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Semelhante a An Oz Mammals Bioinformatics and Data Resource
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An Oz Mammals Bioinformatics and Data Resource
- 1. Vicky Schneider, Andrew Pask, Denis O’Meally, Philippa Griffin, Jeff Christiansen, Mike Charleston, Dominique Gorse, Andrew Treloar, Jason Williams, Rebecca Johnson and Andrew Lonie With comments from Paul Flicek, Michelle Barker, Susanna Sansone, Dave Burt An Oz Mammals Bioinformatics and Data Resource
- 2. • Whole-genome sequencing reads • Exon-capture sequencing reads • RADseq/GBS/exon- capture sequencing reads Raw Processed • Genome assemblies • Gene alignments • Phylogenetic trees • Variant calls • Transcriptome data • Annotations • Sequence alignments • Phylogenetic trees • Microsatellite datasets • Cytological data (images?) • Phenotype information • …..... From Australian Alps on Flickr: https://www.flickr.com/photos/australianalps/69549 40609 CC BY-NC-ND 2.0
- 3. From Australian Alps on Flickr: https://www.flickr.com/photos/australianalps/69549 40609 CC BY-NC-ND 2.0 OMG Project data ● Hugely valuable for ○ Understanding our natural heritage ○ Tackling evolutionary and ecological questions ○ Placental mammal research including human biomedical research ● Uniquely Australian ● Often irreplaceable samples and data We are leading the world in generating these data Could also be leading in sharing the data! +
- 5. Data Life Cycle framework visualising Metadata (contextual information about the data) is key to making this work e.g. Sample - species - tissue type - collection location - museum ID Experiment - sample processing method - technology used - settings
- 6. • A place to store and share data and metadata for the OMG project • A place to store and share existing Oz mammal datasets • A place to share data processing/analysis workflows • A place to access data processing, analysis and visualisation tools (with appropriate compute resources) • Integration with external tools, e.g. Atlas of Living Australia What is not covered by the OMG project?
- 7. • 5 strains x 2 growth conditions of 2 bacterial species • Genomic, transcriptomic, metabolomic and proteomic profiles
- 9. Select datasets using drop-down menu of metadata values: e.g. • ‘all raw transcriptomic datasets from E. coli grown in blood media’ • ‘all datasets from bacterial samples collected from patients in NSW before 2010’ Send to local desktops, HPC systems for analysis Log in Process/analyse/visualise in common cloud-based environment with pre- installed software tools Submit data and metadata to international repository
- 10. • Large collaborative project funded by Research Data Services (RDS), linked with the BPA Antibiotic-Resistant Pathogens Project • Project members from VicNode, QCIF, Melbourne Bioinformatics (formerly VLSCI), Intersect • -> There is expertise in Australia in developing this kind of resource • data storage • research data management • delivering analysis tools in a common cloud environment • linking across storage/management/analysis layers • Many of the pieces can be reused/adapted for different research projects
- 11. Existing Oz Mammal data resources• For within-project collaboration • Focus on data sharing, (storage), community genome annotation • Datasets mostly unpublished as yet Tools: • File downloads • JBrowse • BLAST • Apollo
- 12. http://copo-project.org/ Aims to provide an easy-to-use interface for researches to access interoperable • Metadata annotation services • Data repository services • Data analysis services • Data publishing services
- 13. www.cyverse.org
- 14. • Capture Oz Mammal data and resources that already exist • long-term, secure data storage • Integrate new OMG data and metadata • Enable data sharing within OMG project (and collaborators) • Provide access to Oz Mammal data for the world! What could a well-funded Oz Mammals Data and Bioinformatics Resource do?
- 15. • Capture Oz Mammal data and resources that already exist • long-term, secure data storage • Integrate new OMG data and metadata • Enable data sharing within OMG project (and collaborators) • Provide access to Oz Mammal data for the world! • Access to data processing, analysis and visualisation tools in one place • Integrate external tools, e.g. Atlas of Living Australia • Enable sharing of processing/analysis workflows within the project What could a well-funded Oz Mammals Data and Bioinformatics Resource do?
- 16. • Capture Oz Mammal data and resources that already exist • long-term, secure data storage • Integrate new OMG data and metadata • Enable data sharing within OMG project (and collaborators) • Provide access to Oz Mammal data for the world! • Access to data processing, analysis and visualisation tools in one place • Integrate external tools, e.g. Atlas of Living Australia • Enable sharing of processing/analysis workflows within the project • Enable sharing via submission to appropriate international repositories • encourage best-practice data formats • encourage complete, rich metadata that complies with repository and community standards What could a well-funded Oz Mammals Data and Bioinformatics Resource do?
- 17. • Capture Oz Mammal data and resources that already exist • long-term, secure data storage • Integrate new OMG data and metadata • Enable data sharing within OMG project (and collaborators) • Provide access to Oz Mammal data for the world! • Access to data processing, analysis and visualisation tools in one place • Integrate external tools, e.g. Atlas of Living Australia • Enable sharing of processing/analysis workflows within the project • Enable sharing via submission to appropriate international repositories • encourage best-practice data formats • encourage complete, rich metadata that complies with repository and community standards • Use and build on existing platforms like the OMICS platform • Long-term hosting and maintenance What could a well-funded Oz Mammals Data and Bioinformatics Resource do?
- 19. Current way forward • Drafting a proposal aimed at ANDS/NeCTAR/RDS • No funding scheme yet - but possibly later this year • Engaging with European Bioinformatics Institute (Ensembl Vertebrates), ISA-Tools, Cyverse for potential collaborations and advice • Aligns with broader digital infrastructure strategy currently being mapped at national level Vicky Schneider, Andrew Pask, Denis O’Meally, Philippa Griffin, Jeff Christiansen, Mike Charleston, Dominique Gorse, Andrew Treloar, Jason Williams, Rebecca Johnson and Andrew Lonie With comments from Paul Flicek, Michelle Barker, Susanna Sansone, Dave Burt
- 20. Timescale • Year 1-2: scoping requirements, building, ongoing testing • Year 2-3: building, release, outreach/training, improvement Expertise required • Research Software Engineering • Business Analyst expertise + domain knowledge • Biocuration • Input on Bioinformatics Needs • Input on User Experience Design • Input on Training/Outreach • Project Management For comparison • COPO: 4 FTE for 3 years • Cyverse: 35 FTE for 5 years ( US$100 million over 10 years ) Matt Francey on Flickr: https://www.flickr.com/photos/howfardad/31879952075 CC BY-NC 2.0
- 21. Your thoughts? • Are there OMG project needs not covered in this list? • Any other Oz Mammal portals/resources to be aware of / consider incorporating? • What do you see as the highest priority in data management / accessing compute resources / sharing and storing data for the OMG: • Currently? • A year from now?