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  • 1. Wikis at work A short introduction to 'wikis' and wikis for biology Dan Bolser and Paolo Romano URL for slides: http://
  • 2. Overview of today's course
    • Session 1 (35 min) :
      • What is a wiki? – A gentle introduction to the wiki concept, and a look at Wikipedia.
    • Session 2 (35 min)‏
      • Biological wikis! – A review of some of the most important wikis for biology (BioWikis).
    • BREAK (15 min)‏
  • 3. Overview of today's course
    • Session 3 (35 min)‏
      • Semantic MediaWiki – Software for 'data wikis'.
      • Cell Lines Wiki – A pilot scientific wiki.
    • Practical session (60 min)‏
      • Editing Wikipedia (for the first time?)‏
      • Working with Cell lines Wiki – A gentle introduction to some of the key features.
  • 4.  
  • 5. Session 1
  • 6. What is a wiki?
  • 7. Wiki means QUICK!
  • 8. Wiki is a quicker way to let people put content on the web Old way:
  • 9. Wiki is a quicker way to let people put content on the web Old way:
  • 10. Wiki is a quicker way to let people put content on the web Old way:
  • 11. Wiki is a quicker way to let people put content on the web Old way:
    • Host
    • HTML editor
    • FTP software
    • Domain name
  • 12. Wiki is a quicker way to let people put content on the web Old way:
  • 13. Wiki is a quicker way to let people put content on the web Old way: Wiki way:
  • 14. Wiki means QUICK!
  • 15.
    • There is no longer one single 'point of control' for managing web content.
    • Content is managed by a decentralized community of participating users.
    Wiki is radically different!
  • 16. Is this good or bad?
  • 17. Other advantages of wiki
    • There are many other advantages over 'traditional' web publishing...
      • Notification of changes
      • History of changes
      • Discussion of changes
  • 18. The rise of the wiki
  • 19. Condensed history
    • 1994: Cunningham coined the term 'wiki'.
      • A site (for software developers) with pages that can be edited via the browser, each with a page history.
    • Over the next five years it spawned alternative wiki applications and websites (wiki culture).
      • By 2000, it had developed lots of of spin-off content, most notably MeatballWiki (for general discussion).
    • 2001, Wikipedia launched.
    • 2007, Wikipedia in the worlds top 10 web sites.
  • 20.  
  • 21. Wikipedia
    • Size
      • Stats.
    • Growth‏
      • Research.
    • Rules
      • e.g. Deleting content.
    • Culture
      • e.g. Anatomy of a talk page.
    Almost all of its articles can be edited by anyone with access to the site, and it has about 90,000 regularly active contributors.
  • 22. Wikipedia
    • Size
      • 19.7 million articles
        • 3.7 million in English
        • 847,069 in Italian (4 th out of 282)‏
      • 2.7 billion monthly hits from the US alone.
      • 7 th most popular site in the world.
      • The largest and most popular general reference work.
  • 23. Wikipedia
    • Growth (Kittur)‏
      • Wikipedia has been growing exponentially since 2002 (Voss)‏
      • “ wisdom of crowds” or “elite users”
        • a large number of people with a small number of edits, or
        • a core group who do most of the work?
  • 24. Wikipedia
    • Rules
      • Their are no rules!
      • The 'five pillars' of Wikipedia'
      • Standard deletion procedure...
  • 25. Wikipedia
    • Culture
      • Their are no rules!
      • The 'five pillars' of Wikipedia'
      • Discussion!
        • (Not bureaucracy)‏
  • 26. Moving on...
    • Is WP, or something like it, the future for science?
    • Lets find out in Session 2!
  • 27. Session 1, References
    • http://wikipedia.org/wiki/ History_of_wikis
    • http://wikipedia.org/wiki/ Wikipedia
    • Voss, J. Measuring Wikipedia. In Proceedings of the ISSI 2005 (Stockholm, Sweden, July 24-28, 2005).
    • Kittur A, Chi EH, Pendleton BA, Suh B, Mytkowicz T. Power of the few vs. wisdom of the crowd: Wikipedia and the rise of the bourgeoisie. CHI 2007.
    • http://wikipedia.org/wiki/ Wikipedia:Five_pillars
    • http://meta.wikimedia.org/wiki/ Research: Newsletter/2011-07-25
  • 28.  
  • 29. Session 2
  • 30. Scientific wikis
  • 31. Community annotation
  • 32. Annotation
  • 33. Annotation
  • 34. Community annotation
    • Driven by two key factors:
    • The vast increase in biological data
    • The clear success of Wikipedia
  • 35. BioMoore's Law
    • Over time:
      • Cost per unit of information can be decreased by orders of magnitude.
      • Throughput is increased by orders of magnitude.
        • Fan et al. 2006 . Nat Rev Genet .
    • Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars.
      • Revolution in human genetics.
  • 36. BioMoore's Law
    • Over time:
      • Cost per unit of information can be decreased by orders of magnitude.
      • Throughput is increased by orders of magnitude.
        • Fan et al. 2006 . Nat Rev Genet .
    • Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars.
      • Revolution in human genetics.
  • 37. Community annotation is essential
    • Centralised databases can't cope with annotating the influx of data.
    • Less investment in more specialised data.
      • Fewer people with a stake.
      • Specialists more disparate.
        • Communities are smaller and more focused.
    • Do wikis hold the answer?
