History of Science Online - Course Info - Time tips - Semester Schedule - Weekly Assignments - Timeline - Projects - Course Info: HSCI 3013 - section 995 - Fall 2007

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:

• DEVONthink ($39.95) for initial research and note-taking before I am ready for a focused writing project.
• Scrivener ($35) for early stages of a focused writing project.
• Bookends ($79 with Mellel) for reference management, citation formatting, and pdf cataloging.
• Preview and Skim (free) for annotating pdfs.
• Mellel ($39) or Pages for writing.

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 Bookends 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 Bookends (next step). If a pdf is not likely to be cited, it may be best just to keep it in DevonThink.
      3. If a digital version of the source is available, attach it to the record in Bookends. Set Bookends to move all pdf attachments to a designated folder: ~/Documents/Bookends/Attachments/Files. Use Bookends 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 Bookends reference. This hyperlink will enable quick switching to Bookends from DT, even if Bookends is not open, and it will open Bookends to the linked record. Do this in one of two ways: Drag the Bookends ID# to DevonThink, or Command-Option-Drag any part of the record to DevonThink. The hyperlink can either stand on its own, as a separate note in the folder, or it can be dragged into any rtf note. (The text of the hyperlink may be edited without deleting the link; for example, by copying the formatted citation in Bookends and inserting that text in the link for a more complete citation.) This link will not carry over to Mellel, so it is for DT use only.
   2. Take notes
      1. Go to the Bookends record (using the temporary DT link), and open 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. While in Skim, identify passages worth quoting:
         1. Use commenting and markup tools to annotate the article in Preview or Skim. Highlight passages worth quoting. If using Skim, then a series of comments will contain all passages worth quoting. Preview in Leopard also has excellent commenting and highlighting tools, although it lacks automated exporting of highlighted passages.
         2. Either copy passages worth quoting one by one from Preview and paste them into the DevonThink source folder, or use Skim and follow these two steps to transfer them all at once: (1) In Skim, choose "File –> Export –> Notes as RTF" to export a text file consisting of just the highlighted quotations. (2) Import the quotation text file 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.
      3. Switch back and forth between Preview or Skim and DevonThink to take analytical notes:
         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 Bookends reference into DT (without holding the Command and Option keys, as before). This will produce a bracketed “legacy” citation appearing something like this: {Aaboe, 1958, 5, 209-277}. Add these citations to the primary source quotation notes imported from Skim.
         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. 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.
   5. Export as .rtfd for importing into Pages or Mellel.
       
3. Polish
   1. Import the .rtfd draft into Mellel or Pages. Both word processors will preserve Bookends citations from DevonThink and Scrivener, and both will preserve footnote text from Scrivener. Pages will preserve Scrivener annotations.
   2. If using Mellel, 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.
   3. If using Mellel, 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.)
   4. Format headings to best utilize the outline view in Mellel.
   5. Complete the final polishing of the text and layout in Mellel.
   6. 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 century Kerry Magruder, 2004-07 Search this course website Report typos or broken links

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