Wiki training course

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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