Feasting onbrainswithworkflows
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Feasting onbrainswithworkflows

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About how the workflow paradigm helps collaborative bioinformatics.

About how the workflow paradigm helps collaborative bioinformatics.

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Feasting onbrainswithworkflows Feasting onbrainswithworkflows Presentation Transcript

  • 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
  • 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 biologistMonday, 19 March 2012 BioAID 4
  • My prime interestStructure 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 courseMonday, 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 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
  • 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 graveyardrephrasing David Shotton, University of Oxford 3/19/2012 BioAID 16
  • Which diseases areassociated with myprotein 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 workflowProtocol 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