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.

1. Mahmood Shafeie Zargar for Desautels Doctoral Students Society
Academic Workflow
McGill University
Digital Tools and Techniques
March 3, 2014

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. 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. What Do We Do as Researchers?
Read
Write
Analyze"
(not covered here)
Organize
!4
Interoperability"
is the key

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. 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. 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. “Freehand annotation on tablet? It is possible.”
–Manaf Zargoush
!8

9. “Forget about e-ink readers for PDF reading. They
are not made for that…”
–Mahmood Shafeie Zargar
!9

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. Alternative Means of Reading (McGill)
❖
Browzine: Get access to many
academic journals directly
from your tablet
!11

12. Alternative Means of Reading (McGill)
❖
Browzine: Get access to many
academic journals directly
from your tablet
!12

13. Alternative Means of Reading (McGill)
❖
ebrary: Get temporary access to
some book collections
!13

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. 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. 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. Four New Concepts - (1) Markdown
!17
Mou

18. Four New Concepts - (2) Integrated Writing Environment
!18
Scrivener

19. Four New Concepts - (2) Integrated Writing Environment
!19
Ulysses

20. Four New Concepts - (3) Distraction-Free Writing
!20
Scrivener

21. Four New Concepts - (3) Distraction-Free Writing
!21
Ulysses

22. Four New Concepts - (4) Collaborative Writing
!22
Google Docs

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Credits
❖
Organized by Rozhin Mansouri of DDSS"
❖
Food by Amoo Jamal (Le Chateau d'oncle Jamal )"
❖
Icons made by Adam Whitcroft from flaticon.com"
❖
Photo courtesy of Mahmood Shafeie Zargar at
ofjoy.tumblr.com"
❖
Coolness brought by all of you!
!36