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Lately I’ve been reading a lot of scientific papers. One of the tools I’ve been using is Skim, a free PDF viewer and note taker for Mac OS. Let’s have a peek at it.

skim-logoSkim is available at sourceforge.org. As I write it’s up to version 1.3.19*

They advertise it as being for reading and annotating scientific papers, but it ought to have wider uses with anyone who uses PDF files.

Best feature so far? – split view, which proves useful for viewing figures and body text referring to them at the same time, or to have the references section at hand while you are reading the text.

The initial overall presentation offer few surprises, it’s a viewer, so you get what you might expect: a large window with the contents, a table of content panel to the left (that you can close, and I typically do). To the right you can bring up the notes panel. Across the top is a Toolbar with a range of buttons, that you can customise. (Select ‘View > Customise Toolbar…’ The additions to the right of ‘Add Note’ are in addition to the default tools.)

skim-toolbar

It’s good to see the customisable Toolbar – something I don’t see in enough applications.

You can toogle the Toolbar on and off using command-B. I’m a fan of being able to gain vertical screen height in large document windows, particularly when you are using a laptop, so this is a plus.

Bookmarks can be filed for later reference; there is an accompanying bookmarks editor.

When reading a reference, clicking on URLs and DOIs will bring up the web page or article, respectively.

Pages can be zoomed to fit in the usual ways, including command + and command – to enlarge or reduce. The full list of options are under the ‘PDF’ menu.

Under Preferences there are options I have not tested to allow the document to reflect updates, which should prove useful to those working with TeX, LaTeX or LyX. (Now updated to a new major release since the version reviewed in that link.)

skim-annot-eg-337pxA range of annotations can be added to the document. I’ve shown a mock example to the right.

You will need to save these annotations (command-s). Documents with notes that have not been saved are marked as ‘dirty’ under the list of open documents under the ‘Window’ menu by a solid bullet mark placed to the left of the file. (A tick is placed in front of the current open document.)

You can these have either stored as meta-data associated with the file, or as a separate file.

One catch with storing added annotation as meta-data is that the meta-data can be lost if you email the file to someone else, unless you first bundle the meta-data before sending the document.

To save the annotations as a separate file, select ‘File > Export…’ You will be offered use a file with the same name, but with an extension of ‘.skim’ rather than ‘.pdf’. It seems best to stick to the scheme of using the same filename and set the Preference ‘Automatically save Skim notes backups’ – this way when you save the notes, they will automatically be exported to the accompanying .skim file.

You can edit the colours, lines, borders, etc., associated with the annotations. To edit each element, use ‘Tools > Show Lines’ or ‘Tools > ‘Show > Colours’. The default values can be altered in the Preferences.

You’ll notice I’ve been writing ‘annotations’ rather than ‘notes’. I consider it an annotator rather than a note taker, reminiscent, say, of annotations in Google Docs, for those familiar with that. The written notes are too brief to be considered notes to me – think stickies or scribbles in the margins, rather than notebooks.

Annotations added to a file will not appear in Finder’s Preview of the PDF file, regardless of how you choose to store the annotations. If you select the .skim file, you will see a preview of the lines, circles and remarks you have added.

finder-file-infoA tip for those less familiar with Finder and who decide to use skim regularly. If you select any PDF file, open the information about the file (command-I), as shown to the left, open the ‘Open with’ section, you can select that all files of that type be opened with skim.

I’ve selected the section of the info panel to the left to show off a few features that might be useful to readers.

You can add comments that Spotlight, Mac OS’ internal search engine, can search for. This might appeal to those that like to add meta data to files.

The ‘More Info’ section has details lifted from the PDF files, e.g. the title and authors of the article. In this case the descriptor gives the citation and DOI.

(For those curious about the paper in the example, I have an interest in methods used to determine and explore the three-dimensional structure of genomes.)

Before anyone asks, yes, you can page your way through the preview at the bottom! In fact, the example is on the second page.

If you place your mouse over the preview two arrows will appear to let you paginate through the file. (Illustrated below.) Double clicking the preview will open the file.

Downers?

There is no keyboard shortcut to move to the start or end of a document (you can do this via the ‘Go’ menu, which will offer ‘First’ and ‘Last’ as options when appropriate.)

When you have an item selected in the bookmark, command-O does not open the file selected but the panel to open a brand new new file.

Rendering of an image with many components can still tie up CPU. This may not be the developer’s fault, but I’m left wondering if generation of images/graphs would ideally be a background process if possible. Caching might help too: each time you re-encounter a noisome graph, the CPU gets tied up anew. This ties up the whole program, you can’t ’escape’ this by grabbing the scrollbar and dragging the focus away from the offending image.

Things I’d like to see? (These favour my use, of course – your preferences might be different.)

  • More powerful bookmarking, ideally with tie-ins to bibliographic tools.
  • Genuine note-taking. (Here it would be good to exploit that developing a basic editor using Apple’s built-in code classes is trivial.) This, of course, could be extended almost endlessly and you do have to draw a line at some point.

Final thoughts?

It’s an excellent addition, well worth checking out.

Footnotes

* The version I have used here is 1.3.18.


Other articles on Code for life:

LyX for free word-processing

WWW database servers on Mac OS X 10.6.x, part I: Installing MySQL

Mac OS X — quickly inspecting the contents of a file

Apple drops another cat at your door

What use now is handwriting?

How did you learn to critique the scientific literature?