Mahmood Shafeie Zargar for Desautels Doctoral Students Society

Academic Workflow Digital Tools and Techniques

McGill University March 3, 2014

Dr. John Smith’s Only WorkflowCapture Compose Format & Release

Storage

Word!Family Heritage

EndNote!Department Heritage

Word!Family Heritage

EndNote!Department Heritage

Word!Family Heritage

EndNote!Department Heritage

USB Key!Fault-Intolerant Error-Prone Limited-Capacity Insecure Storage

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One of My WorkflowsDEVONthink!

Desktop Content Management System

Scrivener Integrated Writing

EnvironmentEvernote!Synchronized"Note Taking

Word!Badass Editor

Papers!Reference Library"

& Citation Manager

MindNode!Mind-mapping"

& Outlining

Capture Compose Format & Release

Storage DEVONthink DropBox+

Magic Citations!Reference Library"

& Citation Manager

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What Do We Do as Researchers?Read Write

Organize

Analyze"(not covered here)

Interoperability"is the key

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Reading Digitally vs. on Paper❖ Searchability (text and

annotations) "❖ Exportability of annotations

(highlights and notes) "❖ Transferability (unlimited)"❖ Mobility (volume)"❖ Security (backups, access control,

etc…)"❖ Easy organization"❖ Multicolour highlights (mom’s

favorite!)

❖ Low resolution (exc. Retina)"

❖ Backlight-related stress (exc. e-ink)"

❖ Unfriendly annotation features"

❖ Limited screen real-estate"

❖ Narrow focus while reading"

❖ Limited comparability"

❖ No tactile random access"

❖ Multitasking (Distractibility)

Pros Cons

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Formats (PDF vs. eBook)❖ PDF is not a reading format, but a printing and archival format"

❖ With PDF documents loos the same everywhere, but they remain unadapted to every single screen (why vertical?!)"

❖ Nearly all scientific journals are published in PDF format"

❖ 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)

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Reading PDFs (in a workflow)Integrated

ReaderStandalone"

Reader

Inline Annotation EndNote (m/w)

Acrobat (m/w/i)Foxit (m/w)Preview (m)"

PDFExpert (i)*

Sidecar Annotation

Papers (m/w/i)*"Mendeley (m/w/i)* Skim (m)*

m = Mac"w = Windows"i = iOS

+ = Some export functionality"* = Research-grade export functionality

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–Manaf Zargoush

“Freehand annotation on tablet? It is possible.”

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–Mahmood Shafeie Zargar

“Forget about e-ink readers for PDF reading. They are not made for that…”

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Reading eBooks (in a workflow)

Format Capabilities

iBooks (i/m) ePub

Good Syncing Great Annotation

Export

Kindle"(a/i/m/w/o/d)

mobipocketGreat Syncing"

Some Annotation Export (via Bookcision)

Kobo"(a/i/m/w/d) ePub

Some Syncing"Weak Annotation

Export

m = Mac"w = Windows"o = Online

i = iOS"a = Android"d = Device

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Alternative Means of Reading (McGill)

❖ Browzine: Get access to many academic journals directly from your tablet

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Alternative Means of Reading (McGill)

❖ Browzine: Get access to many academic journals directly from your tablet

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Alternative Means of Reading (McGill)

❖ ebrary: Get temporary access to some book collections

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All Texts: From Vanilla to Rich

❖ Vanilla Text (Simple text editor)"

❖ Typesetting (LaTeX)"

❖ Markup (HTML, XML, etc…)"

❖ Rich Text (Word, Pages, etc…)

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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…)

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WYSIWYG vs. WYGIWYW❖ Pros"

❖ Immediate feedback on both form and content"

❖ Supposedly just one step to the final document"

❖ Very rich user interface with a plethora of options"

❖ Fool-proof"

❖ Cons"

❖ Slow and resource consuming"

❖ Low browsability (not appropriate for very long documents)"

❖ Little structure (despite the existence of TOC)"

❖ Formatting, a mess"

❖ Formatting nearly not reproducible (semi-useless templates) "

❖ Working out formatting and content at the same time"

❖ Lack of standards and convertibility (for rich text formats)"

❖ Not editable everywhere"

❖ Possible loss of formatting in each content transfer"

❖ Weak logics: erratic interface behaviour"

❖ File corruption and data loss a real possibility"

❖ Single output from single source file (source = output)

❖ Cons"❖ Doesn’t look as good at first sight"❖ Not as intuitive"❖ Takes some practice"❖ Not presentable in raw format: always needs transformation"❖ Adds a final “transformation” to the writing process"

