From Laboratory to e-Laboratory

From Laboratory to e-Laboratory?
Introduction for ‘Lab-J’ of the LUMC Human Genetics Department
Marco Roos
Acknowledging the colleagues from BioSemantics, myGrid, OMII-UK, AID, The LUMC BioInformatics Expertise Centre

Introducing
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Me

Liaison biology/bioinformatics – informatics
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Biologist and bioinformatician, e-(bio)science researcher
Coordinator BioSemantics group LeidenHuman Genetics Department Leiden University Medical Centre and Informatics Institute University of Amsterdam
Project or Area Liaison (PAL) OMII-UK
Member BioAssist programme committee NBIC

also about
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You

First about
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Me

My C.V. before e-Sciencebefore 2003
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Molecular & Cellular biology(MSc)
microscopy and image analysis of chromosome structure
‘minor’ computer science
Image analysis methods to measure DNA content in bull sperm cells(civil service)
Chromatin structure & function(PhD molecular cytology)
F.I.S.H., microscopy, image analysis, statistics
3-D chromosome structure during cell cycle (no luck)
DNA movement in Escherichia coli(success)
Human Transcriptome Map (post-doc)
Gene expression to human genome sequence
Analysis of regions of increased gene expression

MotivationStructure and function of DNA in the nucleus
Escherichia coli
Muntiacusmuntjak

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Why bioinformatics?
Lab-J suggests…

23/09/2009
BioAID
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Bioinformatics
A typical bioinformatician

23/09/2009
BioAID
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Bioinformatics
A biologist behind a computer
who (just) learned perl

23/09/2009
BioAID
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/*
* determines ridges in htm expression table
*/
#include "ridge.h"
intselecthtm(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));
}
intis_ridge(PGresult *htmtable, int row, double exprthreshold, intmincount)
/* 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;
inti;
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;
}
intprintresults(PGresult *tuples)
{
inti;
for (i=0; i< PQntuples(tuples) && i < 10; i++)
{
printf("%d, ", i);
printf("%s ", PQgetvalue(tuples,i,0));
}
return TRUE;
}
intvalidquery(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;
}

State of the art applied computer science to a biologist
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Why e-science? What is wrong with bioinformatics?
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Human geneticists think…

Why should a biologist be interested in e-science?
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BioAssistantsguessed…
Involves Computation
Interpretation of results
Biology isn’t that interesting
Reduce reinvention of the wheel
Current lack of standards
Sharing results
Reshaping biology
Synergy between different sciences
Emerging Data driven science

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Why e-Science?
Lots of data to deal with
Single tiny brain
Lots of knowledge to deal with
No computationalsuperpowers
Lots of methodsand algorithms to try and combine
Aneedy biologist

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1070 databasesNucleic 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

23/09/2009
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Traditional data integration in bioinformatics
Local
Database
Local
Database

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The ‘spaghetti’ approach

Some of my observations
Reinvention
How many reannotation pipelines do you need?
Little reuse of components
Reproducibility
Black boxes
Emphasis not on clarity
Can we understand bioinformatics as wet lab protocols?
Focus on technicalities, not biological analysis
Should bioinformaticians write ‘job submission’ scripts?
Data graveyards
Do we need >1000 databases?
Can we understand our own data?
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How did I end up here?
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Marco Roos
Biologist and bioinformatician, Post-doc e-(bio)scienceHuman Genetics Department Leiden University Medical Centre and Informatics Institute University of Amsterdam
Project or Area Liaison (PAL) OMII-UK
Member BioAssist programme committee NBIC

Some examples from field of e-Science
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Enhancement 1: Workflows(Taverna workflow)
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Enhancement 2: exploiting brains
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Exploiting Brains By Web Servicessource: http://biocatalogue.org(launched at ISMB2009)
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>1000 annotated services, >3000 known to Taverna
Includes BioMart, R, Text mining, Kegg, NCBI Pubmed, Ensembl, etc.
Web Services run remotely

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Exploiting more brains by sharing workflowssource: http://myExperiment.org
Social community web site for scientists
2300 registered users in two years
750 workflows

Bioinformatics and e-science
Customized experiments with reusable components
Single purpose,single person, black box
application
My component
Your component
My component
My component
Your component

What do we know of our data?
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Sufficient?

Query discoveries?
Query across experiment?
Fit biological modelling?
Good basis for new experiments?
Flexible enough?

