Thursday, November 29, 2007

Paper pieces.

Somebody really needs to write a science-specific program for compiling papers. Soon, please?

Here's what I'm doing right now, and I'm not joking about this:

Step 1: Drafting using Scrivener . Scrivener is great, I love it. But it can't do references or formatting.

Step 2: Export from Scrivener into a word processor, e.g. Pages or the trial version I downloaded of Nisus Writer. But neither of these can do references.

Step 3: Attempt to create new library of references in Endnote. I used to be able to get it to connect to Pubmed and download the papers into it that way, but for some reason today the searching function wasn't working and the program kept crashing. After 5 tries, I gave up because I didn't really want to use Word anyway.

Step 4: Rapidly and easily create new library of references in BibDesk. Yay! I love BibDesk. I love the new search function, it's super-fast and way better than Endnote. The only drag for me was I had one paper from pre-1968 and the search function couldn't find it. It's online but apparently not in Pubmed. So I had to put it in by hand. Yippee.

Step 5: Convert paper to LaTeX by hand using old templates from last (still unpublished) paper and (still unfunded) grant application. The good news is, the program will automatically put in all my references, format everything, etc. when I TeX the paper. The bad news is, the intermediate version looks like a computer program, and my co-authors will panic if I give them that.

But overall this is pretty ridiculous. While Scrivener can import other file types, there's no linkback to let you open and edit your figures easily in their native applications, e.g. Photoshop or whatever else you use.

And I don't really like the solution that you can export your text as an .rtf file from Scrivener or Nisus and then run it through Endnote after the fact- that's just lame and you have to do it over and over if you change anything?? Not gonna happen.

I love the corkboard feature in Scrivener, I use it a lot. But they should give you the option to write in corkboard mode instead of having it be separate from the text.

Scientific writing is basically always the same. Even the paragraph format could have a template. Why don't we just use templates? It's so ridiculous that we spend all this time on formatting, especially if you're going to submit a paper and then rapidly resubmit to other journals if it doesn't go out for review! Somebody needs to make an easier WYSIWYG program that can let you make custom templates and share them. What do you think? That would be a lot easier and a huge timesaver, right???

And differences that really waste your time are things like whether figures are labeled Figure 1. or Fig.1 and whether the components of figures are labeled with capital A , B, C or lowercase a, b, c and whether they're bold or not or (in parentheses) or not.

Personally, I don't care much about typesetting unless it's inconsistent. But I know some reviewers (and editors) get ticked off about stuff like that.

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At 12:27 AM, Blogger Kelly said...

I'm not as into the creative and Mac-based software tools as you, but I find your points ringing home as I write the first paper of my postdoc.

SOME journals are making what I thought were great strides by having their referencing automatically available as an EndNote output style. I still can't understand why more journals don't do this. The amount of time it takes a journal editorial staff member to make an EN output style is minuscule compared to the time hundreds of authors spend creating the same thing. Even if we don't all use EndNote, it's a start.

I agree that figure labeling is the next logical step for styling in the same way - unfortunately I can't think of a way to implement that automatically in the Word/EndNote model used by so many of us.

Anyway - right on! :)

At 1:00 AM, Blogger Mikael said...

Have you looked at LyX?

At 3:55 AM, Anonymous Anonymous said...

Um, is there a reason word + endnote is insufficient for your needs? Almost everyone I know in the biosciences uses that, with the occasional exception for people with tons of equations...

At 5:45 AM, Blogger stella said...

Why not just use LaTeX all the way and hand it to your co-authors together with Lyx or Kile - Lyx is a very nice GUI (i.e. hides the scary code) for LaTex; Kile lets you see the code a bit more but does some handholding.

I'm in CS so we use LaTex (& Bibtex) for everything. Most conferences also give you LaTeX templates so the whole thing is pretty hassle-free, especially in comparison with your multistep process (I can only imagine).

At 7:51 AM, Anonymous Anonymous said...

Connotea is a great bibliographic resource. You can export as Endnote (*ick*) and BibTex as well as other formats.

At 9:40 AM, Blogger Ms.PhD said...


You can automatically do figure labeling using the cross-referencing thing in Word, but I don't like Word so I avoid that whenever possible. Grants are the only exception where it can actually be easier to just do it in Word, except for their shitty word-wrap around inserted figures.


I tried LyX. I didn't like it. Sorry I can't remember exactly why, it had something to do with troubleshooting and having the code be hidden when I didn't want it hidden, I just gave up and went back to syntax highlighting, I like that better. And there's no way my co-authors will be willing to use a new program, even something as relatively friendly as LyX is way out of their ballpark.


yeah, I refuse to use word + endnote BECAUSE THEY CRASH ALL THE TIME. among other things like being slow and ugly, but that's the main one.


