1. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wiki training course
Dr. Konrad U. F¨rstner
o
February 19th, 2010 @ EBI, Hinxton, UK

2. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

3. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

4. Preface Intro Basics Non-technical issues Recommendations Links Sources
Preface
You get no handouts as
... we want to save trees
... wikis bring their own documentation
... you will get these slides as a pdf file
... we have created a wiki page for you with links

5. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

6. Preface Intro Basics Non-technical issues Recommendations Links Sources
What is a wiki?
A web site which is based on wiki software
That offers the user a fast (Hawaiian: wiki) and easy way to
create and edit interlinked pages within the web browser
By this it enables collaborative knowledge management

7. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wiki engines
There are different wiki engines with different features and
requirements
Their syntax might differ but they are based on common
principles
WikiMatrix.org helps to compare wiki engines
Some engines offer extensions for special functionalities
There are providers of wiki spaces - e.g. wikia.com

8. Preface Intro Basics Non-technical issues Recommendations Links Sources
History in a nutshell
Concept goes back to 70’s ZOG / HyperCard (80’s)
Tim Bernes Lee’s idea of the WWW - editable pages
1995 - WikiWikiWeb of Ward Cunningham
Wikis became popular in the FLOSS scene
2001 Launch of Wikipedia - increased interest in wikis

9. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wikipedia - the best known example
An encyclopedia based on a wiki
Created and maintained by an open community
More than 350 languages/dialects
Free content and open source wiki software
Relatively good proven average quality

10. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wikipedia - Size of the English version

11. Preface Intro Basics Non-technical issues Recommendations Links Sources
Further examples - WikiTravel

12. Preface Intro Basics Non-technical issues Recommendations Links Sources
Further examples - WikiLeaks

13. Preface Intro Basics Non-technical issues Recommendations Links Sources
Further examples - Software/Hardware Manual

14. Preface Intro Basics Non-technical issues Recommendations Links Sources
Further examples - BarCamps

15. Preface Intro Basics Non-technical issues Recommendations Links Sources
Further examples - EMBL Alumni Wiki

16. Preface Intro Basics Non-technical issues Recommendations Links Sources
General observation
Wikis technically reflect the speed of growth of our knowledge
If there is a community it’s likely that there is one or more
wikis for it

17. Preface Intro Basics Non-technical issues Recommendations Links Sources
Examples of how you can use a wiki
Sharing knowledge in a structured form between your
group / lab
collaboration network
community
Labjournal
Write papers
Open Science

18. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

19. Preface Intro Basics Non-technical issues Recommendations Links Sources
Before you start
Every wiki has editing help
Make yourself familiar with the rules of the wiki site

20. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

21. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

22. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

23. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

24. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

25. Preface Intro Basics Non-technical issues Recommendations Links Sources
Basic formating

26. Preface Intro Basics Non-technical issues Recommendations Links Sources
Basic formating

27. Preface Intro Basics Non-technical issues Recommendations Links Sources
Basic formating

28. Preface Intro Basics Non-technical issues Recommendations Links Sources
Basic formating

29. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

30. Preface Intro Basics Non-technical issues Recommendations Links Sources
Creating captions and TOCs

31. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

32. Preface Intro Basics Non-technical issues Recommendations Links Sources
Links to external pages

33. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

34. Preface Intro Basics Non-technical issues Recommendations Links Sources
Links to internal pages and creating pages

35. Preface Intro Basics Non-technical issues Recommendations Links Sources
Links to internal pages and creating pages

36. Preface Intro Basics Non-technical issues Recommendations Links Sources
Links to internal pages and creating pages

37. Preface Intro Basics Non-technical issues Recommendations Links Sources
Links to internal pages and creating pages

38. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

39. Preface Intro Basics Non-technical issues Recommendations Links Sources
Uploading files

40. Preface Intro Basics Non-technical issues Recommendations Links Sources
Uploading files

41. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

42. Preface Intro Basics Non-technical issues Recommendations Links Sources
Inserting images

43. Preface Intro Basics Non-technical issues Recommendations Links Sources
Inserting images

44. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

45. Preface Intro Basics Non-technical issues Recommendations Links Sources
Page history

46. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

47. Preface Intro Basics Non-technical issues Recommendations Links Sources
Comparing versions

48. Preface Intro Basics Non-technical issues Recommendations Links Sources
The basics step by step
Orientation
Creating an account
Exploring the user page
Basic formating
Creating captions and TOCs
Links to external pages
Links to internal pages and creating pages
Uploading files
Inserting images
Page history
Comparing versions
Undo

49. Preface Intro Basics Non-technical issues Recommendations Links Sources
Undo

50. Preface Intro Basics Non-technical issues Recommendations Links Sources
Undo

51. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

52. Preface Intro Basics Non-technical issues Recommendations Links Sources
Non-technical issues - Community Management
Keep in mind - Wikis are filled by people
critical mass, rules, permissions, work flow, complaints, consensus,
vandalism, conflicts, attribution, discussion ...

