Feasting on Brains           with Taverna and myExperiment                        Marco Roos, Katy Wolstencroft           ...
Why should a biologist be interested in workflows?Leiden Students Say…•…        Monday, 19 March 2012        2            ...
Hold those thoughts…    Monday, 19 March 2012   BioAID   3
A biologistMonday, 19 March 2012        BioAID   4
My prime interestStructure and function of DNA in the nucleus                                                   Mouse fibr...
Connecting the dots(example: protein interaction network in yeast)           Monday, 19 March 2012                  BioAID...
Thousands of                            Databases                            Low & High Throughput                        ...
Biomedical knowledge repository    PubMed statistics    http://www.ncbi.nlm.nih.gov/entrez    >20 million citations    >40...
My brain is too small !        3/19/2012         BioAID   9
A typical biologist…              Lots of data              to deal with                                                  ...
Start at the beginning                                        I have a                                        computationa...
‘Old school’ Bioinformatics                                A typical bioinformatician        Monday, 19 March 2012        ...
‘Old school’ Bioinformatics                            A biologist behind a computer                                who (j...
/*       * determines ridges in htm expression table      */      #include "ridge.h"      int selecthtm(PGconn *conn, char...
The ‘spaghetti’ approach        Monday, 19 March 2012   BioAID   15
Computational tools graveyardrephrasing David Shotton, University of Oxford           3/19/2012                           ...
Which diseases areassociated with myprotein of interest‘EZH2’    Monday, 19 March 2012   BioAID   17
Combining expertise                                  Edgar Meij                           Information retrieval expert    ...
Combining expertise                               Sophia Katrenko                               Machine learning expert   ...
Combining expertise                               Willem van Hage                               Semantic web expert       ...
“Collaboration through Web Services”                                Martijn Schuemie                          Bio-text min...
“Collaboration through Web Services”                                Hideaki Sugawara                                Biolog...
e-Science collaboration                                         AIDA                                         toolbox      ...
“Collaboration through Web Services”                                e-bioscientist        Monday, 19 March 2012       BioA...
A nice experiment design        Monday, 19 March 2012   BioAID   25
A not so nice experiment design        Monday, 19 March 2012     BioAID   26
A workflowProtocol for a computational experiment       Monday, 19 March 2012     BioAID   27
Feasting on brilliant brains with Taverna!                               Want this…       Monday, 19 March 2012       BioA...
The enhanced Biologist      Monday, 19 March 2012   BioAID   29
What are the benefits of the Workflow approach?Leiden Students Think…• …        Monday, 19 March 2012      30             ...
Upcoming SlideShare
Loading in …5
×

Feasting onbrainswithworkflows

417 views
381 views

Published on

About how the workflow paradigm helps collaborative bioinformatics.

Published in: Education, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
417
On SlideShare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Feasting onbrainswithworkflows

