Bioinformatics Services in Australia – a collaboration with the European Bioinformatics Institute - Graham Cameron

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Bioinformatics is crucial to all life science research. The European Bioinformatics Institute (EBI) is one of a few major centres in the world that provide data and services for bioinformatics and, with Australia’s membership of EMBL, a natural collaborator of Australia. In 2010 a project was launched to mirror EBI services from the University of Queensland (UQ). The goal was to improve Australian bioinformatics by removing barriers of geographical remoteness.
We have revisited the Mirror’s mission in light of experience and with input from a survey of Australian bioinformatics needs, and are creating the Bioinformatics Resource Australia – EMBL (BRAEMBL) with a mission to:
 enable optimal exploitation of the tools and data of bioinformatics by Australian scientists
 contribute to the global biomolecular information infrastructure in a way which showcases Australian science.
 engage in Australia-wide training in support of these goals
Key findings of the survey and the rationale for the BRAEMBL project will be presented.
BRAEMBL will work with the EBI to create a part of the EBI in Australia and to ensure that Australian scientists have access to the data and methods of bioinformatics and the necessary IT resources, though integrated high-quality services to rival those available anywhere in the world. This will draw on the support of Australian partners including BioPlatforms Australia (BPA) and the existing eResearch infrastructure. It will work with UQ’s Research Computing Centre to be early adopters of modern IT methodologies, in particular cloud computing.
The evolving plan for the BRAEMBL and its contribution to Australian bioinformatics will be presented.

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Bioinformatics Services in Australia – a collaboration with the European Bioinformatics Institute - Graham Cameron

