feasting onbrainswithworkflows

Wednesday 12 April 2023 BioAID 1

Feasting on Brainswith Taverna and myExperiment

Marco Roos, Katy Wolstencroft

acknowledgingCarole 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


Why should a biologist be interested in workflows?

Leiden Students Say…• …


Hold those thoughts…


A biologist


Mouse fibroblast (skin) cells

My prime interestStructure and function of DNA in the nucleus

Esc

heric

hia

coli


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


Thousands of DatabasesLow & 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


Biomedical knowledge repository

PubMed statisticshttp://www.ncbi.nlm.nih.gov/entrez

>20 million citations>400,000 added/year~70,000 searches/month

Does not fit

…

Does not compute

04/12/2023 BioAID 9

My brain is too small !


A typical biologist…

A needy biologist

Tiny brain

Lots of data to deal with

Lots of methodsand algorithms to try and combine

No computationalsuperpowers

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 computerwho (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.\n");fprintf(stderr, "%s", PQerrorMessage(conn));exit(1);

}else printf("Connection ok\n");

sprintf(querystring, "SELECT * FROM chromosomes");printf("%s\n", 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\n", PQgetvalue(tuples,i,0));

}return TRUE;

}

int validquery(PGresult *result, char *querystring){

printf(" in validquery\n");if (PQresultStatus(result) != PGRES_TUPLES_OK) {

printf("Query %s failed.\n", querystring);fprintf(stderr, "Query %s failed.\n", querystring);return FALSE;

}return TRUE;

}


The ‘spaghetti’ approach

04/12/2023 BioAID 16

Computational tools graveyard rephrasing David Shotton, University of Oxford


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


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)


“Collaboration through Web Services”

Bio-text mining expertBioSemantics group,Erasmus University Rotterdam

Martijn Schuemie



Biological Database expert

Hideaki Sugawara


AIDA toolbox

e-Science collaboration



e-bioscientist


A nice experiment design


A not so nice experiment design


A workflowProtocol for a computational experiment


Feasting on brilliant brains with Taverna!

Want this…


The enhanced Biologist


What are the benefits of the Workflow approach?

Leiden Students Think…• …

feasting onbrainswithworkflows

Education

bioaid printfquery

int mincount

int row

proteinprotein interaction

int printresultspgresult

int ifor

int validquerypgresult

int main