❖ Pros"❖ Very simple, minimal clutter"❖ Focus on content while wiring, focus on format while

formatting "❖ Template-based reproducible formatting"❖ Consistent behaviour"❖ Multiple output formats"❖ File transclusion"❖ Highly standardized, highly compatible (Markdown)"❖ Highly structured (LaTeX, Markdown)"❖ Write anywhere, on any editor (LaTeX, Markdown)"❖ Little risk of corruption (LaTeX, Markdown)

WYSIWYG (Word, Pages, etc…) WYGIWYW (LaTeX, Markdown, IWEs…)

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Four New Concepts - (1) Markdown

Mou�17

Four New Concepts - (2) Integrated Writing Environment

Scrivener�18

Four New Concepts - (2) Integrated Writing Environment

Ulysses�19

Four New Concepts - (3) Distraction-Free Writing

Scrivener�20

Four New Concepts - (3) Distraction-Free Writing

Ulysses�21

Four New Concepts - (4) Collaborative Writing

Google Docs�22

Editor ChoicesEditor" Type" Format" Platform Sync. Collaborative

MS Office 365 Word Processor MS Office m, w, i, o" via Skydrive some"Apple iWork Word Processor iWork, Some MS m, i, o" via iCloud" some"

Libre / Open / Neo Office Word Processor ODF , MS m, w" n/a" n/a"Google Docs" Word Processor Google" i, a, o" via GDrive"

!yes"!Quickoffice" Word Processor MS Office" i, a, o" via GDrive" n/a"

WriteRoom Distraction Free Vanilla" m" n/a" n/a"iA Writer, Byword Distraction Free Markdown" m, i" yes" n/a"Writebox, wābisābi Distraction Free" Vanilla" o" n/a" n/a"

TextWrangler, Sublime Text Code Editor Any Text (exc. Rich) m" n/a" n/a"TeXnicCenter LaTeX Editor LaTeX w" n/a" n/a"

TeXWorks LaTeX Editor LaTeX m" n/a" n/a"ShareLatex LaTeX Editor LaTeX o" n/a" n/a"

Marked Markdown Viewer Markdown m n/a" n/a"StackEdit Markdown Editor"

!Markdown" o" n/a" n/a"

Scrivener Integrated Writing" Rich Text Format" m, w"!

n/a" n/a"Ulysses Integrated Writing Markdown" m" n/a" n/a"

OMMWriter Distraction Free" Vanilla m, i" yes" n/a"The Journalist Markdown Editor" Markdown m, i" yes" n/a"

Mou Markdown Editor" Markdown m" n/a" n/a"

m = Mac"w = Windows"o = Online

i = iOS"a = Android"

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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 post-dropbox era

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Note Taking

❖ There are too many apps to be named here"

❖ Some are simple, andsome are just one notch below a full- fledged content management system

Software Saves Type Platform Icon

Notational Velocity Vanilla Text

Bare-bones"(Sync via

Simplenote)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

m = Mac"w = Windows"o = Online

i = iOS"a = Android"

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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)"

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Analog Note Taking, Digital Notebook❖ Livescribe: Audio-annotated notes"

❖ Searchable handwritten notes"

❖ The perfect interview device"

❖ Needs proprietary paper (printable)"

❖ Penultimate"

❖ Just a tablet app"

❖ Searchable handwritten notes"

❖ 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)

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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. MindNode (Mac - Lite version free)"

❖ e.g Mind Manager (Mac & Windows - The best, but not 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)

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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

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Citation Management Software Type Technology

Style Rendering

Library & Sync Tablet Search Refactoring

Citation Formatting Reader

Bookmarklet

Builtin Search

PDF Reconginitio

n

EndNote Standalone ProprietaryExcellent but

not customizable

Weak native sync

Elementary Some NoneWord,

Pages + Tag-based

Bultin, Weak

annotationN/A Best Tries

Papers Standalone CSLGood &

customizableDropbox

synx Very capable

Field-based and Full Text

By author, by journal, by book,

etc…

Most editors +

Tag-based

Bultin, Excellent

annotationYes Good Best

Mendeley Standalone CSLMileage varies &

customizable

Native sync Good

Full Text Some

Word, Pages, OO

+ Tag-based

Builtin, Good but

messy annotation

Yes N/A Good

ZoteroBrowser

Extension CSLVery good & customizable

Native sync

With workarounds

Full Text N/A

Word, Pages, OO

+ Tag-based

Builtin, Good but

messy annotation

Yes N/A Good

BibTeXSeveral

Implementations BibTeX

Excellent for certain

formats, atrocious for

others

N/A N/A N/A N/ALaTeX Tag-

based N/A N/A N/A N/A

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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

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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…

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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

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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)

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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

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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!

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