53. Preface Intro Basics Non-technical issues Recommendations Links Sources
Non-technical issues - Licenses
Open content = contribution to humankinds knowledge,
transfer of prosperity
Use e.g. Creative Commons licences / Public domain

54. Preface Intro Basics Non-technical issues Recommendations Links Sources
Not covered today – For Future advanced training session
Setting up a wiki
Categories, templates and customizations etc.
Access Control Lists
Licenses and their consequences in detail
... and much more

55. Preface Intro Basics Non-technical issues Recommendations Links Sources
Table of content
1 Preface
2 Intro and background
3 The basics step by step
4 Non-technical issues
5 Helpful wiki sites for biologists

56. Preface Intro Basics Non-technical issues Recommendations Links Sources
Yes, again ... Wikipedia
As a source - if you refer to Wikipedia article use the history
to get the version link (...&oldid=xxx) and quote that one
Good way of communicating your research to the public
Increased importance in science - e.g. the journal RNA Biology

57. Preface Intro Basics Non-technical issues Recommendations Links Sources
RNA Biology and Wikipedia

58. Preface Intro Basics Non-technical issues Recommendations Links Sources
OpenWetWare

59. Preface Intro Basics Non-technical issues Recommendations Links Sources
WikiGenes

60. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wikibooks

61. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wikiversity

62. Preface Intro Basics Non-technical issues Recommendations Links Sources
Wikis at EMBL
Gibson Team
Bork group
Russell group
Schneider group
Briggs group
Furlong Group
Next Generation Sequencing (NGS) Wiki
EICAT

63. Preface Intro Basics Non-technical issues Recommendations Links Sources

64. Preface Intro Basics Non-technical issues Recommendations Links Sources
Selected links
http://www.mediawiki.org
http://www.wikimatrix.org
http://en.wikipedia.org/wiki/List_of_wiki_software
http://creativecommons.org
http://openwetware.org
http://www.wikigenes.org
About WikiGenes: http://www.nature.com/ng/journal/v40/n9/full/ng.f.217.html
Speculations on the future of science:
http://www.edge.org/3rd_culture/kelly06/kelly06_index.html
http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Vandalism_studies
Re. quality of Wikipedia: http://www.wired.com/culture/lifestyle/news/2005/12/69844
RNA Biology http://www.landesbioscience.com/journals/rnabiology/guidelines/
http://wikitravel.org
http://wikileaks.org
http://wiki.openmoko.org
http://barcamp.org
http://alumniwiki.embl.org
http://wikibooks.org
http://wikiversity.org

65. Preface Intro Basics Non-technical issues Recommendations Links Sources
Image sources/attribution
http://www.flickr.com/photos/library_of_congress/2179910918
http://commons.wikimedia.org/wiki/File:Kepler-world.jpg
http://commons.wikimedia.org/wiki/File:HNL_Wiki_Wiki_Bus.jpg
http://en.wikipedia.org/wiki/File:Ohain_USAF_He_S-8A_page68.jpg
http://upload.wikimedia.org/wikipedia/commons/b/b1/Doi_trilo.gif
http://www.flickr.com/photos/knilram/64366434/
http://en.wikipedia.org/wiki/Wikipedia:Size_in_volumes
http://en.wikipedia.org/wiki/File:TopTenWikipediasGraph.png
http://commons.wikimedia.org/wiki/File:Koogan_binoculars_01.JPG
http://commons.wikimedia.org/wiki/File:
Kevincole_-_Western_honey_bees_(Apis_mellifera)_(by).jpg
http://commons.wikimedia.org/wiki/File:Chiodini_wiki.jpg
http://www.flickr.com/photos/library_of_congress/2179123671/
http://wiki.creativecommons.org/images/6/62/Creativecommons-informational-flyer_eng.pdf
http://en.wikipedia.org/wiki/File:Orion_aveugle_cherchant_le_soleil.jpg
http://commons.wikimedia.org/wiki/File:Apollo_15_launch_medium_distance.jpg
http://commons.wikimedia.org/wiki/File:Traces.JPG
http://commons.wikimedia.org/wiki/File:EMBL_Heidelberg.jpg
http://commons.wikimedia.org/wiki/File:GSUSA_All_Abouts_Thank_you.JPG
http://commons.wikimedia.org/wiki/File:Z_The_End_Notorious.png

66. Preface Intro Basics Non-technical issues Recommendations Links Sources
About this document
A
Created in L TEX using the beamer class, TeX Live and Emacs.
All these programs run on OpenBSD.
http://www.latex-project.org
http://latex-beamer.sourceforge.net
http://www.tug.org/texlive/
http://www.gnu.org/software/emacs
http://www.gimp.org/
http://www.openbsd.org
Published under the Creative Commons Attribution 3.0 License (*)
http://creativecommons.org/licenses/by/3.0/
by Konrad F¨rstner
o
http://konrad.foerstner.org
(*) Excepting the EMBL Logo
Document version 1.3 2010/02/19