      • Wikipedia as a model…
  • 38. But Wikipedia isn’t always the answer ...
    • Wikipedia is an educational resource.
      • All articles are encyclopaedic in style.
      • Explicitly forbids data from ‘original research’:
        • http://wikipedia.org/wiki/Wikipedia:No_original_research
          • “ Wikipedia does not publish original research” .
      • No tools for the specific analysis, presentation, or collection of ‘biological’ data.
    • BioWikis!
  • 39. BioWikis
    • Wikis with a biological subject matter, customized for analysis, presentation and collection of specific biological data and biological data types:
  • 40. Wikis for biology
  • 41. Proteopedia
    • http://proteopedia.org/
    • Aim – To make knowledge about proteins accessible.
    • Features:
      • Interactive 3D viz.
      • Contributions linked to publications.
    • Problems
      • Doesn't work on all browsers.
      • Can be slow.
    • Reference
      • Hodis, E. et al., 2008. Proteopedia - a scientific “wiki” bridging the rift between three-dimensional structure and function of biomacromolecules. Genome biology, 9(8), p.R121.
  • 42. WikiPathways
    • http://wikipathways.org
    • Aim – The curation of biological pathways.
    • Features:
      • Interactive pathway editing.
      • Integrated to many biological databases.
    • Problems
      • Doesn't work on all browsers.
      • Can be slow.
    • Reference
      • Pico, A.R. et al., 2008. WikiPathways: pathway editing for the people. PLoS biology, 6(7), p.e184.
  • 43. EcoliWiki
    • http://ecoliwiki.net/
    • Aim – Share info related to non-pathogenic E. coli.
    • Features:
      • Very extensive and well structured domain information.
      • Referencing is good.
    • Problems
      • Big resource
      • Specific focus, could it be applied to others?
    • Reference
      • EcoliWiki, 2007. EcoliHub’s subsystem for community annotation. http://ecoliwiki.net.
  • 44. CHDWiki
    • http://goo.gl/info/Zxg8H
    • Aim(?) – Geneticists, clinicians, and mol. biologists working on Congenital Heart Defects.
    • Features:
      • Curated gene lists.
      • PPI browser.
    • Problems
      • Very old MediaWiki fork
      • Used?
    • Reference
      • Barriot, R. et al., 2010. Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome medicine, 2(3), p.16.
  • 45. SEQwiki
    • http://seqwiki.org
    • Aim – a catalogue of analysis tools and, technologies for NGS.
    • Features
      • Structured data.
      • Linked to an established forum.
    • Problems
      • Data can become error prone.
      • Data is difficult to centrally manage.
    • Reference
      • Li J.W., et. al. 2012. The SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis. Nucleic Acids Research 2012 Database special issue.
  • 46. Listing of biowikis...
    • http://bioinformatics.org/wiki/BioWiki
  • 47. BioWikis
    • There is a variety of different systems.
    • All seek to 'recognize' contributors (biologists) in a way more familiar to scientists than Wikipedia.
    • Most have features not found in Wikipedia.
      • Some projects use the base of Wikipedia to successfully build integrated 'sub-projects'...
  • 48. The MCB Portal in Wikipedia
    • http://en.wikipedia.org/wiki/ Wikipedia:MCB
    • Aim – Better organize information related to molecular and cell biology on Wikipedia.
    • Features
      • Integrated with WP
    • Problems
      • The project can be confusing to those unfamiliar with Wikipedia.
    • Reference
      • ...
  • 49. Gene Wiki
    • http://en.wikipedia.org/wiki/ Portal:Gene_Wiki
    • Aim – applying community intelligence to gene annotation.
    • Special features:
      • Semi-automatic gene curation system.
    • Problems
      • The project can be confusing to those unfamiliar with Wikipedia.
    • Reference
      • Huss, J.W. et al., 2008. A gene wiki for community annotation of gene function. PLoS biology, 6(7), p.e175.
  • 50. Wikis for Cancer?
  • 51. Some aditional references
    • Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nature reviews. Genetics 7, 632-44 (2006).
    • The Molecular modelling blog post http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/
    • http://bifx.org/wiki/BioWiki
    • Daub, J. et al., 2008. The RNA WikiProject: community annotation of RNA families. RNA (New York, N.Y.), 14(12), pp.2462-4.
    • Stehr, H. et al., 2010. PDBWiki: added value through community annotation of the Protein Data Bank. Database, p.baq009-baq009.
    • Flórez, L.A. et al., 2009. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database : the journal of biological databases and curation, p.bap012
  • 52.  
  • 53. Session 3
  • 54. Semantic MediaWiki
  • 55. Semantic MediaWiki (a data wiki engine)‏
    • What is SMW?
    • Motivation
    • Frontend
      • What you see as a user of SMW.
    • Backend
      • What you do as a SMW site developer...
    • Data
    • Properties and types
    • Classes
    • Templates
    • Forms
    • Queries
  • 56. References
    • SMW Homepage: http://semantic-mediawiki.org
    • MW Templates: http://www.mediawiki.org/wiki/Help:Templates
    • SF Homepage: http://www.mediawiki.org/wiki/ Extension:Semantic_Forms
    • SMW #ask: http://semantic-mediawiki.org/wiki/ Help:Inline_queries
    • SMW demo sites:
      • http://pgscdemo.referata.com
      • http://discoursedb.org
      • http://sandbox.referata.com
  • 57. Cell Lines Wiki