Preface Intro Basics Non-technical issues Recommendations Links Sources

Wiki training course

Dr. Konrad U. Forstner

February 19th, 2010 @ EBI, Hinxton, UK

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

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

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

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

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 tocreate and edit interlinked pages within the web browser

By this it enables collaborative knowledge management

Preface Intro Basics Non-technical issues Recommendations Links Sources

Wiki engines

There are different wiki engines with different features andrequirements

Their syntax might differ but they are based on commonprinciples

WikiMatrix.org helps to compare wiki engines

Some engines offer extensions for special functionalities

There are providers of wiki spaces - e.g. wikia.com

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

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Wikipedia - Size of the English version

Preface Intro Basics Non-technical issues Recommendations Links Sources

Further examples - WikiTravel

Preface Intro Basics Non-technical issues Recommendations Links Sources

Further examples - WikiLeaks

Preface Intro Basics Non-technical issues Recommendations Links Sources

Further examples - Software/Hardware Manual

Preface Intro Basics Non-technical issues Recommendations Links Sources

Further examples - BarCamps

Preface Intro Basics Non-technical issues Recommendations Links Sources

Further examples - EMBL Alumni Wiki

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 morewikis for it

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 / labcollaboration networkcommunity

Labjournal

Write papers

Open Science

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

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

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

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

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

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

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Basic formating

Preface Intro Basics Non-technical issues Recommendations Links Sources

Basic formating

Preface Intro Basics Non-technical issues Recommendations Links Sources

Basic formating

Preface Intro Basics Non-technical issues Recommendations Links Sources

Basic formating

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Creating captions and TOCs

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Links to external pages

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Links to internal pages and creating pages

Preface Intro Basics Non-technical issues Recommendations Links Sources

Links to internal pages and creating pages

Preface Intro Basics Non-technical issues Recommendations Links Sources

Links to internal pages and creating pages

Preface Intro Basics Non-technical issues Recommendations Links Sources

Links to internal pages and creating pages

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Uploading files

Preface Intro Basics Non-technical issues Recommendations Links Sources

Uploading files

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Inserting images

Preface Intro Basics Non-technical issues Recommendations Links Sources

Inserting images

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Page history

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Comparing versions

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Undo

Preface Intro Basics Non-technical issues Recommendations Links Sources

Undo

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

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 ...

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

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

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

Yes, again ... Wikipedia

As a source - if you refer to Wikipedia article use the historyto 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

Preface Intro Basics Non-technical issues Recommendations Links Sources

RNA Biology and Wikipedia

Preface Intro Basics Non-technical issues Recommendations Links Sources

OpenWetWare

Preface Intro Basics Non-technical issues Recommendations Links Sources

WikiGenes

Preface Intro Basics Non-technical issues Recommendations Links Sources

Wikibooks

Preface Intro Basics Non-technical issues Recommendations Links Sources

Wikiversity

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

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

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

Preface Intro Basics Non-technical issues Recommendations Links Sources

About this document

Created in LATEX 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 Forstnerhttp://konrad.foerstner.org

(*) Excepting the EMBL Logo

Document version 1.3 2010/02/19