Jeremy BarkerChief Executive OfficerChief Executive Officer

Queensland Facility for Advanced Bioinformatics

QFAB Alliance

• ARC Centre of Excellence in Bioinformatics• University of Queensland• Institute for Molecular BioscienceInstitute for Molecular Bioscience• Australian e‐Health Research Centre • Queensland University of Technology • Griffith Universityy• QPI&F (Emerging Technologies)• National Computational Infrastructure (formally APAC)• Queensland Cyber Infrastructure Foundation

Supported by Queensland Smart State funding

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Driving your research further

QFAB helps life science researchers unlock the full value of their research data by delivering the required experiencetheir research data by  delivering  the required experience, breadth of skills and data infrastructure through a dedicated bio/informatics node

Projects

Skills

QFABTools

Data

QFAB

Data

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Driving your research further

What we do:

• Help life science researchers unlock the full value• Help life science researchers unlock the full value of their research data through the tailored application of bioinformaticspp

Jeremy Barker

DominiqueGMhairi

IT/GRIDS i li t

IT/GRID Infrastructure

Research & Support Research

BioinformaticsTools, Data & Skills

GorseMhairiMarshall

NickRhodes

MelissaDavis

SpecialistInfrastructure & Support Specialist CommunityDavid

Innes

DavidWoodAmanda

MatthewBryant

Pierre-AlainChaumeil

CasSimons

Ki A h

Anrug Nayak

WoodAmanda Miotto

Kim-Anh Le Cao

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Systems Biology Platform

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Platform Architecture

MetacoreIngenuitySRS R GenePatternMetacoreIngenuitySRS R GenePattern

Web

Workflow engine

QFAB

• 25 nodes• 200 cores• 200 cores• 16 - 32 GB/node• 25 TB storage

Mirror of PublicEBI NCBI QFAB

Databanks• UCSC• Ensembl

EBI, NCBI Web Services Customised

Web Services

The most comprehensive curatedThe most comprehensive curated 

database of spider toxins

• Glenn King group • Collaborators• Glenn King group

– Tomas Miljenovic

– Volker Herzig

• Collaborators

– Robert Raven

– Quentin Kaas

– David Wilson

– Glenn King

– Pierre Escoubas

– Graham Nicholson

www.arachnoserver.org Photo courtesy of Bastian Rast

ArachnoServer

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UCSC Genome Browser Mirror

ARC LIEF t l d bARC LIEF grant led by John Mattick and Mike Pheasant

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• http://genome.qfab.org

• Updated every fortnight

UCSC Genome Browser Mirror

D di d f• Dedicated resources for partners – private data and compute power

UCSC Genome Browser Mirror

Koala Child Obesity

• Gary Leong– Paediatric endocrinologist at the Mater 

Children’s Hospital

– Researcher at Institute for MolecularResearcher at Institute for Molecular Bioscience (IMB)

• Identifying biomarkers in children which indicate the propensity for  the de elopment of obesit related illnessdevelopment of obesity related illness such as diabetes or heart disease

Data capture and integration

• WebsiteWebsite• Forms and database 

for data captureCli i l th l– Clinical pathology

– Psychometric– Dietary– Behavioural– Human movement– Metabolites– MRI– Gene expression

14http://koala.imb.uq.edu.au

Secure infrastructure

• Dedicated serversDedicated servers

• De‐identified data

S• Secure access

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Nuclear Receptors in Breast Cancer

Western Australian Institute for M di l R h

QFABProject Leader: Melissa Davis

ACBProfessor Mark Ragan

•Bioinformatics and systems biologyMedical Research

Professor Peter Leedman

Breast Cancer Tissue Microarray•miRNA assoc with cancer

•Bioinformatics and systems biology•Data integration

Western Australia

Queensland

Northern Territory Institute for Molecular BioscienceProfessor George Muscat

•Core facility containing multiple Applied Biosystems 7900HT qPCR instruments•Expression analysis (TLDA)

NewSouth Wales

South Australia

Westmead Millennium InstituteA/Professor Christine Clarke

Hanson InstituteDame Roma Mitchell Cancer Research

LaboratoriesProfessor Wayne Tilley

p y ( )

Victoria

Wales

ACT

A/Professor Christine Clarke

Prince Henry’s Institute

•Explant tissue culture of primary tumor cells•Image analysis and histopathology •Digital tumour imaging

