Feasting On Brains With Taverna Public

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

Feasting on your brain!

Please help me by filling out the form

preferably on

http://www.tinyurl.com/TavernaBrains

What can Taverna do for me?

Benelux bioinformaticians think…

Introducing myself A biologist

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

How did I end up here?

Marco Roos

Biologist and bioinformatician (e-bioscientist) at the Informatics Institute, University of Amsterdam (BioRange/VL-e)

Project or Area Liaison (PAL) OMII-UK/myGrid

Member BioAssist programme committee NBIC

Member UK All Hands e-Science Foundation

Components controlling structure & function of DNA

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

1070 databases Nucleic Acids Research Jan 2008 (96 in Jan 2001)

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

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

Start at the beginning I have a computational question…

‘ Old school’ Bioinformatics A typical bioinformatician

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

/* * 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. "); fprintf(stderr, "%s", PQerrorMessage(conn)); exit(1); } else printf("Connection ok "); sprintf(querystring, "SELECT * FROM chromosomes"); printf("%s ", 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("%s ", PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(" in validquery "); if (PQresultStatus(result) != PGRES_TUPLES_OK) { printf("Query %s failed. ", querystring); fprintf(stderr, "Query %s failed. ", querystring); return FALSE; } return TRUE; }

The ‘spaghetti’ approach

Computational tools graveyard rephrasing David Shotton

Database survival: <20% ‘no problems’

Data graveyard quoting David Shotton

Old school bioinformatics for biologists

Lots of data, knowledge, and methods to deal with

Bioinformaticians make spaghetti and graveyards

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

What about…

e -Science?

‘ enhanced science’

Research and development from the field of computer science to enhance science with their methodologies

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

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

An e-science approach

Combining expertise

Collaborating and sharing

Technology

Combining expertise Edgar Meij Information retrieval expert

Combining expertise Sophia Katrenko Machine learning expert

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

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

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

e -Science collaboration AIDA toolbox

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

“ Collaboration through Web Services” Biological Database expert Hideaki Sugawara

“ Collaboration through Web Services” e -bioscientist

A nice experiment design

A not so nice experiment design

A workflow Protocol for a computational experiment

10/06/09 BioAID

Sharing and publishing my designs

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

Bio AID Disease discovery workflow 10/06/09 BioAID

An insightful computational experiment

Feasting on brilliant brains with Taverna! Want this…

Feasting on brilliant brains with Taverna! … need this

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

Some?

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

myExperiment users