My digital social science engine

I’ve spent a considerable amount of time optimising my workflow and identifying the right software for each step. As a result I’m indebted to lots of other nerdy knowledge worker blogs on the web.

Let’s go!

An admission: I do love and support Linux. However, since a former employer had Mac OS running, it gave me sort of a rationale for my betrayal. So the setup I’m presenting is for Mac. Some of the software is available for Linux and Windows, too.
Love Linux!

1. Search: I mostly use G**g**-Scholar for search. I do so with the free and open source browser Firefox and two plugins: Zotero and the Zotero-to-BibDesk auto-import utility.

Firefox

2. Research library: The Zotero-to-BibDesk auto-import utility syncs my Zotero database with my Bibdesk database. The free and open source Bibdesk allows me to save my reference data in a Latex format with uniquely identifiable and portable reference keys. Bibdesk also serves as an iTune-like research library, where I can assign keywords, comments and ratings. I can also tick whether I’ve already read a text or collect texts in a reading list.

Bibdesk

3. Annotation: From inside Bibdesk I can start the (once again) free and open source PDF reader Skim. Skim allows me to highlight and comment PDFs. After having done so, I can copy everything highlighted or commented to a text editor, complete with an indication of the relevant page numbers.

Skim

4. Page number adjustments: Often the digital PDF page numbers and the nominal page numbers of ebooks and journal articles will not be congruent. This will impinge upon the page numbers indicated after copying from Skim to your favourite text editor. It’s a hassle to adjust the page numbers for each individual entry. For page number adjustments I have only found one solution: Adobe Acrobat Professional, which comes with a rather hefty price tag (particularly considering that you only really need it for this one task). It can save lots of work, though.

5. Database and draft editor: I use Scrivener as a database and for drafts. It’s lightweight, has tons of functions and hardly every crashes. It’s great as a complex outliner (for simpler outlines, I recommend OmniOutliner). Scrivener is proprietary but value for money. You can just copy your highlights and annotations, from Skim, alongside the citation keys from Bibdesk, to Scrivener and then rearrange them according to the structure of your research project. If you do it properly, you will always know what are your own thoughts and what you took from which page of what publication, thus avoiding plagiarism.

Scrivener

6. Compile it all into a beautiful text: I use TexShop for setting the final text in LaTex. TexShop works harmoniously with Bibdesk. Of course, you may often need to exchange documents with people who don’t use Scrivener of LaTex. Then you will need to use OpenOffice or Word for the final draft. Combining that with Bibdesk is a little more of a hassle, though rudimentary Plugins do exist.

TexShop

7. Get published or die trying.

3 comments

  1. Nathan

    I use exactly the same tools and workflow that you use, but I don’t keep any references in Zotero; I use the Zotero-to-BibDesk add-on to send all references only to BibDesk. I’ve been very satisfied with this tool set for at least five years.

    I would mention that Pandoc is also a supremely useful addition to this tool set. If you write in MultiMarkdown format in Scrivener, you can use Pandoc to convert from MultiMarkdown format (or many other formats) to almost any file format you would need, and I have found that if you use hierarchical headings in your document, Pandoc does a better job of preserving them upon conversion than does Scrivener’s native compilation.

    • NinoDavidJordan

      Hi Nathan,
      thanks for sharing. By now I’m using Scrivener and Bibtex for the main structuring and Sublime Text -> Pandoc for the actual paper writing. I’m looking into linking Scrivener better with Pandoc but I haven’t had the patience to really figure it out yet.
      Cheers, Nino

      • Nathan

        Hi Nino: That’s great. Sometimes I also use other tools beside Scrivener to write, especially for shorter documents. There are rumors that a future version of Scrivener will have better (easier) support for Pandoc.

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