Model-based data integration
Computer readable model
Biologist readable model
Biological concepts (‘myModel’)
Data
Marshall et al., International Workshop on Knowledge Systems in Bioinformatics 2006
Post et al., Bioinformatics 2007

Model based data integrationExample: UCSC genome browser
partOf

Semantic Web (Linked Open Data)
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Empower me with a ‘virtual brain’
*
My ws
Your ws
My ws
My ws
Your ws
* From P.J. Verschure, Journal of Cellular Biochemistry 2006, vol. 99(1), pg 23-34

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Query
Add query to semantic model
Retrieve documents from Medline
Add documents (IDs) to semantic model
Extract proteins (Homo sapiens)
Add proteins to semantic model
Calculate ranking scores
Add scores to semantic model
Create biological cross references
Add cross references to semantic model
Convert to table (html)
Workflow and Semantic Web

Concept web from a users point of view
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e-Laboratories and e-Laboratory factories

e-Galaxy for NBIC
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Galaxy as front end
Workflows & Web Services
Grid enabled Taverna
MOLGENIS
Semantic/Concept Web
myExperiment/BioCatalogue
Scientific Research Objects

Vacancy! (software engineer)

SRO = a pack of models
- Tool models
- Data/ui models
- Flow models
+Attached data
SRO enactment = a running e-laboratory
Tools
Uses tools services
Model
SROs
my protocols
my data
my protocols
my data
Portal to workflows
2.0
mashup
data
Flows
mashup
tools
e-biologist
e-bioinformatician
Uses data services
Portal to workflows
Data
programmatic interaction
user interfacing

e-Galaxy mock-up
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Suggestions by semantic components
Your Scientific Research Object
Underlying workflow
Related research and documents
Adlsjfladjslfadsflkjalfdadsf
Adfljadlfkjaladlfjlakdjflkjadf
Adflkjlakjlkjadsflakdfjlfladoioewn
Jlakdsfooiuwfjaoijaoisdflvoaijdf
MOLGENIS
Convert
Import/Export
Research Objects
Store
Configure
Run

e-Science requirement: Reuse
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E-Laboratorycomponent

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http://www.epigenius.org/(mock-up)

Research and development aims
Automated support for hypothesis formation
E.g. on epigenetic mechanisms
Apply Workflow, Semantic Web, Concept Web
Concept-based meta-analysis
Automated triple creation from computational analysis
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Research and development ambitions
Co-develop e-Laboratories
e-Galaxy
epiGenius
BioBanking
Help BEC with support environment
Concept Web services
Web services
E-Laboratory components
Transparent creation of triples
Personal semantic repositories
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Liaison
Bioinformatics Expertise Centre LUMC
Statistical and computer science expertise
Generic support
NBIC
BioAssist core software development
Grid tools, Concept Web, e-Labs
BioSemantics Rotterdam
Text mining
Concept profile meta-analysis
AIDUniversity of Amsterdam
e-Science experts
Grid tools
You?
OMII-UK
Manchester, Southampton, Edinburgh
(ca. 30 engineers)
Taverna, myExperiment, e-Labs
Concept Web
Content, tools and infrastructure
W3C Health Care & Life Sciences Interest Group
Semantic Web experts
Linked Open Data

‘e’ for enhance, not enforce
Please help me to help you
Register for:
http://snipurl.com/biosemanticsusers
(http://www.myexperiment.org/groups/211)
Allows me to
Give you preferential treatment
Not spam everybody
Keep you informed
Ask your opinion (user driven development!)
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Visit the BioSemantics web sitehttp://www.biosemantics.org/
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Word of warning
Computer scientists are scientists too!
Need to publish
Score by papers, not by software
Addressed by OMII-UK and BioAssist
Compare
“How can I use it in the clinic?”
“How can I use it in the lab?”
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Dissemination
Come by for help or information
Internal ‘mini-courses’?
Send me suggestions!
Course Managing Life Science Information for PhD students, 2010
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Thank you for your attention
Lots of accessible data
Communitybrain power
Knowledge basesto query
Other people’scomputationalsuperpowers
Web Services, Workflows, and their creatorsavailable
Anenhanced biologist
Homo biologicusenhancis

Demontration
SysMo-SEEK (e-Lab)
BioCatalogue
myExperiment
Taverna
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