Using Scrivener for scientific writing

I am a new user of Scrivener 2.8 for Mac. I am in academia/science and most of my writing includes tables- typically consisting of 3 columns and 20-25 rows. My questions are per below:

  1. Is there a smooth way to interface Scrivener with Microsoft excel content, so that I can see my excel datasets easily? If I create a link to the excel file in scrivener, will the link get updated whenever I update the dataset? Any additional tricks to make this process smoother?

2)I am having a hard time using the inbuilt tables in scrivener. For instance, when I copy a group of rows from one table to the next, it pastes the content of multiple rows into one row. I have not yet figure out how to overcome this problem and would greatly appreciate any insight/tips/tricks to make this process and in general working with tables easier.

  1. Are there scrivener forums/websites/youtube videos that are geared towards those using the app for academic/scientific writing (for instance to discuss issues such as references, tables, figures, etc)

Thanks very much!

Hi axf10,

I’ve used Import > “Research Files as Alias…” to import excel files into my research folder in Binder before. You get a Quicklook view of your excel file and it makes referencing your data while writing in split view relatively straightforward. Open in external editor makes it easy to launch excel. You can also import the XLSX file directly and then have it properly part of the project (less likely to break links).

I don’t use tables much so can’t comment much on your other questions. I’m not sure if a markdown workflow (which is better for academic/scientific writing overall IMO) would be more flexible in this case as markdown tables do have some limitations in formatting. But for example I vaguely remember there are some tricks to import CSV files as a markdown table, so you maintain the CSV files and a Pandoc workflow would render them into tables…

Can you please tell me more about “markdown workflow”? Where can I find additional information? Thanks again!

My two cents (I am a long time users of Scrivener and a full time scientist/academic, professor in a US Department of Psychiatry, neuroscientist, and writing science all the time):

You eventually will have to compile your manuscript in something else that is not Scrivener. I would add all these other elements to your manuscript when you need to get out of the Scrivener environment. Scrivener is an amazing organizer. I’d definitely use the Research Files alias option to have quick access to data you need to have access to. But I wouldn’t agonize over tables and figures and indeed you may even decide to use your favorite reference manager after you compiled. Also, you are not gonna find many people using Scrivener, which means your collaborators eventually will force you to get your manuscript into a Word format

I work in a similar way that marcoiac suggest.
Create rough figures from my data and keep the figures in the Research section, and finalize tables in Word. As for references, I use Papers 3 which integrates fairly well with both Scrivener (citekeys) and Word (creating reference list).
Markdown? No, I don’t see the point of introducing a third way of handling my manuscript. The journals want Word-files.

The major point about markdown is that you can generate a well formatted document with proper outlining for any output format including Word without much effort. Without markdown I see many people having to do a tedious search replace of formatting into styles to generate the hierarchy in Word from Scrivener directly. Then they need to deal with things like quotation style and figures with captions etc… In markdown you simply use a specialised syntax and heading styles, quotations, citations, footnotes[1] and figure / table captions are all created and styled in Word without any other intervention. I would argue the easiest way to get a well laid out, properly styled Word document for a journal is to use Scrivener with Markdown (using Pandoc for conversion). Perhaps when Scrivener 3 comes out this will change, but until then RTF export to Word loses too many features to make it worth it (IMO)…

To find out more about markdown, there is a subforum here dedicated to it, and Chapter 22 of the Scrivener user manual. Basically markdown is a structured writing system, so:

#Important finding

…is a major heading, in word it will get the “Heading 1” style without any manual intervention.

![Figure 5. This is a caption](fig5.png)

…will become a styled figure with a styled caption without any work on your part. I personally prefer to use Pandoc for final conversion which works well if you use Scrivener compile to markdown.

[1] Scrivener footnotes are converted to markdown automatically on export so you can still benefit from Scrivener footnotes.

I agree with nontroppo. The inalienable robustness of markdown makes it the most reliable writing medium I have yet found. No more time wasted rectifying problems when bold, italics, headings, etc go missing in the garbled world of Word and RTF and HTML and …

With markdown, the “formatting” can never be lost because it is hardwired in the DNA of the writing itself. It is a beautiful way to work, if your brain functions that way.

yeah, if you do know markdown, you definitely want to use it in scrivener. if you don’t know it, given the steep learning curve, i am not sure it’s worth investing your time on it, since after you move your document into, say, word formatting, there will be many more changes due to collaborators comments and edits, reviewers critiques, journal editors corrections, and, for grant application, your institutional grant officials changes, the uploading system your institution uses to upload your grants, etcetera

if your final output needs to go through many other stages outside scrivener, not sure it’s worth your time to learn multimarkdown

I solve it by not using bold, italics, headings, etc, until the manuscript is getting ready for submission. Why bother with that while writing?

My point is that even if you need to go outside of Scrivener, the conversion pathway scrivenerMarkdown>pandoc>word automagically creates a more robust and well formatted Word document than scrivenerRTF>word — I spend less time in Word before sending my revision to my collaborators.

I’ve recently switched over to using Pandoc citations directly, so I don’t even need to scan my document with Bookends/Endnote anymore, my bibliography is already well formed. Again, “normal” writing using ScrivenerRTF and you need an extra step in Word.

My major time waster is dealing with collaborator feedback from a Word document, but that is the same issue whether writing in RTF, Markdown, or Klingon; it is a problem when dealing with non-Scrivener users

Yeah, that’s something I almost invariably do too :slight_smile:

I guess I just give up using Scrivener (and switch permanently to Word for a given project) when anything I worked on leaves Scrivener land. I know that it’s a major time waster to reimport data into Scrivener

Most of the times I don’t even use Scrivener anymore for specific projects because I don’t even write first drafts anymore. Still an incredibly useful app for organizing material, note taking, etcetera. And for short write ups like reviews. But in those cases formatting is not even an issue

I’ll have to check your Pandoc citations thing though, at least for fun!

For me, it’s easier to “format” as I write, rather than going through tens of thousands of words afterwards and adding italics etc at a late stage. And with MMD, I never lose formatting in the way that RTF, Word, and others regularly lose and corrupt formatting.

Personally, markdown didn’t present a steep learning curve…especially for the basics, such as bold, italics, and headings (my brain just works that way, I guess). And, of course, you can persuade others to use Scrivener and MMD. :stuck_out_tongue:

Complete respect for other people’s preferences.

Well, scientific articles seldom consist of tens of thousands of words, I think? I had to check it up. Five thousand words are more like a normal article, and the tricky part is not the text, but tables and figures. And the statistics. And the logic. And actually reading all those articles one refer to.

But Scrivener is superb for getting the logic flow, keeping figures and tables together with the manuscript in a handy way, and simply simplify the writing process. As for headings, italics and such, different journals have different standards so I will have to change the text in the anyhow.

Irrespective of length, I prefer to use MMD for its reliable robustness.

Have done a lot of scientific thesis / dissertation writing and copy-editing; most works in excess of 100,000 words. When writing for clients, I use the Oxford Style Manual ( … b&lang=en&). If clients have their own in-house style guides for publishing, they can reformat and typeset as they wish.

Appreciate that we all have different ways of working. :smiley:

Simple formatting is very easy, but Tables less so, and if you want to have the whole arsenal, including critic markup, it does require a little learning. The real problem though is what you said, since not many people use it (at least regular academics/scientists), you don’t practice it much and I often wonder if it’s worth the effort given the little payoff you have when you collaborate with others on scientific writing

For me, it is. Even if only at a first-draft stage. The integrity of my own work.

But not for everyone.

Thanks so much everyone for your help!