•3D tissue culture•Illumina microarray analysis• Tissue bankPrince Henry s Institute

Professor John FunderProfessor Peter Fuller

Professor Evan SimpsonTasmania

Australian Regenerative Medicine Institute (ARMI)Prof Nadia Rosenthal•Core facility containing Applied

Tissue bank

•Generation of genetically modified mice•Access to EMBL mice including international consortia

Prof Nadia Rosenthaly g ppBiosystems 7900HT qPCR and DNA sequencing•Micro RNA analyses

Biomarkers and drug targets discovery

Clinical specimens

Determine cohorts

QFAB support31

1. Data management & integration

Preliminary Experimental Data

TLDA Expression profiling

Public dataExpression array data

Literature4. Data mirrors & Sys. Biology Tools

5 Pathway and network analysis

2. Support of interpretation & analysis

3. Biostatistics

p p gRTPCR validation

Interpretation & analysis

Molecular interaction data4

5. Pathway and network analysis

5231

1

Additional Data sources:Functional annotation,

miRNA data, Human-mouse

Identification of regulated pathways & candidates 4

5

Clinical Outcomes

Proposed treatments for underserved patients with

currently untreatable breasthomology, etc.Inference

“Drivers” vs “Bystanders”

4 5 currently untreatable breast cancer subtypes

3

Experimental Data

Expression in normal cells Expression in target cells

Target Validation

Mouse KO & disease models

Prioritisation

Candidate “Drivers”

522

331

Targeted Validation Tissue Microarrays

4 52 31Target selection

Plone DemoARCHER Project – Prof Ian Atkinson 

at James Cook University

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Plone Demohttp://plone.jcu.edu.au/qfab

y

2 ‐ Informatics support

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Network modelling

The Pregnane X receptor (PXR) network

Shapes = Classes of proteins

Colour = Differential gene expression between 2 cohorts

QFAB Future Directions

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NCI ‐ SF

National Computational Infrastructure – Specialised Facility

Townsville

Partners:

B i b

TownsvilleQPSF

QFAB

A t li R h BrisbaneQCIF

PerthCanberra S dne

Adelaide

SAPAC

NCI SF

Australian Research Community

IVECCanberra

NCISydney

AC3

MelbourneVEPACVEPAC

HobartTPAC

HPC and QFAB

National Computational Infrastructure (NCI) Specialised Facility in Bioinformatics

The NCI specialised facility will provide high performance computing for Australian researchers tuned specifically for the needs of bioinformatics research

• Access to 1000’s of CPUs

• “Fat” nodes with up to 500Gb of memory

• Local access to large public data sets

• Wide range of commonly used bioinformatics tools

• Available early 2010y

The Chemical Biology Platform

MetadrugMOESystems Biology Platform

Workflow engine

PubM

PrivateBioinformatics

Cheminformatics

PubMed

Private

Chemical Biology

Services Services

PublicQFAB and Public

Shared

Chemical Biology Repository

PublicDatabanks

QFAB and Public Services

Network Analysis Experimental Data

Combining Genomics, proteomics, metabolomics and cheminformatics

yInterconnecting compound/metabolites

with their predicted targets andother associated network objects.

pImport and overlay

any experimental dataCompound

Predicted

Chemical properties, QSAR, etc…

DB SimilarityDB SimilaritySearchSearch

Similar DB

Metabolites

Compounds

Lists of Targets (genes/proteins)Lists of Targets (genes/proteins)for the input molecule and for metabolites

Based on the known targetsfor the Similar Compounds

Functional Enrichment AnalysisBased on the Predicted Targets:

-Drug target networks-Toxicity networks

-Canonical Pathway Maps-Process networks-Disease Networks

Predicted Primary and Secondary Effects of a Compound of interestPredicted Primary and Secondary Effects of a Compound of interest

Summary

• We pride ourselves in developing tailoredWe pride ourselves in developing tailored bioinformatics solutions to meet research needs

– Enable collaboration between scientists within disparate research areas

– Enable reasoning across data sources

– Develop workflows for easy and efficient data iprocessing

– Provide scalable infrastructures to meet future growthgrowth

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Contacts

Jeremy Barker

Chief Executive Officer

j.barker@qfab.org

(07) 3346 2611

Dominique Gorse

Technical Manager

d gorse@qfab org

htt // f b

d.gorse@qfab.org

(07) 3346 2624

http://qfab.org

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