Every Wednesday night, between 19:30 and 20:30 UK time , a ‘brood’  of doctoral researchers from different time-zones gather under the Twitter hashtag #phdchat, for a synchronous chat about different aspects of doctoral research. The week before last, the selected topic was the Literature Review. I mentioned that I often used Skim alongside Scrivener (on a Mac), and was asked if I could explain my workflow a bit, which is what I’ve tried to do here.
Please bear with me: these are not comprehensive instructions for these programs, but a brief introduction to each of them, followed by a description of how I integrated them into my thesis-writing workflow. Feel free to ask questions in the comments and I’ll do my best to help, or better yet, refer you to better source to provide you with answers :)
(I used a fantastic little program called ‘Skitch‘ to add the numbers, arrows and circles to the images in this post)
First, a bit of an introduction to the software:
:!: Skim is open-source software, but currently only available for Mac OSX.
Skim is a PDF viewer that has added functionality of a powerful note-taker. You can highlight, underline, and enclose shapes sections of the text of a PDF. You can add your own notes and annotations – either directly onto the PDF, or ‘anchored’ to a particular location within the text. The ability to take ‘snapshots’ enhances the experience by allowing you to ‘grab’ areas of the PDF into notes, and that includes images, charts, tables and figures.
Reading and taking notes electronically is not for everyone, or for all circumstances, but it can be very useful. This is just how I did it. I would read the hard copy of a PDF and make my notes by hand in illegible scrawls, THEN input my notes into the electronic copy in Skim. Why? Because Skim allows you not just to view your notations on screen, but also to search, edit, and add to your clippings and notes, and to export these to a Rich Text Format document (RTF), which you can then import into your writing program or your bibliographic database, in fact any application that can handle text. We’ll come back to Skim in a moment.
:!: Scrivener 2.0 is for Mac OSX, but a Windows version is currently in beta testing phase- and also a Linux version.
Scrivener is a powerful ‘content-generation’ tool. It is so much more than a ‘word-processor’, with it’s capability of handling huge projects (a 100,000-word novel or thesis doesn’t tax it in the slightest) in multiple sections, drag-and-drop functionality, notes and keyword integrations, integral handler for imported documents, images and more. And yet at the same time, Scrivener is so much less than a ‘word-processor’- in all the right ways – reducing clutter and redundant functionality, removing irrelevant software bloat.
Don’t be daunted though: Scrivener puts you firmly in charge as master of your writing and research, with a fully customisable interface and comprehensive keyboard shortcuts. You can use as little or as much of its power as you choose – nothing gets in the way. Scrivener’s raison d’etre is to get you to the completion of a first draft (or second, or third…).
I first tried out Scrivener back in the early days of my research (2007), when I was looking for software that could file and retrieve all my research-related scribblings, annual reports, and conference abstracts in a single, freely-accessible place, yet allowed me to search across all the different types of document, and to use the text as a basis for writing my thesis. Scrivener came up trumps, and by a long mile too. It has come a long way since then, the most recent overhaul to 2.0 being an absolute bargain at only $45 (currently £29.59) full price, with an educational licence being a mere £25.15. Frankly, you can’t afford not to have this tool in your research armoury. If you’re not sure, you can download the fully-functional free trial and take 30 days to find out how Scrivener can work for you. That’s 30 days of use, not just 30 days from download date, so take your time :)
How I used Skim with Scrivener to write my thesis
In this section I assume that you have had a little experience of the software. Workflow is a very a personal thing. There is no holy grail or magic bullet: you must find out what works best for you, and be aware that this might change, as your research and writing progresses, and as your expectations of your workflow increase (they will). Both Skim and Scrivener are extremely powerful and flexible – I doubt I’ve encountered even half the possibilities – so, with the caveat that this is just my workflow, not the workflow, I’ll get on with it.
Skim: Annotate your PDF
Open your PDF in Skim, and annotate it. Here I’m just using a recent published article related to my doctoral research. In the screenshot below, I have closed the Contents pane and opened the Notes pane (to the right of the document).
First select the ‘Text Tool’ button
This makes the ‘Add Note’ functions available. Here I’ve used:
Text Note (shown in pale yellow)
NB I have started the note with ‘!’ to indicate to myself that it is a ‘to do’ item.
Box (shown in green)
Anchored Text Note (shown in pink)
Highlight (shown in orange)
Skim takes the text you input or select, and indexes it in the Notes pane on the right of the application.
All these notes can be edited in the notes pane. For this example, I have:
added some of my own thoughts (a crude summary of Berridge’s position) to the Anchored Note
added my own note to the Highlight (where I have identified a link to a paper I’ve already read).
Skim: Save your PDF and Notes
So, you’ve now got a whole load of notes from the PDF paper you’ve read and annotated with Skim. Be sure to save the document. Before we go any further, it’s worth knowing how Skim handles notes, annotations and the PDFs so that the next bit will make more sense. I quote directly from the Skim documentation:
“Normally, Notes and highlights you add to a PDF document are not saved in the PDF data, but are added to the file as extended attributes.”
Because of this, you have several options, but I will focus on four which are (to me) most useful in different circumstances:
Save PDF as normal
Why: You want to edit / add notes at a later date, in Skim.
