Academic Workflow: Digital Tools & Techniques


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I present some of the digital tools available for the researchers on today's market to my fellow doctoral students in McGill University Desautels School of Management, and I offer them with my experiences while trying to make an end-to-end digital research workflow.

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Academic Workflow: Digital Tools & Techniques

  1. 1. Mahmood Shafeie Zargar for Desautels Doctoral Students Society Academic Workflow McGill University Digital Tools and Techniques March 3, 2014
  2. 2. Dr. John Smith’s Only Workflow Capture Compose Format & Release Word! Family Heritage Word! Family Heritage Word! Family Heritage EndNote! Department Heritage EndNote! Department Heritage EndNote! Department Heritage Storage USB Key! Fault-Intolerant Error-Prone Limited-Capacity Insecure Storage !2
  3. 3. One of My Workflows Capture Format & Release Compose DEVONthink! Desktop Content
 Management System Papers! Reference Library" & Citation Manager Evernote! Synchronized" Note Taking Scrivener
 Integrated Writing
 Environment Word! Badass Editor Magic Citations! Reference Library" & Citation Manager MindNode! Mind-mapping" & Outlining Storage DEVONthink !3 + DropBox
  4. 4. What Do We Do as Researchers? Read Write Analyze" (not covered here) Organize !4 Interoperability" is the key
  5. 5. Reading Digitally vs. on Paper Pros ❖ ❖ Cons ❖ Low resolution (exc. Retina)" ❖ Backlight-related stress (exc. eink)" ❖ Unfriendly annotation features" ❖ Searchability (text and annotations) " Limited screen real-estate" Exportability of annotations (highlights and notes) " ❖ Transferability (unlimited)" ❖ Mobility (volume)" ❖ Security (backups, access control, etc…)" ❖ Narrow focus while reading" ❖ Limited comparability" ❖ ❖ ❖ No tactile random access" Easy organization" Multicolour highlights (mom’s favorite!) ❖ !5 Multitasking (Distractibility)
  6. 6. Formats (PDF vs. eBook) ❖ PDF is not a reading format, but a printing and archival format" ❖ ❖ Nearly all scientific journals are published in PDF format" ❖ ❖ With PDF documents loos the same everywhere, but they remain unadapted to every single screen (why vertical?!)" Supported by most academic reader softwares" eBook formats (ePub, mobipocket, etc…) are designed as reading formats" ❖ Viewers change the size and flow of the text to fit to your screen" ❖ Some academic journals are testing the format" ❖ Supported by absolutely no academic reader software (as of today) !6
  7. 7. Reading PDFs (in a workflow) Integrated 
 Reader Inline
 Annotation Standalone" Reader Acrobat (m/w/i) Foxit (m/w) Preview (m)" PDFExpert (i)* EndNote (m/w) Sidecar
 Papers (m/w/i)*" Annotation Mendeley (m/w/i)* m = Mac" w = Windows" i = iOS Skim (m)* + = Some export functionality" * = Research-grade export functionality !7
  8. 8. “Freehand annotation on tablet? It is possible.” –Manaf Zargoush !8
  9. 9. “Forget about e-ink readers for PDF reading. They are not made for that…” –Mahmood Shafeie Zargar !9
  10. 10. Reading eBooks (in a workflow) Format iBooks 
 (i/m) Kindle" (a/i/m/
 w/o/d) Kobo" (a/i/m/w/d) Capabilities ePub Good Syncing
 Great Annotation Export mobipocket Great Syncing" Some Annotation Export (via Bookcision) ePub Some Syncing" Weak Annotation Export m = Mac" i = iOS" w = Windows" a = Android" o = Online d = Device !10
  11. 11. Alternative Means of Reading (McGill) ❖ Browzine: Get access to many academic journals directly from your tablet !11
  12. 12. Alternative Means of Reading (McGill) ❖ Browzine: Get access to many academic journals directly from your tablet !12
  13. 13. Alternative Means of Reading (McGill) ❖ ebrary: Get temporary access to some book collections !13
  14. 14. All Texts: From Vanilla to Rich ❖ Vanilla Text (Simple text editor)" ❖ Typesetting (LaTeX)" ❖ Markup (HTML, XML, etc…)" ❖ Rich Text (Word, Pages, etc…) !14
  15. 15. All Texts: From Vanilla to Rich ❖ Vanilla Text (Simple text editor)" ❖ Markdown (Markdown, MultiMarkdown, etc…)" ❖ Typesetting (LaTeX)" ❖ Markup (HTML, XML, etc…)" ❖ Rich Text (Word, Pages, etc…) !15
