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Step 5: Convert paper to LaTeX by hand using old templates from last (still unpublished) paper and (still unfunded) grant application.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.