1. Digital Tools for Academic Research
Sidiropoulos John
www.organognosi.com
email: organognosi@gmail.com
twitter: @organognosi
mobile: +44 7510 570990

2. The Problem
I do not remember where I have read this.
Where is this file in my hard drive?
I cannot find it!
I spend too much time trying to
organize my ebooks and papers.
I cannot find my notes from the paper I read
last week.

3. The Solution:
Digital Tools for Academic Research
Hypertext
Links
Wikis
Additional/alternative solutions
Tags
Search engines
Databases

4. Hypertext
Hypertext is a text structure that cannot
be conveniently printed. (As We Will
Think - Nelson: 252)
The biggest and most well known
hypertext system is the World Wide
Web (WWW).

5. Links
The defining characteristic of hypertext
Immediate access to information or data
Effective organizational tool
Kinds of Links
Between different documents
Between different sections of the same
document
Between text files and media files

6. Links between Documents
The references in a book or paper can be live
links to the original sources
e.g. Sorites Paradox and Vagueness - Sidiropoulos
Links to local files - e.g. A Critique
of Deflationism - Gupta: 286
URL: x-devonthink-item://644047E6-B393
-466E-B4E9-980AB5201172?page=4
Links to Google Books
e.g. Vagueness - Willimason: 35
URL: http://books.google.co.uk/
books?id=9ZEB6JNAkKsC&pg=PA35

7. Internal Document Links
Clickable table of contents
e.g. Hypertext marks in LaTeX: 2
Clickable index
e.g. Hypertext marks in LaTeX:448
Clickable endnotes/footnotes
e.g. Sorites Paradox and Vagueness -
Sidiropoulos: 5
Clickable references to specific
PDF pages e.g. Sorites Paradox
and Vagueness - Sidiropoulos: 11

8. Links to Audio and Video Files
TunesLinker - http://bit.ly/14qlx4k
Links to specific files
e.g. Night Bird - Deep Forest
Links to specific time points
e.g. Hypertext and Computer-Augmented-
Thought - 11:19

9. Ways of Writing Hypertext
HTML (HyperText Markup Language)
Wikis
LaTeX
e.g. Sorites and Vagueness - Sidiropoulos
Creation of links using AppleScript
e.g. Create MediaWiki and RTF links to
iPhoto pictures

10. Wikis
The easiest way to create hypertext
Demo MediaWiki
Links to other pages - e.g. [[Vagueness]]
Markup syntax: MediaWiki Cheat Sheet
Wiki programs
MediaWiki
ConnectedText
VoodooPad
Wikispaces

11. MediaWiki - Tips
For each book, article that I read I
create a separate wiki page
Name template: @Title - Surname
For each important concept I create a
separate wiki page.
Name template: Concept and specifier
I insert pertinent tags or categories to the
wiki pages.
I try to write anything new that I learn.
My wikis are the personal repositories
of my knowledge.

12. Advantages of Hypertext
Every source is just one click away!
You can organize your sources, notes and
thoughts in an associative manner which
can preserve the context.
Facilitates the creation of new connections.
Facilitates analysis - modular organization
of content (imitation of index cards).
Facilitates synthesis - creation of
dynamic documents (transclusion).

13. Problems with Hypertext
The links can break.
It requires the learning of new skills
(new programs, markup languages)
New dangers (security, backup)
Digitization of source material
Copyright (open access movement)

14. My Favorite Mac Applications
for reading and annotating documents:
Skim (PDF), Clearview (ePub, chm)
for bibliography management: BibDesk
for writing: Scrivener, Scapple, LaTeX
for notes management: MediaWiki
for documents management:
DEVONthink (PDFs), Calibre (ePub, chm)
for automating my workflow:
Script Debugger

15. OrganoGnosi
http://www.organognosi.com
Development of custom scripts and
applications
Private tuitions