1) The document discusses using a wiki as a laboratory information management system (LIMS) to store metadata and track samples from multiple next generation DNA sequencers. 2) Key benefits of the wiki LIMS include flexibility to handle a variety of sample types and details, full version history and audit trail, and the ability to initiate and track tasks. 3) The wiki can be accessed and edited via a web browser and customized using Perl scripts to read and write wiki pages programmatically.

1. WikiLIMS BioTeam.net

2. Dilbert 1

3. 1st Next Gen Sequencer Centerpiece of a lab Generates new workflows These cannot be known in advance When they order 2 more sequencers Still want a single repository for all runs

4. Tasks/Workflows Production Few tasks, all repeated many times Rigorous standards Ideal for software Research Many one-off tasks Ad hoc standards Difficult for software

5. Sequencer’s Input Infinite variety of Samples, handling and lab prep All details might matter Usually only a few do

6. The 454 Solution A single strict [A-Z0-9]+ field Intended as an external primary key Makes sample tracking an upstream problem Part of the results directory name R_TIMESTAMP_MACHINEID_USER_YOURFIELD Clean technical solution

7. These are Researchers Apparently they wanted a LIMS Found a way to cram it in PROJIDxxSPECIESxxSAMPLExxDESCxxNOTES More or less consistent

8. Additional Details 3 machines Signs of strain by the 50th run Difficult to look across machines Too many DESCRIPTION variants Desire to rename old data

9. Dilbert 2

10. Key Terms Wiki Fast in Hawaiian LIMS Laboratory Information Management System Mediawiki Software that runs Wikipedia

11. Wikipedia/ UC Berkeley

12. flexible --- database 1/3 flexible database

13. flexible --- database 2/3 No need to abuse a ‘comments’ field. Everything is a comment until you make it structured.

14. flexible --- database 3/3 No need to abuse a ‘comments’ field. Everything is a comment until you make it structured.

15. Full History Audit Trail Full History Differences between any 2 versions

16. Version Differences

17. Next Gen Data Store File data raid Meta data wiki

18. Next Gen Data Analysis File data raid Meta data wiki People Programs

19. Next Gen Data Analysis File data raid Meta data wiki People Programs

20. Automatic data capture - Raw Most structured content can be captured and recorded by programs as it is generated

21. Automatic data capture - Pretty 1/3 All captured automatically, at the 454 machine

22. Automatic data capture - Pretty 2/3 All captured automatically, at the 454 machine

23. Automatic data capture - Pretty 3/3 All captured automatically, at the 454 machine

24. File Browser Access raw files

25. Next Gen Data Analysis CGI File data raid Meta data wiki People Programs

26. Custom HTML Tricks you’ve never seen wikipedia do. Adding a record via a form. Run custom perl/php code. Generate *any* html on the fly. AJAX

27. Project Dashboard Steer the ongoing analysis

28. User Interface Traditionally LIMS UI Must be done up-front Can be hardest part to get right Wiki provides a minimal UI Instantaneous and consistent Focus on data first Improve it when and where needed

29. As Details Emerge Users can edit data with only a browser Won’t make 5000 changes by hand But 50 is faster and cheaper than calling in a coder Write software only for the heavy lifting Cost effective only if we will do something many times Deferred until patterns emerge and become tedious

30. Reading Wiki From Perl use Perlwikipedia; $bot = Perlwikipedia->new; $bot->set_wiki($hostname, $directory); $bot->login($username, $password); $pagetext = $bot->get_text("Main Page");

31. Edit Wiki Pages @pages = $bot->get_all_pages_in_category( "Category:Is_a_454_Run"); foreach $page (@pages) { $oldtext = $bot->get_text($page); $newtext ="$oldtext changed by bot"; $bot->edit($page, $newtext, $comment); }

32. Dilbert 3

33. SPARQL PREFIX abc: <http://mynamespace.com/exampleOntologie#> SELECT ?capital ?country WHERE { ?x abc:cityname ?capital. ?y abc:countryname ?country. ?x abc:isCapitalOf ?y. ?y abc:isInContinent abc:africa. } Select all African capitol cities from wikipedia

34. DBpedia.org Use SPARQL to query directly against wikipedia Make a local relational cache Query with SQL You hide your SQL behind a layer anyway…..right?

35. Concerns It can’t scale see http://en.wikipedia.org No theoretical basis This is a semantic web

36. Conclusion Extremely flexible database Unifies next gen, microarrays, inventory, … History of all changes Initiate/steer tasks Perl for deep customization The human intelligence of a wiki