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Course Info: HSCI 3013 - section 995 - Fall 2008

A Digital Academic Workflow

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There's more than one way to skin a cat, and more than just a few tools for creating a paperless workflow for academic research and writing. I've noted some of the possibilities on the Affordable Mac apps for academic tasks page. On this page I'll sketch some of my favorite apps and my own strategies for using them. But people have different working styles, and various projects have different needs as well. Maybe these tips will give you some ideas, but the great thing is how many excellent choices are available for academic projects on the Mac.

My basic workflow involves these applications:

See the comments on the previous page about each of these apps, but here are some tips and strategies for putting them together into a coherent workflow consisting of three stages: Research, Draft, Polish.

  1. Research
    1. Initial set-up
      1. To begin, open Sente and create a bibliographic record for the source. In this case, suppose the source is a journal article.
      2. If the source is a printed photocopy, scan it using DEVONthink Pro Office to create a pdf with an OCR-generated text layer (DevonThink Pro Office's OCR is excellent, although Acrobat Professional can also convert to text). Then export the pdf from DevonThink for management in Sente (next step). If a pdf is not likely to be cited, it may be best just to keep it in DevonThink.
      3. Use Sente to see if a digital version of the source is available, and if so, Sente will create a bibliographic record and download the file. Use Sente to catalog, find and display all pdfs that are likely to be cited in any project.
      4. Open DEVONthink and create a source folder that will contain quotations and notes associated with this article. Create this source folder within a folder for the currrent project, or whatever folder hierarchy seems most useful for organizing the research.
      5. If desired, create separate folders within the DT source folder for primary and secondary notes (place quotations in the primary folder and comment notes in the secondary folder).
      6. Create a hyperlink from the DevonThink source folder for the article to the Sente reference. This hyperlink will enable quick switching to Sente from DT, even if Sente is not open, and it will open Sente to the linked record.
    2. Take notes
      1. Go to the Sente record (using the DT link), and view the pdf. Tip: If using Skim, then in OS X preferences, set Skim as the default pdf reader, so that the pdf will open in Skim for markup.
      2. Sente supports automatic importation of quotations and images into notes. Take simple notes within Sente; transfer to Devonthink when finished or when notetaking becomes more complex.
      3. In Sente, identify passages worth quoting:
        1. Use commenting and markup tools to annotate the article in Preview or Skim. Highlight passages worth quoting. Note: Preview in Leopard has excellent commenting and highlighting tools, and although it lacks automated exporting of highlighted passages, Sente will do this quite easily.
        2. Create simple notes containing passages worth quoting one by one in Sente. When ready to transfer them into the DevonThink source folder, just drag and drop selected notes and/or the entire reference (including all notes) from Sente into the DevonThink source folder, perhaps in a "Primary" source folder. Split it into multiple source notes, if desired.
        3. If an article is central enough to the writing project to make it worthwhile, index the article in the DevonThink source folder. This makes the entire content of the article, not just the imported highlighted quotes, accessible to DT's artificial intelligence functions. However, it's a good idea not to dump everything indiscriminately into DT; the human brain should play a pre-processing, filtering role.
      4. Switch back and forth between Sente and DevonThink as needed. Write detailed analytical notes in DevonThink:
        1. Take notes, write summaries of important points, and make comments on the article in the source folder in DevonThink, perhaps in a "Secondary" source folder. Keep notes relatively short, in chunks. Multiple shorter notes are better than fewer long ones. It will be easy to combine them later, if desired.
        2. To create a citation in a note that will carry over into Scrivener and Mellel, drag and drop a Sente reference into DT. This will produce a bracketed citation appearing something like this: {Aaboe, 1958, 5, 209-277}.
        3. To format text (e.g., italics), use the Styles drop-down menu on the DevonThink ruler. In general, minimize formatting; save that for final polishing in the word processor. However, type non-Roman characters in Unicode.
        4. Organize and edit selected notes using DevonThink features such as drag and drop re-ordering of notes, outlining, and note merging (Data Menu).
        5. If desired, Replicate or duplicate selected notes (Data Menu) to facilitate classification. (Replicated notes will not go out of sync since any changes made to one will immediately appear in the other. Duplicated notes allow one to preserve a copy with the original content when the duplcated copies are edited.)
    3. Repeat the note-taking process with other sources, whether print or digital, books or web resources, primary or secondary.
    4. When a project becomes more focused, export to OmniOutliner or Scrivener to prepare the draft.
  2. Draft
    1. Create a new project in Scrivener for producing a draft. (Others might use OmniOutliner or Circus Ponies Notebook in this role, but I prefer the elegant drafting environment of Scrivener.)
    2. Drag and drop selected DevonThink notes from various source folders directly into Scrivener. It's that simple!
    3. Identify additional related notes that might be useful using DevonThink's search features (including fuzzy searching) and artificial intelligence (for example, the "See Also..." button and the Concordance). At any time, drag and drop them into Scrivener also.
    4. Integrate Scrivener and Sente: Command-Y works in both. In Scrivener it takes you from Scrivener to Sente and in Sente it takes you from Sente back to Scrivener and pastes in a citation to the active reference in Sente.
    5. Organize and edit selected notes into a coherent draft using Scrivener's powerful features such as note metadata and keywords, drag and drop re-ordering of notes, outlining, note splitting and merging, multi-pane comparison of notes and media, split-window editing and full screen writing.
    6. Export as .rtfd for importing into Pages.
  3. Polish
    1. Import the .rtfd draft into Pages. Both Pages and Mellel will preserve Sente citations from DevonThink and Scrivener, and both will preserve footnote text from Scrivener. Pages (but not Mellel) will preserve Scrivener annotations.
    2. If using Mellel,
      1. Convert draft styles to Mellel "character styles." In Mellel, choose “File –> Replace Styles...” to change imported styles to appropriate character styles (e.g., change all italics to Garamond style, italic variation). After changing to appropriate character styles, then choose the appropriate paragraph styles (e.g., Body). Note: It is important to replace character styles before changing paragraph styles; selecting the Body style before changing character styles will result in loss of italics and other character formatting.
      2. Then convert the temporary legacy citations in the draft into citation objects. Choose Edit – Bibliography – “Convert Text to Citations...”. (After converting, and before scanning, if using footnotes instead of in-text references, and if citations have not already been marked as footnotes in Scrivener, then create the footnotes and move the citation objects into them.)
      3. Format headings to best utilize the outline view in Mellel.
    3. Complete the final polishing of the text and layout in Pages or Mellel.
    4. In Sente, choose Scan document or in Mellel, press the "Scan" button in the Bibliography pallette, to convert citation objects to formatted footnote references and to add a formatted bibliography.

Then publish!

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HSCI 3013. History of Science to 17th centuryCreative Commons license
Kerry Magruder, 2004

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