. You can see the lightbulbs go on over their heads that this is SOOO much better! I think End Note is actually on it’s way out- looks like Mendeley may overtake it soon.
But of course we have some sticklers in the department who insist on doing things manually. They are also the same people who would not allow our major to pick one consistent style to use for all student work.
As for the LaTeX people out there- the fact that you keep citing how math uses it is NOT a selling point. Who would ever take writing advice from a mathematician.?!
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February 13, 2018 at 9:32 am
As for the LaTeX people out there- the fact that you keep citing how math uses it is NOT a selling point. Who would ever take writing advice from a mathematician.?!
I can feel the burn from here.
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February 13, 2018 at 4:09 pm
Ugh I hate Endnote. But I do use Mendeley (which isn’t perfect, but gets the job done, costs nothing for now, and has never corrupted my files when I was facing a rapidly approaching deadline).
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February 13, 2018 at 8:25 pm
“They are also the same people who would not allow our major to pick one consistent style to use for all student work.”. Who cares about this? Honestly, why would that matter to anyone enough to keep tabs on who is preventing this homogenization of style?
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February 14, 2018 at 6:10 am
It’s true that unstructured things like acknowledgements would still have to be manually reformatted; LaTeX isn’t magically intelligent. But an awful lot of other changes between journal formats are very automatable and LaTeX handles them well. I haven’t heard about GUI front ends like Overleaf, but they sound like they might make LaTeX less scary for beginners.
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February 14, 2018 at 10:48 am
I’m trying to convey that reformatting a manuscript for submitting to another journal is never a process that can be automated like reference styles can be.
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February 15, 2018 at 8:01 am
When I was in academia, I used LaTeX to write the research plans for R01 applications. They were beautiful aesthetically and a lot easier to make beautiful and properly formatted in LaTeX than in Word. I enjoyed the learning curve — but maybe that’s my personality. I tried submitting LaTeX files to journals a few times, but I found that they would just ask for Word files anyway and quickly gave that up.
Not being in academia anymore …I work at an agency that helps pharma companies publish. We need to archive all edits/changes and tracked-changes in Word makes that possible. We used Mendeley for years and recently switched to Endnote, which has caused headaches for the writers. We basically cannot create the bibliography until the very very end — and realize how eff-ed up it is because fields were entered incorrectly in the database and the database will need to be fixed before submitting.
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February 15, 2018 at 3:47 pm
About the latex vs MS Word “controversy”.
I’m a long time user of Latex, probably from before you were born. . .
But MS Word is really good. It’s just that most people don’t know how to use it properly. I couldn’t believe some of the messed up MS Word documents with a mishmash of different fonts and styles that experienced writers send me.
If you are concerned about separating content and format, then learn to use use styles and themes.
Also, in the latest version of word (Word for Office 365) you can type your equations in latex style
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February 27, 2018 at 8:57 pm
Main issue with Mendeley is it’s owned by Elsevier, and is therefore inherently evil. Some colleagues in Pharma (i.e. no academic library access) are reporting on problems with Mendeley not allowing usage/citation of articles that are not documented to be purchased or owned by the company. Wait till Elsevier bricks your Mendeley database when the library chooses to unsubscribe from a journal. What about citing things where you’ve only read the abstract on PubMed (C’mon, you know you do it) and Mendeley checks to see if you’ve actually downloaded and read the PDF before allowing you to cite it?
When the product is free, you and your personal information ARE the product.
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March 1, 2018 at 12:37 pm
Only if it is non open-source. There really are free things that are free without secret strings attached. Zotero would be the most Mendely-like thing in that category.
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March 1, 2018 at 2:10 pm
No grant was ever won or lost on how it was referenced. As the Wiccin’s say, “An it harm none, do what thou wilt”.
Except use LaTeX. That crap is way too complex for a job that just simply isn’t that hard to do.
I use Papers. It’s simple, inexpensive, and easy to use. I can focus on writin’ zee science, not silly formatting asshattery.
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