  1. 1. Feasting on Brains with Taverna and myExperiment Marco Roos, Katy Wolstencroft acknowledging Carole Goble, Dave de Roure, Alan Williams, Jiten Bhagat, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem van Hage, M. Scott Marshall, Pieter Adriaans, NBIC, OMII-UK, the myGrid teamMonday, 19 March 2012 BioAID 1
  2. 2. Why should a biologist be interested in workflows?Leiden Students Say…•… Monday, 19 March 2012 2 BioAID
  3. 3. Hold those thoughts… Monday, 19 March 2012 BioAID 3
  4. 4. A biologistMonday, 19 March 2012 BioAID 4
  5. 5. My prime interestStructure and function of DNA in the nucleus Mouse fibroblast (skin) cells Escherichia coli Monday, 19 March 2012 BioAID 5
  6. 6. Connecting the dots(example: protein interaction network in yeast) Monday, 19 March 2012 BioAID 6
  7. 7. Thousands of Databases Low & High Throughput Proteomics, Genomics, Transcriptomics, Protein sequence prediction, Phenotypic studies, Phylogeny, Sequence analysis, Protein Structure prediction, Protein- protein interaction, Metabolomics, Model organism collections, Systems Biology, Epidemiology, etcetera … All with a splendid interface … all different, of courseMonday, 19 March 2012 7 BioAID
  8. 8. Biomedical knowledge repository PubMed statistics http://www.ncbi.nlm.nih.gov/entrez >20 million citations >400,000 added/year ~70,000 searches/month … Does not compute Monday, 19 March 2012 BioAID 8
  9. 9. My brain is too small ! 3/19/2012 BioAID 9
  10. 10. A typical biologist… Lots of data to deal with Tiny brainLots of knowledgeto deal with Lots of methods No and algorithms to try computational and combine superpowers A needy biologist Monday, 19 March 2012 BioAID 10
  11. 11. Start at the beginning I have a computationa l question… Monday, 19 March 2012 BioAID 11
  12. 12. ‘Old school’ Bioinformatics A typical bioinformatician Monday, 19 March 2012 BioAID 12
  13. 13. ‘Old school’ Bioinformatics A biologist behind a computer who (just) learned perl Monday, 19 March 2012 BioAID 13
  14. 14. /* * determines ridges in htm expression table */ #include "ridge.h" int selecthtm(PGconn *conn, char *htmtablename, char *chromname, PGresult *htmtable) { char querystring[256]; sprintf("SELECT * FROM %s WHERE chrom = %s ORDER BY genstart", 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, "movmed39expr")) < 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("dbname=htm port=6400 user=mroos password=geheim"); if (PQstatus(conn)==CONNECTION_BAD) { fprintf(stderr, "connection to database failed.n"); fprintf(stderr, "%s", PQerrorMessage(conn)); exit(1); } else printf("Connection okn"); sprintf(querystring, "SELECT * FROM chromosomes"); printf("%sn", 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("%d, ", i); printf("%sn", PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(" in validqueryn"); if (PQresultStatus(result) != PGRES_TUPLES_OK)Monday, 19 March 2012 { BioAID printf("Query %s failed.n", querystring); 14
  15. 15. The ‘spaghetti’ approach Monday, 19 March 2012 BioAID 15
  16. 16. Computational tools graveyardrephrasing David Shotton, University of Oxford 3/19/2012 BioAID 16
  17. 17. Which diseases areassociated with myprotein of interest‘EZH2’ Monday, 19 March 2012 BioAID 17
  18. 18. Combining expertise Edgar Meij Information retrieval expert Monday, 19 March 2012 BioAID 18
  19. 19. Combining expertise Sophia Katrenko Machine learning expert Monday, 19 March 2012 BioAID 19
  20. 20. Combining expertise Willem van Hage Semantic web expert (and bass guitar player) Monday, 19 March 2012 BioAID 20
  21. 21. “Collaboration through Web Services” Martijn Schuemie Bio-text mining expert BioSemantics group, Erasmus University Rotterdam Monday, 19 March 2012 BioAID 21
  22. 22. “Collaboration through Web Services” Hideaki Sugawara Biological Database expert Monday, 19 March 2012 BioAID 22
  23. 23. e-Science collaboration AIDA toolbox Monday, 19 March 2012 BioAID 23
  24. 24. “Collaboration through Web Services” e-bioscientist Monday, 19 March 2012 BioAID 24
  25. 25. A nice experiment design Monday, 19 March 2012 BioAID 25
  26. 26. A not so nice experiment design Monday, 19 March 2012 BioAID 26
  27. 27. A workflowProtocol for a computational experiment Monday, 19 March 2012 BioAID 27
  28. 28. Feasting on brilliant brains with Taverna! Want this… Monday, 19 March 2012 BioAID 28
  29. 29. The enhanced Biologist Monday, 19 March 2012 BioAID 29
  30. 30. What are the benefits of the Workflow approach?Leiden Students Think…• … Monday, 19 March 2012 30 BioAID

×