E Science4 Chromatin Research

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Information about E Science4 Chromatin Research
Education

Published on October 15, 2008

Author: MarcoRoos

Source: slideshare.net

Description

Presentation about developments on the web and e-Science that could change we perform chromatin research now or in the future.

Chromatin research in cyberspace Developments in e-Science and on the web for scientific communities By Marco Roos acknowledging Carole Goble, Jeremy Frey, David de Roure, Alan Williams, Mark Wilkinson, Ben Good, Katy Wolstencroft, Scott Marshall, Jano van Hemert, Wendy Bickmore and many others for slides and inspiration

Introduction and disclaimer Marco Roos Biologist and bioinformatician Post-doc e-(bio)science, University of Amsterdam (BioRange/VL-e) Project or Area Liaison (PAL) OMII-UK Member BioAssist programme committee NBIC Not the biggest expert on Web developments

Marco Roos

Biologist and bioinformatician

Post-doc e-(bio)science, University of Amsterdam (BioRange/VL-e)

Project or Area Liaison (PAL) OMII-UK

Member BioAssist programme committee NBIC

Research flow

Technology

Knowledge flow

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

Some?

Many?

Research flow

A ‘million minds’ helping you hypothesize WikiPathways WikiProtein and Knewco’s Concept Web

Research flow

Electronic Laboratory journals and blogs Jeremy Frey, University of Southampton Electronic laboratory notebook Encourage exchange & collaboration Flexible

Electronic laboratory notebook

Encourage exchange & collaboration

Flexible

OpenWetware.org – Is Maniatis a relic of the past?

Data flow & computation

I need more than excel

Bioinformatics A typical bioinformatician

Bioinformatics A biologist behind a computer who (just) learned perl

/* * determines ridges in htm expression table */ #include &quot;ridge.h&quot; int selecthtm(PGconn *conn, char *htmtablename, char *chromname, PGresult *htmtable) { char querystring[256]; sprintf(&quot;SELECT * FROM %s WHERE chrom = %s ORDER BY genstart&quot;, 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, &quot;movmed39expr&quot;)) < 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(&quot;dbname=htm port=6400 user=mroos password=geheim&quot;); if (PQstatus(conn)==CONNECTION_BAD) { fprintf(stderr, &quot;connection to database failed. &quot;); fprintf(stderr, &quot;%s&quot;, PQerrorMessage(conn)); exit(1); } else printf(&quot;Connection ok &quot;); sprintf(querystring, &quot;SELECT * FROM chromosomes&quot;); printf(&quot;%s &quot;, 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(&quot;%d, &quot;, i); printf(&quot;%s &quot;, PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(&quot; in validquery &quot;); if (PQresultStatus(result) != PGRES_TUPLES_OK) { printf(&quot;Query %s failed. &quot;, querystring); fprintf(stderr, &quot;Query %s failed. &quot;, querystring); return FALSE; } return TRUE; }

‘ Old school’ bioinformatics approach Local Database Local Database

Theme Not an e-Science approach

The ‘spaghetti’ approach

Example Demonstration An e -science approach for automated knowledge extraction from literature Roos, Marshall, et al., ISMB/ECCB, Vienna, 2007

Demonstration

An e -science approach for automated knowledge extraction from literature

An e-science approach Combining expertise Collaborating and sharing Technology

Combining expertise

Collaborating and sharing

Technology

Which diseases may be associated with my protein of interest EZH2

Biological knowledge extraction Biological question/model Computational experiment Extracted knowledge I want to do it my way >17 million citations +400,000/yr

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

05/06/09 BioAID

A workflow Protocol for a computational experiment

05/06/09 BioAID

Sharing and publishing my designs

Bio AID Disease Discovery workflow 05/06/09 BioAID AIDA AIDA OMIM service (Japan) AIDA ‘ Taverna shim’ Taverna ‘shim’

Bio AID Disease discovery workflow 05/06/09 BioAID

Bio AID Disease discovery workflow 05/06/09 BioAID

An insightful computational experiment

/* * determines ridges in htm expression table */ #include &quot;ridge.h&quot; int selecthtm(PGconn *conn, char *htmtablename, char *chromname, PGresult *htmtable) { char querystring[256]; sprintf(&quot;SELECT * FROM %s WHERE chrom = %s ORDER BY genstart&quot;, 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, &quot;movmed39expr&quot;)) < 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(&quot;dbname=htm port=6400 user=mroos password=geheim&quot;); if (PQstatus(conn)==CONNECTION_BAD) { fprintf(stderr, &quot;connection to database failed. &quot;); fprintf(stderr, &quot;%s&quot;, PQerrorMessage(conn)); exit(1); } else printf(&quot;Connection ok &quot;); sprintf(querystring, &quot;SELECT * FROM chromosomes&quot;); printf(&quot;%s &quot;, 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(&quot;%d, &quot;, i); printf(&quot;%s &quot;, PQgetvalue(tuples,i,0)); } return TRUE; } int validquery(PGresult *result, char *querystring) { printf(&quot; in validquery &quot;); if (PQresultStatus(result) != PGRES_TUPLES_OK) { printf(&quot;Query %s failed. &quot;, querystring); fprintf(stderr, &quot;Query %s failed. &quot;, querystring); return FALSE; } return TRUE; }

e -Science is about using many brains Want this…

e -Science is about leveraging the use of more brains … need this

Upcoming: e -Laboratories Obesity e-Labs, SysMo, BioAssist,… your e-Laboratory?

Research flow

Traditional peer-reviewed loosing its monopoly? WikiPathways WikiProtein and Knewco’s Concept Web Publish & share research packs

Conclusion E-science and the web enable the use of many minds Wiki’s for hypotheses Blogs for lab journals and protocols Workflows for computational experiments e -Laboratories to enable it for you

E-science and the web enable the use of many minds

Wiki’s for hypotheses

Blogs for lab journals and protocols

Workflows for computational experiments

e -Laboratories to enable it for you

http://staff.science.uva.nl/~roos/ChromatinWorkgroup/

Thank you for your help and attention Acknowledgements Carole Goble, Jeremy Frey, David de Roure, Alan Williams, Mark Wilkinson, Ben Good, Katy Wolstencroft, Scott Marshall, Jano van Hemert, Wendy Bickmore and many others for slides and inspiration http://adaptivedisclosure.org http://myexperiment.org http:// nbic.nl http://vl-e.nl http://mygrid.org.uk http:// omii.ac.uk Share your thoughts on http:// staff.science.uva.nl/~roos/ChromatinWorkgroup / This was a PAL to peer presentation; PAL = Project and Area Liaison for OMII-UK, an organisation founded to deliver and sustain e-science products

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