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As high-throughput DNA sequencing continues to become cheaper and more widely accessible, the bottleneck in genomics research has become one of bioinformatics rather than data generation. Sequencing service providers and equipment manufacturers are attempting to address this by providing a range of analysis options, but ultimately most researchers using genomics technologies will need support and resources beyond these standard offerings.
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2013 Winter School Mark Crowe, July 2013
Genomics infrastructure for NGS
Expertise infrastructure
• What is your experimental goal? • Is NGS really the right technology? • How will you manage:
– Data collecFon? Data storage? Analysis? StaFsFcs?
When to ask advice
BEFORE you start your project
Sequencing infrastructure
agrf.org.au www.ramaciotti.unsw.edu.au
• ACRF centres • Local (department/insFtute) services
Bioinformatics infrastructure
• ‘Support’ rather than research – Accessible to biologists – Stable and documented
• SoWware, hardware and experFse
EMBLBRAustralia
The challenges of Bioinformatics support
In house
Outsource
Collabora1on
Cloud
Infrastructure So5ware
Training Sta1s1cs
Exper1se
Cost
Going it alone
• Networking and community for bioinformaFcians
• Yammer channel • Conference and naFonal bioinformaFcs society • Web, twiZer
australianbioinformatics.net @ausbionet
• Training – 3 day NGS analysis workshops
• Embedded bioinformaFcians – Associated with BPA infrastructure
• Reference datasets – Dedicated bioinformaFcs support
www.bioplatforms.com.au
Genomics Virtual Lab
www.genome.edu.au
Galaxy: simplifying bioinformatics
GVL on the cloud
• NeCTAR research cloud – a free resource for Australian researchers
• GVL provides Galaxy and CloudBioLinux NeCTAR instances
hZp://nectar.org.au
• The NCI NaFonal Facility supports Australian research through the use of high-‐end computaFonal resources
• The NCI Specialised Facility in BioinformaFcs offers NCI support tailored for the life science community
www.ncisf.org
NCI-SF infrastructure
• Computer scienFsts, bioinformaFcians, and IT professionals
• High Performance CompuFng – 384 compute nodes – 3144 CPU cores – 11.5TB RAM – 24 Teraflops of performance – 280TB shared disk
• 35TB of BioinformaFcs databanks
• >150 bioinformaFcs tools and applicaFons
Access to NCI-SF
• Directly, through Partner shares: – UQ – CSIRO – QCIF (CQU, GU, JCU, QUT, UQ, USQ, USC) – QCMG – QFAB
• Through NaFonal Merit ApplicaFon Scheme h=p://nf.nci.org.au/accounts/
• BioinformaFcs Resource Australia – EMBL • Developed out of the EBI mirror project • Enable opFmal exploitaFon of the tools and data of bioinformaFcs by Australian scienFsts
• Contribute to the global biomolecular informaFon infrastructure in a way which showcases Australian science
EMBLBRAustralia
braembl.org.au
BRAEMBL resources
• FTP site – mirror of 13TB of EBI data • Local ENSEMBL browser • ProgrammaFc access to data and tools via Web Services technologies
• Survey on bioinformaFcs needs
Most useful thing?
About QFAB
QFAB delivers bioinformaFcs services to analyse and manage large-‐scale datasets
Our support includes experimental design and data capture through to NGS and ‘omics analyses.
qfab.org @QFAB_Bioinfo
ComputaFonal Biology K. Le Cao X. Chua R. Legaie J. Straube
Organisation
IT/GRID Specialist
IT/GRID Infrastructure
Research
& Support Specialist
Research Community
Bioinformatics/Statistics Tools, Data & Skills
Senior Management Team J. Barker D. Gorse M. Desselle S. Rudd M. Crowe
Data Specialists J. Parsons P. Chaumeil A. Kunert N. Rhodes
Currently recrui1ng a Computa1onal Biologist to join the team
Other bioinformatics providers
• Victorian Life Science ComputaFonal IniFaFve (VLSCI) and Life Science ComputaFon Centre
• Centre for ComparaFve Genomics, WA
www.vlsci.org.au ccg.murdoch.edu.au
Useful links • qfab.org • agrf.org.au • www.ramaciotti.unsw.edu.au • australianbioinformatics.net • bioplatforms.com.au • genome.edu.au • ncisf.org • braembl.org.au • vlsci.org.au • ccg.murdoch.edu.au
• [email protected] • @QFAB_Bioinfo