How: File –> Save As… –> “PDF”
Result: Skim saves the PDF with notes in the extended attributes.
:!: When you re-open this file with Skim, it will be as you left it, and you can edit and add more notes.
Other PDF viewers may not be able to display the extended attributes, in which case the PDF will be displayed as it was before you annotated it.
Sometimes, if you send your annotated PDF over email, the extended attributes are stripped out, and the recipient will therefore see the PDF displayed as it was before you annotated it.
Save the PDF file with notes and highlights included
Why: You want a copy of the PDF in which your notes are visible in other PDF viewers.
How: File –> Export… –> “PDF With Embedded Notes”
Result: This makes a copy of the file, and will “flatten’ the PDF. Your notes will be incorporated in the PDF data.
You will be able to view your notes and highlights in other PDF viewers.
:!: You will NOT be able to edit these notes if you open the resulting PDF in Skim: the notes have been embedded into the PDF.
To edit your notes, go back to the copy you saved in ‘i.’ above.
Save the PDF and Notes in a bundle
Why: You want to send the PDF with editable Notes by email, or you want to archive it.
How(1): To save: File –> Save As… –> “PDF Bundle”
How(2): To save a copy: File –> Export… –> “PDF Bundle”
Result:This will result in a “package” (essentially a folder with files in it, that Mac OSX handles as a singular entity) containing the unmodified PDF and files containing your Notes.
To see the contents of the package, use the Finder to navigate to the file, and select ‘Show package Contents’ from the contextual menu. You will see that the Notes have been saved in two different formats: RTF and TXT.
If you send the package over email, the Notes will accompany the PDF to its destination.
Save Notes and Highlights as text
Why: You want to use your notes elsewhere – such as in Scrivener, in your research database (e.g. DevonThink), or in a bibliographic database (e.g. EndNote; Zotero; Mendeley; BibDesk; Sente; Papers; etc).
How: File –> Export… –> “Notes as RTF” or “Notes as Text”
Result:This will result in an RTF file containing your notes. When opened in Text Editor, it looks like this:
I used a combination of i. and iv. to integrate Skim with Scrivener. It makes sense now to get your notes back into Scrivener where they are searchable and easily available to you whilst you write. It also makes sense to have them connected in some way to the PDF, so you can refer to it later if you need to clarify your notes. So here’s how I do just that.
Scrivener: import your PDF, then open it with Skim
Import your PDF into Scrivener by dragging from the Finder and dropping into the relevant part of the file structure in your Scrivener project.
Here, I have created a folder called ‘Papers’ in the ‘Research’ folder, and imported my annotated PDF (see Section ‘i.’ above) into it. :!: Scrivener makes a copy of the PDF and inserts it into the Scrivener project package. This is important to remember: if you wish to edit this version of your PDF, you should open it from within Scrivener.
Open the selected PDF by clicking on it in the binder so it shows in the editor. :!: Note that Scrivener’s PDF viewing framework does not show your Skim Notes. That’s ok, they are still there, and will show up in Skim in the next step.
Select the ‘Open in External Editor’ button in the status bar. :!: Note that this button remembers the last programme you used to open this file: if It wasn’t Skim, or if you are unsure, then you’ll need to click and hold the button to access a list of applications from which you can choose Skim.
Your PDF will open in Skim, and your Notes and annotations will be visible, searchable, and editable as usual. Now we have our PDF exactly where we want it for quick reference – right inside the Scrivener project. Let’s get the Notes in next.
Scrivener: import your Notes
This is a process that you may want to repeat periodically to ensure the Notes in Scrivener are up to date with the latest version of the Notes you make in Skim.
Open the RTF file. Select the text [cmd + a] and copy it [cmd + c]
Back in Scrivener, ensure the PDF is selected in the binder and displayed in the editor (see A and B above).
Open the Inspector [opt + cmd + i]
Ensure that Document Notes are visible, and paste in the text [cmd + v]
Now your Notes are attached to, and associated with, the PDF inside your Scrivener project – they are accessible and searchable whilst you are writing up. Here’s how I used this in my Scrivener writing workflow:
:!: The default behaviour of the inspector is to show metadata from the currently-selected editor pane (i.e. the one you are editing). So to make sure the Document Notes of the secondary pane (where your PDF is displayed) are visible, select the 2nd editor pane, and then ‘lock’ the inspector by clicking the padlock icon, indicated in the image by ‘!’. Then, when you return to your working document, the PDF notes remain visible.
That’s it. It looks long and difficult, but it isn’t really, and once you’ve done it twice it’s easy to remember :D
 UK time is UTC/GMT, with Summer daylight saving (UTC/GMT+01:00) between the last Sunday in March and the last Sunday in October. See the London page at timeanddate.com for clarity.
 There is another way. You can select your Scrivener project in the Finder, and open the package by selecting “Show Package Contents” from the contextual menu. The PDF will be saved in the folder called “Docs”, but will have been given a numeric file name (e.g. ‘342.pdf’). You can open the PDF from there. But this method isn’t really advised: inadvertent changes to the Scrivener project package from outside of Scrivener itself can have DIRE consequences. You have been warned.