  16. 16. WYSIWYG vs. WYGIWYW WYSIWYG (Word, Pages, etc…) ❖ WYGIWYW (LaTeX, Markdown, IWEs…) Pros" ❖ Cons" ❖ ❖ Doesn’t look as good at first sight" ❖ Supposedly just one step to the final document" ❖ Not as intuitive" ❖ Very rich user interface with a plethora of options" ❖ Takes some practice" ❖ ❖ Immediate feedback on both form and content" Fool-proof" ❖ Not presentable in raw format: always needs transformation" ❖ Adds a final “transformation” to the writing process" Cons" ❖ Slow and resource consuming" ❖ Low browsability (not appropriate for very long documents)" ❖ Very simple, minimal clutter" ❖ Little structure (despite the existence of TOC)" ❖ ❖ Formatting, a mess" Focus on content while wiring, focus on format while formatting " ❖ Formatting nearly not reproducible (semi-useless templates) " ❖ Template-based reproducible formatting" ❖ Working out formatting and content at the same time" ❖ Consistent behaviour" ❖ Lack of standards and convertibility (for rich text formats)" ❖ Multiple output formats" ❖ Not editable everywhere" ❖ File transclusion" ❖ Possible loss of formatting in each content transfer" ❖ Highly standardized, highly compatible (Markdown)" ❖ Weak logics: erratic interface behaviour" ❖ Highly structured (LaTeX, Markdown)" ❖ File corruption and data loss a real possibility" ❖ Write anywhere, on any editor (LaTeX, Markdown)" ❖ Single output from single source file (source = output) ❖ Little risk of corruption (LaTeX, Markdown) ❖ !16 Pros"
  17. 17. Four New Concepts - (1) Markdown !17 Mou
  18. 18. Four New Concepts - (2) Integrated Writing Environment !18 Scrivener
  19. 19. Four New Concepts - (2) Integrated Writing Environment !19 Ulysses
  20. 20. Four New Concepts - (3) Distraction-Free Writing !20 Scrivener
  21. 21. Four New Concepts - (3) Distraction-Free Writing !21 Ulysses
  22. 22. Four New Concepts - (4) Collaborative Writing !22 Google Docs
  23. 23. Editor Choices Editor" MS Office 365 Apple iWork Libre / Open / Neo Office Google Docs" Quickoffice" WriteRoom iA Writer, Byword Writebox, wābisābi TextWrangler, Sublime Text TeXnicCenter TeXWorks ShareLatex Marked StackEdit Scrivener Ulysses OMMWriter The Journalist Mou Type" Word Processor Word Processor Word Processor Word Processor Word Processor Distraction Free Distraction Free Distraction Free" Code Editor LaTeX Editor LaTeX Editor LaTeX Editor Markdown Viewer Markdown Editor" ! Integrated Writing" Integrated Writing Distraction Free" Markdown Editor" Markdown Editor" Format" MS Office iWork, Some MS ODF , MS Google" MS Office" Vanilla" Markdown" Vanilla" Any Text (exc. Rich) LaTeX LaTeX LaTeX Markdown Markdown" Rich Text Format" Markdown" Vanilla Markdown Markdown !23 Platform m, w, i, o" m, i, o" m, w" i, a, o" i, a, o" m" m, i" o" m" w" m" o" m o" m, w" ! m" m, i" m, i" m" Sync. via Skydrive via iCloud" n/a" via GDrive" ! via GDrive" n/a" yes" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" yes" yes" n/a" m = Mac" i = iOS" w = Windows" a = Android" o = Online Collaborative some" some" n/a" yes" ! n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a" n/a"
  24. 24. Before Writing: Capturing Those Tiny Bits of Information ❖ You used to have a Moleskin… 
 Good old times…" ! ❖ Good news: The productivity app market has exploded during the last decade" ❖ A variety of products to capture not only text, but every sort of structured and unstructured information" ❖ Most either sync across platforms or are ready for the postdropbox era !24
  25. 25. Note Taking Software ❖ ❖ There are too many 
 apps to be named here" Notational Velocity Some are simple, and
 some are just one
 notch below a full-
 fledged content 
 management system Saves Type Bare-bones" Vanilla Text (Sync via Simplenote) Platform m The Journalist Markdown, Images Journal" (Sync via iCloud) m, i Evernote Rich Text, Images, PDFs, Audio Versatile" (Native Sync) m, w, i, a, o VoodooPad HTML / Rich Text Wiki 
 (No Sync / Dropbox) m !25 m = Mac" i = iOS" w = Windows" a = Android" o = Online Icon
  26. 26. Evernote in a Workflow ❖ Looks up your calendar, the time and the location to add metadata to your notes" ❖ Present on every device (and web) for your note taking pleasure" ❖ Does image search (character recognition)" ❖ Can search PDFs (not free)" ❖ Saves web clips" ❖ Can fetch Kindle annotations (Using Bookcision)" ❖ Lets you make simple todo lists" ❖ Lets you share notebooks" ❖ Syncs with digital pens" ❖ Livescribe " ❖ Penultimate" ❖ Can keep your business cards and recipes (mom’s favorite!) " ❖ Has limited but sufficient export functionality" ❖ Can transcribe your audio notes (automatic on Android, through Dragon Dictate on iOS, several additional services offered including human transcription e.g. Quicktate)" !26
  27. 27. Analog Note Taking, Digital Notebook ❖ Livescribe: Audio-annotated notes" ❖ ❖ The perfect interview device" ❖ ❖ Searchable handwritten notes" Needs proprietary paper (printable)" Penultimate" ❖ ❖ Searchable handwritten notes" ❖ ❖ Just a tablet app" Better with the proprietary pen" McGill’s Xerox Scanner" ❖ Not fancy!" ❖ Free OCRd PDF (but not for handwritten text)" ❖ Evernote can search in the image of a handwritten text (not perfect) !27
  28. 28. Mind-mapping and Outlining ❖ Andrew Van de Ven thinks tossing around ideas recorded on tiny cards helps theorizing!" ❖ Well, you got it…" ❖ Too many online and offline solutions for tossing around and structuring ideas:
 ❖ ❖ e.g Mind Manager (Mac & Windows - The best, but not free)" ❖ ❖ e.g. MindNode (Mac - Lite version free)" e.g. Just google it!