Sadly my co-authors are just not computer people at all. I actually had one of them ask me, when I told him to hit the 'reload' button on his browser, he didn't know what I was talking about. I'm not kidding. Another one is incapable of using a spellchecker.

I've never heard of Kile, though. I'm using iTexMac or SubEthaEdit, that kind of thing. I've heard TeXMate kicks butt, but I'm so overloaded with apps right now I haven't gotten around to trying it. I'm learning how to use version control...


I haven't gotten into the web-based bibliography stuff. I'm tired of passwords and the not-so-infrequent problems I have with my wireless connections at work being too slow to use sometimes for half a day or whole days, randomly. Maybe I should give it another shot, but I don't think I'm ready yet to deal with losing one more app to the internet. I know it's the future, and all that, but I hate the idea of giving up independent control and having it all live on some big computer in the sky.

At 10:23 AM, Blogger ScienceGirl said...

I am with Stella - latex+bibtex all the way. I am using TeXShop on my mac for that, and it is great. It also works well with the versioning systems that compare text line by line - so you and your co-writers can work on different sections/paragraphs and not step on each other's feet.

In the research lab I am in, nothing else goes - the advisor sets the rules. I am sorry to hear there are people out there unwilling to learn the tools of the trade...

At 10:38 AM, Anonymous Anonymous said...

i'm in a life sciences field, where latex is not often used. however, i used latex for my dissertation, as i was scared to give all of the power to MS Word (due to its crashing 'feature'). i looked at scrivener, and was initially interested, but the $$ kept me from using it regularly. i wish they had an academic discount :) if you haven't tried Papers for storing article PDFs, i absolutely love it!

At 12:18 PM, Anonymous Anonymous said...

I'm learning how to use version control...

Do you mean something like mercurial? It's quite good, a lot easier to use than Git. I love being able to pull in changes from coauthors, see colourised 'diff' output of changes between versions, and not have to deal with stupid filenames like blah-01.tex, blah-final.tex, blah-final-really.tex, and so on.

At 2:07 PM, Anonymous Anonymous said...

can you post or provide a link to LaTeX templates for biological/medical manuscripts and grant applications?

At 3:11 PM, Anonymous Anonymous said...

Well, I've written several papers, 2 grant proposals, a thesis, and a fellowship application over the last 5 years, using Word 2000 or more recently Word XP with Endnote 7. Quite frankly, they've been stable - no crashes as far I can recall, certainly nothing recently. Maybe your system has other problems?

Now Adobe PDF reader, that crashes all the time. :)


At 3:24 PM, Blogger Sacha DC said...

the rules:

1. To study a subject best, understand it thoroughly before you start.

2. Always keep a record of data - it indicates you've been working.

3. Always draw your curves, then plot your reading.

4. In case of doubt, make it sound convincing.

5. Experiments should be reproducible - they should all fail in the same way.

6. Do not believe in miracles - rely on them.

At 7:44 PM, Anonymous Anonymous said...

Looks like you caught DrugMonkey's attention again. I really don't understand that guy.

At 6:35 AM, Blogger Mikael said...

I have a growing suspicion that attitudes toward (or against, as it where) Word depend a lot on scientific discipline. In my corner of the world - Mathematics - Word is so unthinkable that you can actually make people laugh by suggesting it.

As a contrast, my wife - who works in linguistics - uses Word for everything. As do my historian friend. They both are in a discipline where the benefits from something like LaTeX are no longer quite as visible, and where the learning curve required to tackle it is significant enough for it to basically ban the TeX family from the discipline.

The only place I have seen close up that lived in between was my stint in the private sector. We'd produce the documentation for our software library in a highly automated TeXed build, but all non-software-documentation documents we needed to produce were done in Word with company template files.

As for me, I've been writing raw LaTeX code since I was in 11th grade. My English teacher in my 12th grade wanted to learn it herself after seeing my essays.

At 11:43 AM, Blogger eilf said...

Hi, having been given a brief lesson in LaTex yesterday I can say that I am with you completely on the scariness of it to anyone used to using WYSIWYG programs, though I also see it's benefits (I think). I agree with you completely that users should be able to intuitively work out how to use a program - isn't that what program designers are for?
I found your blog because endnote is crashing adobe reader 9 and I was looking for a solution - I will come back to read some more, keep up the good work.

At 11:43 PM, Anonymous Custom Thesis Writing said...

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