This document summarizes a presentation about using the Taverna workflow system and myExperiment repository for collaborative bioinformatics research. It discusses how Taverna allows researchers to combine multiple computational methods and online data sources into reproducible workflows. The presenter describes their own experiences with early "spaghetti code" approaches to bioinformatics and how e-Science tools now enable more insightful experiments through collaboration and sharing of workflows.

1. Feasting on Brains with Taverna Tutorial and demonstration by Marco Roos acknowledging Carole Goble, Dave de Roure, Alan Williams, Jiten Bhagat, Katy Wolstencroft, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem van Hage, Scott Marshall, Pieter Adriaans, NBIC, OMII-UK, the myGrid team

4. Introducing myself A biologist

5. My prime interest Structure and function of DNA in the nucleus Escherichia coli Mouse fibroblast (skin) cells

7. Components controlling structure & function of DNA

8. Connecting the dots (example: protein interaction network in yeast)

10. A typical biologist… A needy biologist Tiny brain Lots of data to deal with Lots of methods and algorithms to try and combine No computational superpowers Lots of knowledge to deal with

11. Start at the beginning I have a computational question…

12. ‘ Old school’ Bioinformatics A typical bioinformatician

13. ‘ Old school’ Bioinformatics A biologist behind a computer who (just) learned perl

14. /* * determines ridges in htm expression table */ #include &quot;ridge.h&quot; int selecthtm(PGconn *conn, char *htmtablename, char *chromname, PGresult *htmtable) { char querystring[256]; sprintf(&quot;SELECT * FROM %s WHERE chrom = %s ORDER BY genstart&quot;, htmtablename, chromname); htmtable = PQexec(conn, querystring); return(validquery(htmtable, querystring)); } int is_ridge(PGresult *htmtable, int row, double exprthreshold, int mincount) /* determines if mincount genes in a row are (part of) a ridge */ /* pre: htmtable is valid and sorted on genStart (ascending) /* post: { if (mincount<=0) return TRUE; if (row>=PQntuples(htmtable)) return FALSE; if(PQgetvalue(htmtable, 0, PQfnumber(htmtable, &quot;movmed39expr&quot;)) < exprthreshold) { return FALSE; } return(is_ridge(htmtable, ++row, exprthreshold, --mincount)); } int main() { PGconn *conn; /* holds database connection */ char querystring[256]; /* query string */ PGresult *result; int i; conn = PQconnectdb(&quot;dbname=htm port=6400 user=mroos password=geheim&quot;); if (PQstatus(conn)==CONNECTION_BAD) { fprintf(stderr, &quot;connection to database failed.&quot;); fprintf(stderr, &quot;%s&quot;, PQerrorMessage(conn)); exit(1); } else printf(&quot;Connection ok&quot;); sprintf(querystring, &quot;SELECT * FROM chromosomes&quot;); printf(&quot;%s&quot;, querystring); result = PQexec(conn, querystring); if (validquery(result, querystring)) { printresults(result); } else { PQclear(result); PQfinish(conn); return FALSE; } PQclear(result); PQfinish(conn); return TRUE; } int printresults(PGresult *tuples) { int i; for (i=0; i< PQntuples(tuples) && i < 10; i++) { printf(&quot;%d, &quot;, i); printf(&quot;%s&quot;, PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(&quot; in validquery&quot;); if (PQresultStatus(result) != PGRES_TUPLES_OK) { printf(&quot;Query %s failed.&quot;, querystring); fprintf(stderr, &quot;Query %s failed.&quot;, querystring); return FALSE; } return TRUE; }

15. The ‘spaghetti’ approach

16. Computational tools graveyard rephrasing David Shotton

17. Database survival: <20% ‘no problems’

18. Data graveyard quoting David Shotton

20. e -Science? ‘ enhanced science’ Research and development for enhancing science

22. Which diseases are associated with my protein of interest ‘EZH2’

23. Biological knowledge extraction Biological question/model Computational experiment Extracted knowledge >17 million citations +400,000/yr

25. Combining expertise Edgar Meij Information retrieval expert

26. Combining expertise Sophia Katrenko Machine learning expert

27. Combining expertise Willem van Hage Semantic web expert (and bass guitar player)

28. Combining expertise Towards a knowledge framework Computer scientist and bioinformatician Scott Marshall

29. The AIDA toolbox, Web Services for knowledge extraction and knowledge management

30. e -Science collaboration AIDA toolbox

31. “ Collaboration through Web Services” Bio-text mining expert BioSemantics group, Erasmus University Rotterdam Martijn Schuemie

32. “ Collaboration through Web Services” Biological Database expert Hideaki Sugawara

33. “ Collaboration through Web Services” e -bioscientist

34. A nice experiment design

35. A not so nice experiment design

36. A workflow Protocol for a computational experiment

37. 10/06/09 BioAID

38. 10/06/09 BioAID

39. Sharing and publishing my designs

40. Bio AID Disease Discovery workflow 10/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’

41. Bio AID Disease discovery workflow 10/06/09 BioAID

42. Bio AID Disease discovery workflow 10/06/09 BioAID

43. An insightful computational experiment

44. Feasting on brilliant brains with Taverna! Want this…

45. Feasting on brilliant brains with Taverna! … need this

46. How many brains do you want to use? – One?

47. Some?

48. Many? Some statistics >4000 Taverna users >3000 Web Services in Taverna >400 workflows on myExperiment >1000 registered myExperiment users in one year

49. myExperiment users

54. For feasting on brains with Semantic Web formats and tools (and workflows) please visit poster 31