Genomics Virtual Laboratory Mike Pheasant (UQ) Andrew Lonie - - PowerPoint PPT Presentation

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Jan 18, 2024 157 likes •379 views

Genomics Virtual Laboratory Mike Pheasant (UQ) Andrew Lonie (VLSCI) What is the Genomics Virtual Laboratory? NeCTAR funded nationally distributed platform for genomics, built on the Research Cloud and RDSI NeCTAR? Research Cloud? RDSI?

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Genomics Virtual Laboratory

Mike Pheasant (UQ) Andrew Lonie (VLSCI)

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What is the Genomics Virtual Laboratory? NeCTAR funded nationally distributed platform for genomics, built on the Research Cloud and RDSI

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NeCTAR? Research Cloud? RDSI?

NeCTAR = National eResearch Collaboration Tools and Resources

http://www.nectar.org.au

NeCTAR Research Cloud

http://www.nectar.org.au/research-cloud

RDSI = Research Data Storage Initiative

http://www.rdsi.uq.edu.au/

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What is the Genomics Virtual Laboratory?

NeCTAR funded nationally distributed platform for genomic analyses:

Infrastructure

Workflow management system
Bioinformatics toolkit (for command-line users)
Visualisation services
Scalable compute infrastructure

Resources

Tutorials and exemplar workflows targetted at common high throughput

genomics tasks

Data catalogues and coordination centres
Subscription based support

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What is the Genomics Virtual Lab?

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Workflow platforms

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Workflow platforms

Interactive platforms for developing genomics workflows and interactive data analysis

Galaxy
Genepattern, others possible (Bioflow, ...)

What's Galaxy? "an open, web-based platform for performing accessible, reproducible, and transparent genomic science."

http://galaxyproject.org Accessible: Users without programming experience can easily specify parameters and run tools and workflows Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis Transparent: Users share and publish analyses via the web

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Visualisation platforms

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Cluster-on-the-cloud

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Cluster-on-the-cloud

CloudBioLinux - Linux with comprehensive, actively maintained suite of bioinformatics tools

http://cloudbiolinux.org/

CloudMan: platform for launching and scaling CloudBioLinux clusters and Galaxy clusters on the cloud

http://usecloudman.org

Research Cloud: ~25000 CPUs to be spread across 6-10 research centres around Australia, to host research activities 'on demand'

http://www.nectar.org.au/research-cloud

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Data catalogues

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Data catalogues

UCSC databases Ensembl databases ENCODE dbSNP, Hapmap ICGC, COSMIC BPA Framework Datasets

sarcoma
wheat
soil diversity

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Tutorials and workshops

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Tutorials and education resources

NGS School - summer schools, 2 day workshops Galaxy based online tutorials:

Intro to NGS
Genome Browsers
Common analyses

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Differential gene expression

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Variant calling

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ChIPseq

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...

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Exemplar best practice workflows

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Exemplar workflows

Variant calling:

○ GATK best-practice ○ microbial ○ cancer-optimised

RNA-seq differential expression
Fusion gene discovery from RNA-seq
MicroRNA analysis
De novo genome and transcriptome assembly
Metagenomics
ChIP-seq
Variant annotation
Pathway analysis
Methylation

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Support

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Genomics Informatics Network

Institutional subscriptions:

genomics support (% of FTE)
large compute and data resources
managed instances of GVL
new GVL tool development
advocacy to funding bodies for resources
communities of best practice

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Or...roll your own GVL

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Progress and timelines

Dec 2012 Prototype at Qld (UQ) and Vic (UoM)

Galaxy
UCSC browser + databases
Bioinformatics cluster-on-the-cloud
Initial tutorials and exemplars

Jun 2013 Production at Qld (UQ) and Vic (UoM), prototype @ other Research Cloud nodes Data coordination centres, data catalogues Dec 2013 Additional workflows and tutorials Additional nodes Jun 2014 Operations (support centres - subscriptions)