Genomics infrastructure for NGS -...
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2013 Winter School Mark Crowe, July 2013 Genomics infrastructure for NGS
Transcript of Genomics infrastructure for NGS -...
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
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
