The document discusses developments in e-Science and online tools for scientific communities. It describes how electronic lab notebooks, wikis, blogs and workflows can enable collaboration and knowledge sharing. Computational experiments using web services allow combining various experts' tools and data. E-science approaches leverage many minds to generate hypotheses, publish results and enable virtual laboratories.

1. Chromatin research in cyberspace Developments in e-Science and on the web for scientific communities By Marco Roos acknowledging Carole Goble, Jeremy Frey, David de Roure, Alan Williams, Mark Wilkinson, Ben Good, Katy Wolstencroft, Scott Marshall, Jano van Hemert, Wendy Bickmore and many others for slides and inspiration

3. Research flow

4. Technology

5. Knowledge flow

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

7. Some?

8. Many?

9. Research flow

10. A ‘million minds’ helping you hypothesize WikiPathways WikiProtein and Knewco’s Concept Web

11. Research flow

13. OpenWetware.org – Is Maniatis a relic of the past?

14. Data flow & computation

15. I need more than excel

16. Bioinformatics A typical bioinformatician

17. Bioinformatics A biologist behind a computer who (just) learned perl

18. /* * 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; }

19. ‘ Old school’ bioinformatics approach Local Database Local Database

20. Theme Not an e-Science approach

21. The ‘spaghetti’ approach

24. Which diseases may be associated with my protein of interest EZH2

25. Biological knowledge extraction Biological question/model Computational experiment Extracted knowledge I want to do it my way >17 million citations +400,000/yr

26. Combining expertise Edgar Meij Information retrieval expert

27. Combining expertise Sophia Katrenko Machine learning expert

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

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

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

31. e -Science collaboration AIDA toolbox

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

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

34. “ Collaboration through Web Services” e -bioscientist

35. A nice experiment design

36. A not so nice experiment design

37. 05/06/09 BioAID

38. A workflow Protocol for a computational experiment

39. 05/06/09 BioAID

40. Sharing and publishing my designs

41. Bio AID Disease Discovery workflow 05/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’

42. Bio AID Disease discovery workflow 05/06/09 BioAID

43. Bio AID Disease discovery workflow 05/06/09 BioAID

44. An insightful computational experiment

45. /* * 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; }

46. e -Science is about using many brains Want this…

47. e -Science is about leveraging the use of more brains … need this

48. Upcoming: e -Laboratories Obesity e-Labs, SysMo, BioAssist,… your e-Laboratory?

49. Research flow

50. Traditional peer-reviewed loosing its monopoly? WikiPathways WikiProtein and Knewco’s Concept Web Publish & share research packs

52. http://staff.science.uva.nl/~roos/ChromatinWorkgroup/

53. Thank you for your help and attention Acknowledgements Carole Goble, Jeremy Frey, David de Roure, Alan Williams, Mark Wilkinson, Ben Good, Katy Wolstencroft, Scott Marshall, Jano van Hemert, Wendy Bickmore and many others for slides and inspiration http://adaptivedisclosure.org http://myexperiment.org http:// nbic.nl http://vl-e.nl http://mygrid.org.uk http:// omii.ac.uk Share your thoughts on http:// staff.science.uva.nl/~roos/ChromatinWorkgroup / This was a PAL to peer presentation; PAL = Project and Area Liaison for OMII-UK, an organisation founded to deliver and sustain e-science products