Motivation: modernizing (life) science
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Homo biologicus in his natural habitat
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A mailing list for the Homo biologicus
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Sharing a calendar for the Homo biologicus
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/*
* 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
/* determines if mincount genes in a
/* pre: htmtable is valid and sorted
/* post:
{
if (mincount<=0)
row, double exprthreshold, int mincount)
row are (part of) a ridge */
on genStart (ascending)
return TRUE;
if (row>=PQntuples(htmtable)) return FALSE;
}
int main()
{
if(PQgetvalue(htmtable, 0, PQfnumber(htmtable, "movmed39expr")) < exprthreshold)
{
return FALSE;
}
return(is_ridge(htmtable, ++row, exprthreshold, --mincount));
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;
}
14/09/2009
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;
}
BioAID
6
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
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Homo biologicus’ bioinformatics
Local
Database
Local
Database
14/09/2009
BioAID
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Homo digitalis in his natural habitat
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Homo digitalis in his natural habitat
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Workflows
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Semantic Web (Linked Open Data)
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Homo biologicus
Lots of data
to deal with
Single tiny brain
Lots of knowledge
to deal with
Lots of methods
and algorithms to try
and combine
No
computational
superpowers
A needy biologist
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Homo biologicus enhancis
Lots of
accessible data
Knowledge bases
to query
Web Services,
Workflows,
and their creators
available
Community
brain power
Other people’s
computational
superpowers
An enhanced biologist
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e-Laboratories and e-Laboratory factories
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Context: BioAssist Bioinformatics Support
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An existing & acknowledged ‘e-Laboratory’
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In the e-Laboratory Factory
• Galaxy as front end
• Workflows & Web Services
• Grid enabled Taverna
• MOLGENIS
• Semantic/Concept Web
• myExperiment/BioCatalogue
• Scientific Research Objects
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Scientific Research Object 1.0
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Anatomy of a Research Object
Research questions on SROs
• How to record & represent scientific
collections?
– OAI-ORE serialised in RDF
– Life cycle modeled on scientific publication:
Draft->Review->Publication->Deprecation
• How do we describe the resources within
our Research Object?
– Dublin Core , SIOC, Research Object Upper Model (ROUM)
• How to capture/represent Trustworthiness?
• How much are scientists willing to share?
A pilot
• Create an executable Scientific
Research Object that holds
– Galaxy tool models + resources
– Taverna workflow(s)
– MOLGENIS data models and UI models
– Metadata on the experiment
• Tab delimited, linked to concepts
• Samples, subjects, observations, etc.
– Other (references) to datasets
• Execution through Galaxy
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SRO = a pack of models
- Tool models
SRO enactment = a running e-laboratory
- Data/ui models
- Flow models
+Attached data
Model
SROs
Tools
my protocols
my data
my protocols
my data
mashup
data
Flows
e-bioinformatician
programmatic interaction
user interfacing
Data
2.0
mashup
tools
e-biologist
e-Galaxy mock-up
Your Scientific Research Object
Running workflow
MOLGENIS
Convert
Import/Export
Research Object
Store
Configure
Run
MOLGENIS
Convert
Import/Export
Research Objects
Store
Configure
Run
Related research and
documents
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e-Galaxy mock-up
Running workflow
MOLGENIS
Convert
Import/Export
Research Objects
Store
Configure
Run
Related research and
documents
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25
e-Galaxy mock-up
Suggestions
by semantic components
Your Scientific Research Object
Underlying workflow
MOLGENIS
Convert
Import/Export
Research Objects
Store
Configure
Run
Related research and
documents
Adlsjflad jslf adsflkj alfd adsf
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e-Science requirement: Reuse
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http://www.epigenius.org/ (mock-up)
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E-Lab Vacancies in the Netherlands (blatant advertisement)
http://snipurl.com/elabjobs [OMII-UK(myGrid)/NBIC collaboration]
• Software engineer e-Laboratories
– Taverna components for Galaxy/Liferay
– Semantic/Concept Web meta-analysis
• e-biologist (PhD student)
– Workflow & semantic web applied to
epigenetics => epiGenius portal
• Grid engineers & post-doc medical applications
– http://www.vl-e.nl/vlemed/vacancies.html
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BioAssist Requirements
• Help bioinformaticians help biologists
• Serve bioinformatics community
– Analysis pipelines parse large datasets
– Local/external, small/large databases
– Data for humans and machines
– Knowledge for humans and machines
* Plugin developed by Richard Holland (Eagle Genomics) for SARA and NBIC
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More specifically Requirements and tools
• Analysis pipelines that parse large datasets
Taverna with plugin for Grid access*
Taverna platform for e-Labs
• Biological databases (small and large)
MOLGENIS
REST/SOAP/CSV
Galaxy/Taverna
• Data to be exchanged by humans and machines
Scientific Research Objects/myExperiment PACKs
• Biological meaning disclosed and linked
Concept Web and Semantic Web
Semantically enabled Taverna
* Plugin developed by Richard Holland (Eagle Genomics) for SARA and NBIC
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MOLGENIS research portal generator:
Input:
model of
my research
Output:
auto-generates
software files
Rich user interfaces
for biologists
plugin your
handwritten scripts
(tools,workflows)
Programming interfaces
for bioinformaticians
Connect to R
statistics
m<-find.markers()
544 markers downloaded.
…
library(qtl)
#qtl analysis here
Workflow
ready webservices
Rich documentation
and UML diagrams
add.data(qtl, name = “QTLs”)
2,448,000 data elements added.
CSV exchange
format
strain.txt
specie s.txt
protocol.txt
probe.txt
m ark er.txt
in vestigation.txt
ind ivid ual.txt
gene .txt
data.txt
constant.properties
data
Strongly
typed
framework
t
Data storage optimized
for HTP genomics
db
files
http://www.molgenis.org
Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243
A putative scenario
in addition
With Galaxy
With ‘e-Galaxy’
• Select genome annotation
track from UCSC genome
browser, load into Galaxy
• Combine with other data
resources and local data
• Perform a region selection
algorithm
• Collect regions of interest
• Save successful steps
• Data disclosed with
MOLGENIS
• References to datasets
stored in SRO
• Run region selection
workflow (show process)
• Run meta-analysis
– Parse metadata for concepts
– Run meta-analysis
– Present additional information
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