  1. 1. Bioinformatics Services in Australia – a collaboration with the European Bioinformatics Institute BRAEMBL Bioinformatics Resource Australia – EMBL Bioinformatics Resource Australia EMBL EMBL Australia
  2. 2. Bioinformatics
  3. 3. Focus – central dogma Genomes–Genes–Transcripts–Proteins–Structures–Interactions–Pathways–Systems Molecular information and its phenotypic correlates
  4. 4. EMBL Australia Bioinformatics Infrastructure • Shared data and tools of bioinformatics • Global databases and systems to explore and exploit them • E.g. – GenBank, PDB, UniProt, Ensembl etc.
  5. 5. EMBL Australia You can’t do biology without exploiting this information infrastructure
  6. 6. EMBL Global Information Ecosystem • data collection • data curation • service Australia • EBI (European Bioinformatics Institute) • NCBI • SIB (Swiss Institute of Bioinformatics) • etc.
  7. 7. The EBI: European Bioinformatics Institute EMBL Australia • Part of EMBL – The European Molecular Biology Laboratory • About 500 staff and $80 million p.a. • Australia is an Associate Member of EMBL • Special relationship with the EBI
  8. 8. EMBL Australia EMBL, EBI, Mirror • Australian science needs bioinformatics • Perceived disadvantage in Australia – Geography – Size – Infrastructure • Exploit the EBI ?
  9. 9. EMBL Australia EBI Mirror Project • Copy EBI data and software • Offer services directly to Australia • Funding from various government schemes
  10. 10. EMBL Australia Beyond Mirror • • • • Did mirror some EBI services Across-the-board mirroring impossible Alternatives? Re-examine the mission This talk is about what I am trying to achieve
  11. 11. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show case Australian science in global databases • Training in support of these goals
  12. 12. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show cases Australian science in global databases • Training in support of these goals
  13. 13. EMBL Australia Surveying the community • • • • • February 2013 Solicited input from 500 – 1000 individuals 210 responses 50% Wet 50% Dry
  14. 14. EMBL Australia Demography Northern Territory, 0 Tasmania, 3 ACT, 7 New Zealand, 1 SME, 4 Large commercial, 5 Health, 1 Gov. State, 5 Gov. Commonwealth, 3 CSIRO, 16 South Australia, 18 Western Australia, 12 New South Wales, 47 Academic institute/university, 165 Queensland, 54 Victoria, 63 Figure 1. Geographical source of responses Figure 2. Sector of respondents
  15. 15. EMBL Australia Bioinformatics ubiquitous 50 45 40 35 30 25 20 15 10 5 0 Wet Full-time bioinformatician Use bioinformatics as a core tool Dry Use bioinformatics tools occasionally Rarely/never use bioinformatics tools, but would like to Figure 4. Use of Bioinformatics
  16. 16. EMBL Australia Normal methods of bioinformatics Transcriptomics Taxonomy Systems biology Proteomics Physiology Pharmacology Plant biology… Pathology Neurobiology Molecular biology Microbiology Metabolomics Marine biology Livestock biology Genomics Genetics Evolutionary biology Ecology Developmental biology Cell biology Bioinformatics… Biochemistry 0 Nucleic Acids Genes Genomes Gene expression Protein Sequences Main Protein Motifs Plus Proteomics Pathways Molecular interactions Small molecules 3D Structures Images 0% 50 Figure 5. Scientific domains 100 Very useful 50% Somewhat useful 100% Not useful Figure 6. Usefulness, percentage of respondents
  17. 17. Disadvantaged access ? Data Western Australia Victoria Tasmania Not at all South Australia Queensland Somewhat New Zealand New South Wales A lot Australian… 0 IT resources 20 40 60 40 60 Expertise Western Australia Western Australia Victoria Victoria Tasmania Tasmania South Australia South Australia Queensland Queensland New Zealand New Zealand New South Wales New South Wales Australian… Australian… 0 20 40 60 0 20
  18. 18. Inadequate Don't need None, want some Adequate or High performance compute None, want some External External From collaborators From collaborators In organisation In organisation In group -30 -10 Don't need In group 10 30 50 -30 Software -10 External From collaborators 30 50 Bioinformatics support staff None, want some External From collaborators In organisation In organisation In group -10 10 Don't need None, want some -30 Databases Don't need In group 10 30 50 -30 -10 10 30 50
  19. 19. Training Very useful Somewhat useful Not at all useful Structure analysis Network and pathway analysis Statistical analysis NGS analysis Sequence clustering/phylogeny Sequence Alignment Database Searching 0 100 Figure 9. Usefulness of training 200 • Three quarters of respondents indicated “very useful” for at least one topic • Only four indicated no interest in any training • Demand – Programming – Statistics
  20. 20. Expertise Training My Speciality Funding Community Storage Software Compute Data Access Data Complexity Network Data Quantity Data Quality Compute Infrastructure 0 20 Offer training Access to Expertise Be a hub for bioinformatics Community building My Speciality Compute power Access to data Create or improve software Funding 40 60 Figure 10. Areas of greatest difficulty 0 20 40 60 Figure 11. Areas where BRAEMBL could make greatest contribution 80
  21. 21. EMBL Australia Survey Conclusions • • • • • • • • Bioinformatics is important “central dogma” Wet and dry Geographic disadvantage not crippling Scientists like it in their own group Lack of (access to) expertise Training and community building Programming and statistics
  22. 22. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show cases Australian science in global databases • Training in support of these goals
  23. 23. EMBL Australia Spectrum of service – tides of change Style of usage     Historic/traditional Search-and-browse In the distant past done locally Molecular searching Commonly local 15 years ago Programmatic access All local up to about 6 years ago Methods development Still almost all done locally Today All done on remote information centres Through web forms submitted to data centres Extensive use of programmatic access to remote machines (REST) Emerging possibility of virtual machines at remote data centres.
  24. 24. EMBL Australia Spectrum of service – tides of change Style of usage     Historic/traditional Search-and-browse In the distant past done locally Molecular searching Commonly local 15 years ago Programmatic access All local up to about 6 years ago Methods development Still almost all done locally Today All done on remote information centres Through web forms submitted to data centres Extensive use of programmatic access to remote machines (REST) Emerging possibility of virtual machines at remote data centres.
  25. 25. Inadequate EMBL Adequate or Australia Don't need None, want some High performance compute None, want some External External From collaborators From collaborators In organisation In organisation In group -30 -10 Don't need In group 10 30 50 -30 Software -10 External From collaborators 30 50 Bioinformatics support staff None, want some External From collaborators In organisation In organisation In group -10 10 Don't need None, want some -30 Databases Don't need In group 10 30 50 -30 -10 10 30 50
  26. 26. EMBL Australia Ensure access to: • • • • Data Software methods Hardware Expertise
  27. 27. Research needs bioinformatics
  28. 28. Bioinformatics expertise
  29. 29. Software methods
  30. 30. Shared databases
  31. 31. Computers and stuff
  32. 32. Bioinformatics
  33. 33. Outsourcing
  34. 34. We need more
  35. 35. Too much
  36. 36. Increased Outsourcing Made possible by SOA’s Virtualisation Cloud computing
  37. 37. Users find outsourcing hard
  38. 38. BRAEMBL’s job it to make it easy
  39. 39. EMBL Australia The IT forecast – generally cloudy • Move the method to the data not the data to the method • Why own computers? • Why own storage? • Buy naked compute from a vendor (e.g., Amazon) • Make data visible to the cloud
  40. 40. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show case Australian science in global databases • Training in support of these goals
  41. 41. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show case Australian science in global databases • Training in support of these goals
  42. 42. EMBL Australia Projects of iconic Australian interest • Barrier reef species • Koala • (Sheep)
  43. 43. EMBL Sea-quence project • Sea-quence project unites Great Barrier Reef and Red Sea scientists • Supported by Rio Tinto, Bioplatforms Australia (BPA) and ReFuGe 2020 • Convened by the Great Barrier Reef Foundation • Sequence – 10 corals – algal symbionts – bacteria and viruses Australia
  44. 44. EMBL Australia Collaboration with the EBI • • • • Get the data into the best possible database At the best possible quality Quickly Identifiably Australian Ensembl - Ensembl Genomes - ENA Do the things the EBI won’t prioritise Mini-team in place at BRAEMBL
  45. 45. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show case Australian science in global databases • Training in support of these goals
  46. 46. EMBL Australia Back to basics - Mission • Optimal exploitation of shared tools and data of bioinformatics • Show case Australian science in global databases • Training in support of these goals
  47. 47. EMBL Australia Expertise building • Short courses on bioinformatics services in collaboration with the EBI, BPA, CSIRO and others • Australian Bioinformatics Network to build Community • User support
  48. 48. EMBL Currently on a crusade to persuade Australia to Australia turn BRAEMBL into a sustainable infrastructure • As part of EMBL-Australia • With an annual budget of $3 to $5 million • With substantial security (~5 years) for about 40% of that budget • With a truly infrastructural mindset • $5 million is at best 2% of the global budget for such centres
  49. 49. EMBL Australia Infrastructure mindset • Academic institutions value – Publications – High quality graduates – Grants won • This is different – – – – The mission is to serve researchers throughout Australia It only makes sense as a long-term project It must support careers of engineers It needs sustained and talented leadership
  50. 50. EMBL Service Mission • BRAEMBL will flourish best in a research context • It will produce some publications • Its staff won’t seem so different from researchers Australia • Don’t take comfort in those similarities as the reason to do this • The project will only do well if its unique service mission is embraced enthusiastically
  51. 51. A part of the EBI in Australia

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