 Secret sauce: Adding nodes should be easy and intuitive, otherwise paper remains the superior solution!" ! ❖ Specific outlining tool for the aficionado: Omni Outliner (Mac) !28
  29. 29. Citation Software vs. Paper Libraries ❖ There used to be Thomson Education, Endnote and Refworks" ❖ Created the ISO standard for Citation Styles" ❖ Styles in proprietary format" ❖ This means you have to wait forever for any style correction to be released (but then it will be impeccable)" ! ❖ Many alternative citation management apps today, some free" ❖ Most rely on the open-source Citation Style Language" ❖ This means a large community of users keeping CSL files up-to-date !29
  30. 30. Citation Management Software EndNote Type Standalone Technology Excellent but Proprietary not customizable Papers Standalone CSL Mendeley Standalone CSL Zotero BibTeX Browser Extension Several Implementations Style Rendering CSL BibTeX Library & Sync Weak native sync Tablet Elementary Search Refactoring Citation Formatting Some Word, Pages + Tag-based None Reader Bultin, Weak N/A annotation Field- By author, Most Bultin, Good & Dropbox based by journal, Very capable editors + Excellent customizable synx and by book, Tag-based annotation Full etc… Text Word, Builtin, Mileage Native Full Pages, OO Good but varies & Good Some sync Text + Tagmessy customizable based annotation Very good & customizable Excellent for certain formats, atrocious for others Native sync With workarounds Full Text N/A Word, Builtin, Pages, OO Good but + Tagmessy based annotation N/A N/A N/A N/A LaTeX Tagbased !30 PDF Book Builtin Recon mar Search ginitio klet n N/A Best Tries Yes Good Best Yes N/A Good Yes N/A Good N/A N/A N/A
  31. 31. Mekentosj Papers ❖ Made by researchers for researchers " ❖ Just got acquired by Springer (not a startup anymore)" ❖ 3rd version (last version still beta/buggy)" ❖ Early tablet adopter" ❖ There is a Windows version now" ❖ Excellent search and integration (Finder/Spotlight)" ❖ Excellent refactoring" ❖ Easy annotation and export" ❖ Easy search and import" ❖ Citation system works nearly anywhere !31
  32. 32. Content Management ❖ Put those file tags to good use (Windows and Mac)" ❖ Hierarchical organization and file trees are so 2000" ! ❖ Many note taking apps can function as a content management system" ❖ Evernote (Multiplatform)" ❖ Circus Ponies Notebook (Mac)" ❖ ❖ Note taking, mind mapping, handwritten notes, etc." SOHO Notes (Mac)" ! ❖ The holy grail: DEVONthink [pro] (Mac)" ❖ Import anything from anywhere, then view it, annotate it, index it, search it, tag it, archive it" ❖ ❖ Including web links, web clips, RSS feeds, emails (from mail application), etc…" Inbox folder, floating inbox doc, browser bookmarklet, extensive integration in MacOS (inc. Spotlight), limited tablet edition, in-app Dropbox sync, etc… !32
  33. 33. After Writing: Safeguarding Those Precious Pearls of Wisdom ❖ Make regular backups" ❖ Use Time Machine if you have a Mac" ❖ Plenty of automatic backup solutions for Windows" ❖ Probably your external hard drive comes with one !33
  34. 34. Syncing & Storage ❖ Sync your documents instead of using a USB key" ❖ Portable flash memories are bound to fail" ❖ Syncing is free and most providers offer a free versioning system" ❖ Edit everything in your “cloud” folder and stay online while editing" ❖ Syncing makes sharing a piece of cake (opt for Google Drive if you need advanced sharing options) !34
  35. 35. Security ❖ Make sure you have the right to save human subject data on the server you are using" ❖ Certain schools or research funds won’t allow you to save the data in countries with less restrictive privacy laws (inc. US)" ❖ Tri-council explicitly asks you and holds you responsible for encrypting human subject data" ❖ You can always use a free software like TrueCrypt !35
  36. 36. Credits ❖ Organized by Rozhin Mansouri of DDSS" ❖ Food by Amoo Jamal (Le Chateau d'oncle Jamal )" ❖ Icons made by Adam Whitcroft from" ❖ Photo courtesy of Mahmood Shafeie Zargar at" ❖ Coolness brought by all of you! !36