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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 team



Monday, 19 March 2012               BioAID                               1
Why should a biologist be interested in workflows?




Leiden Students Say…
•…




        Monday, 19 March 2012        2               BioAID
Hold those thoughts…




    Monday, 19 March 2012   BioAID   3
A biologist
Monday, 19 March 2012        BioAID   4
My prime interest
Structure and function of DNA in the nucleus

                                                   Mouse fibroblast (skin) cells
        Escherichia coli




                           Monday, 19 March 2012                   BioAID          5
Connecting the dots
(example: protein interaction network in yeast)




           Monday, 19 March 2012                  BioAID   6
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 course




Monday, 19 March 2012   7                       BioAID
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
My brain is too small !




        3/19/2012         BioAID   9
A typical biologist…


              Lots of data
              to deal with
                                                   Tiny brain


Lots of knowledge
to deal with



   Lots of methods                              No
   and algorithms to try                        computational
   and combine                                  superpowers



                            A needy biologist
           Monday, 19 March 2012    BioAID             10
Start at the beginning


                                        I have a
                                        computationa
                                        l question…




       Monday, 19 March 2012   BioAID         11
‘Old school’ Bioinformatics




                                A typical bioinformatician




        Monday, 19 March 2012               BioAID           12
‘Old school’ Bioinformatics




                            A biologist behind a computer
                                who (just) learned perl



        Monday, 19 March 2012            BioAID             13
/*
       * 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
The ‘spaghetti’ approach




        Monday, 19 March 2012   BioAID   15
Computational tools graveyard
rephrasing David Shotton, University of Oxford




           3/19/2012                             BioAID   16
Which diseases are
associated with my
protein of interest
‘EZH2’




    Monday, 19 March 2012   BioAID   17
Combining expertise




                                  Edgar Meij




                           Information retrieval expert


       Monday, 19 March 2012             BioAID           18
Combining expertise




                               Sophia Katrenko




                               Machine learning expert


       Monday, 19 March 2012             BioAID          19
Combining expertise




                               Willem van Hage




                               Semantic web expert
                               (and bass guitar player)


       Monday, 19 March 2012              BioAID          20
“Collaboration through Web Services”




                                Martijn Schuemie




                          Bio-text mining expert
                          BioSemantics group,
                          Erasmus University Rotterdam
        Monday, 19 March 2012          BioAID            21
“Collaboration through Web Services”




                                Hideaki Sugawara




                                Biological Database expert


        Monday, 19 March 2012               BioAID           22
e-Science collaboration




                                         AIDA
                                         toolbox




        Monday, 19 March 2012   BioAID         23
“Collaboration through Web Services”




                                e-bioscientist


        Monday, 19 March 2012       BioAID       24
A nice experiment design




        Monday, 19 March 2012   BioAID   25
A not so nice experiment design




        Monday, 19 March 2012     BioAID   26
A workflow
Protocol for a computational experiment




       Monday, 19 March 2012     BioAID   27
Feasting on brilliant brains with Taverna!


                               Want this…




       Monday, 19 March 2012       BioAID    28
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             BioAID

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Feasting onbrainswithworkflows

  • 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 team Monday, 19 March 2012 BioAID 1
  • 2. Why should a biologist be interested in workflows? Leiden Students Say… •… Monday, 19 March 2012 2 BioAID
  • 3. Hold those thoughts… Monday, 19 March 2012 BioAID 3
  • 4. A biologist Monday, 19 March 2012 BioAID 4
  • 5. My prime interest Structure and function of DNA in the nucleus Mouse fibroblast (skin) cells Escherichia coli Monday, 19 March 2012 BioAID 5
  • 6. Connecting the dots (example: protein interaction network in yeast) Monday, 19 March 2012 BioAID 6
  • 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 course Monday, 19 March 2012 7 BioAID
  • 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. My brain is too small ! 3/19/2012 BioAID 9
  • 10. A typical biologist… Lots of data to deal with Tiny brain Lots of knowledge to deal with Lots of methods No and algorithms to try computational and combine superpowers A needy biologist Monday, 19 March 2012 BioAID 10
  • 11. Start at the beginning I have a computationa l question… Monday, 19 March 2012 BioAID 11
  • 12. ‘Old school’ Bioinformatics A typical bioinformatician Monday, 19 March 2012 BioAID 12
  • 13. ‘Old school’ Bioinformatics A biologist behind a computer who (just) learned perl Monday, 19 March 2012 BioAID 13
  • 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. The ‘spaghetti’ approach Monday, 19 March 2012 BioAID 15
  • 16. Computational tools graveyard rephrasing David Shotton, University of Oxford 3/19/2012 BioAID 16
  • 17. Which diseases are associated with my protein of interest ‘EZH2’ Monday, 19 March 2012 BioAID 17
  • 18. Combining expertise Edgar Meij Information retrieval expert Monday, 19 March 2012 BioAID 18
  • 19. Combining expertise Sophia Katrenko Machine learning expert Monday, 19 March 2012 BioAID 19
  • 20. Combining expertise Willem van Hage Semantic web expert (and bass guitar player) Monday, 19 March 2012 BioAID 20
  • 21. “Collaboration through Web Services” Martijn Schuemie Bio-text mining expert BioSemantics group, Erasmus University Rotterdam Monday, 19 March 2012 BioAID 21
  • 22. “Collaboration through Web Services” Hideaki Sugawara Biological Database expert Monday, 19 March 2012 BioAID 22
  • 23. e-Science collaboration AIDA toolbox Monday, 19 March 2012 BioAID 23
  • 24. “Collaboration through Web Services” e-bioscientist Monday, 19 March 2012 BioAID 24
  • 25. A nice experiment design Monday, 19 March 2012 BioAID 25
  • 26. A not so nice experiment design Monday, 19 March 2012 BioAID 26
  • 27. A workflow Protocol for a computational experiment Monday, 19 March 2012 BioAID 27
  • 28. Feasting on brilliant brains with Taverna! Want this… Monday, 19 March 2012 BioAID 28
  • 29. The enhanced Biologist Monday, 19 March 2012 BioAID 29
  • 30. What are the benefits of the Workflow approach? Leiden Students Think… • … Monday, 19 March 2012 30 BioAID