EMBL-EBI Powerpoint Presentation - BioModels

BioModels Database
www.ebi.ac.uk/biomodels
Chen Li (chenli AT ebi.ac.uk)
EBI is an Outstation of the European Molecular Biology Laboratory.

Infrastructure
EBI
Application Servers Cluster
Node 1
Users . . .
Node 2
computing­intensive tasks,
external formats' conversions
and some user­driven tasks
will be running on
clusters
...
biomodels.caltech.edu

BioModels Pipeline
Submit Consistency
Check
Curation Annotation Public
Curation
&
Simulation
Non­curated­Models
Non­curated
Models
Curated­Models Search
Curated
Models
Annotations Annotations

SBML models
• Storage
• File system?
• Native XML database?
• RDBMS(models currently are stored in MySQL with full history)
• Version control (in the future)
• libSBML
• Using Apache Lucene to index models.

Annotations
• When a model is being submitted, BioModels Database
parses the model and fetch MIRIAM annotations, and
retain the non­MIRIAM annotations.
• Fetch reference information from external resources
(Gene Ontology, UniProt, ChEBI and Taxonomy etc.) via
directly accessing their databases or Web Services.
• Stored annotations in MySQL database.
• Merge annotations into SBML models when publishing
them.

Annotations
• MIRIAM compliant.

External formats
Level 1 Version 1
Level 1 Version 2
Level 2 Version 1
Level 2 Version 2
Level 2 Version 3
Version 1.0
Version 1.1
Level 2 Version 1
Level 2 Version 3
BioPAX
VCell
XPP-Aut

External formats
• Currently, provides CellML, SciLab, XPP, BioPAX and
VCell.
• BioPAX and VCell → Java converters
• CellML, SciLab and XPP → XSLT
• PDF → SBML2Latex (Java)
• There are SVG, GIF and dynamic Java Applet are
available for reaction networks.
• Conversions are running on clusters at EBI.

Online simulation
• A simple embedded simulation tool is also provided.
• The links to the JWS online simulation.

Model of Month (web interface)

Model of Month (RSS)

Enhanced web interface
• AJAX
• View models­tree built based on Gene Ontology
• Annotation tool
• Sub­model generation
• etc.
• Mathematical equations
• And many
others

Web Services
Client
SOAP services
Target services
BioModels DB
-for more information …
http://www.ebi.ac.uk/biomodels/webservices.html
WSDL

Web Services
• java.lang.String helloBioModels()
• . . .
• java.lang.String[] getModelsIdByChEBI(java.lang.String text)
• java.lang.String[] getModelsIdByChEBIId(java.lang.String ChEBIId)
• java.util.TreeMap getSimpleModelsByChEBIIds(java.lang.String[] ChEBIIds)
• java.util.TreeMap getSimpleModelsRelatedWithChEBI()
• . . .
• java.lang.String getSubModelSBML(java.lang.String modelId, java.lang.String[]
elementsIds)
• etc.

Web Services
Code:
import uk.ac.ebi.biomodels.*;
public class HelloBioModels {
}
public static void main(String args[]) throws Exception{
}
Result:
BioModelsWSClient client = new BioModelsWSClient();
System.out.println(client.helloBioModels());
Hello BioModels

Web Services
Code:
import uk.ac.ebi.biomodels.*;
public class HelloBioModels {
}
public static void main(String args[]) throws Exception{
}
Result:
BioModelsWSClient client = new BioModelsWSClient();
client.setEndPoint("http://biomodels.caltech.edu/services/BioModelsWebServices");
System.out.println(client.helloBioModels());
Hello BioModels

Web Services
Code:
import uk.ac.ebi.biomodels.*;
public class HelloBioModels {
}
public static void main(String args[]) throws Exception{
}
Result:
BioModelsWSClient client = new BioModelsWSClient();
client.setProperty("http.proxyHost", "your.http.proxy.host");
client.setProperty("http.proxyPort", "yourHttpProxyPort");
client.setProperty("socks.proxyHost", "your.socks.proxy.host");
client.setProperty("socks.proxyPort", "yourSocksProxyPort");
System.out.println(client.helloBioModels());
Hello BioModels

Web Services
Code:
import uk.ac.ebi.biomodels.*;
import java.util.ArrayList;
import java.util.TreeMap;
import java.util.Iterator;
public class GetSimpleModelsByChEBIIds {
}
public static void main(String args[]) throws Exception {
}
BioModelsWSClient client = new BioModelsWSClient();
TreeMap resultSet = client.getSimpleModelsByChEBIIds(new String[]{"CHEBI:15355", "CHEBI:27897"});
Iterator iter = resultSet.keySet().iterator();
while (iter.hasNext()) {
}
Result:
CHEBI:15355
CHEBI:27897
// print result set out
BIOMD0000000002 Edelstein1996_EPSP_AChSpecies 8983160 2007­01­04T23:01:47
BIOMD0000000062 bhartiya2003 tryptophan operon 12787031 2007­02­22T23:11:55

Open source
• http://sourceforge.net/projects/biomodels/
• Source code, database schema
• Feature request and bug report

Acknowledgements
• EBI
• Nicolas Le Novère
• Lukas Endler
• Nicolas Rodriguez
• Melanie Stefan
• Camille Laibe
• Vijayalakshmi Chelliah
• SBML team (Caltech)
• Michael Hucka
• Sarah Keating
• Harish Dharuri
BioModels Database is funded by:
• BioModels Database
Scientific Advisory Board
• Upinder Bhalla
• Michael Hucka
• Pedro Mendes
• Ion Moraru
• Herbert Sauro
• Jacky Snoep
National Institute
of General
Medical Sciences
• Journals supporting BioModels
Database
• Molecular Systems Biology
• All PLoS Journals
• All BioMedCentral Journals
• Programs used for curation
• Copasi
• CellDesigner/SBMLodeSolver
• Jarnac/JDesigner
• MathSBML
• RoadRunner
• SBMLeditor
• XPP­Aut
• JigCell
The community of Systems Biology
for their contributions of models and
comments.