Australian Biosciences Data Capability: ABDC

A national research infrastructure providing

bioinformatics resources to life science researchers in Australia

What are we looking to do here?

● The prospect of an NCRIS investment in an Australian Research Data Cloud

creates a requirement for a statement of bioscience data and software

infrastructure needs

● → Setting out the biosciences framework for an Australian Bioscience Data

Capability (ABDC) has become urgent

● So, we are here proposing an approach that should lead to a

community-driven framework; and discussing the nature of the framework in

the context of local and global developments

Key National Research Infrastructure

DIGITAL DATA AND ERESEARCH

● Tier 1 HPC (e.g. NCI, PAWSEY)

● Australian Research Data Cloud

● AREN (Network)

● AAF (Authentication)

HUMANITIES, ARTS, SOCIAL SCIENCE

● Integrated coordinated platform

● Platforms for indigenous

research

● Platforms for social sciences

CHARACTERISATION

● Microscopy network

● Biomedical imaging network

● Neutron stuff (OPAL)

● Synchrotron

ADVANCED FABRICATION &

MANUFACTURING

● Materials on a micro/nano scale

● Bioengineering, fabrication

● New classes of fabricated

devices

ADVANCED PHYSICS AND ASTRONOMY

● Optical and SKA

● International accelerators

● Precision measurement

● Nuclear (OPAL)

EARTH & ENVIRONMENTAL SYSTEMS

● Environmental prediction

● Earth monitoring, exploration

● Remote sensing

● Agriculture networks

● Marine systems

BIOSECURITY

● Prevention of exotic diseases

● Biosecurity testing facility

network

COMPLEX BIOLOGY

● Omics data translation network

● Plant phenomics

● Networked biobanks

● Bioinformatics and automation

THERAPEUTIC DEVELOPMENT

● Drug discovery, manufacturing

● Bioengineering

● Health translation

● Population, tissue, microbial,

genomics datasets

Key National Research InfrastructureA strategy is needed to relate those in red

DIGITAL DATA AND ERESEARCH

● Tier 1 HPC (e.g. NCI, PAWSEY)

● Australian Research Data Cloud

● AREN (Network)

● AAF (Authentication)

HUMANITIES, ARTS, SOCIAL SCIENCE

● Integrated coordinated platform

● Platforms for indigenous

research

● Platforms for social sciences

CHARACTERISATION

● Microscopy network

● Biomedical imaging network

● Neutron stuff (OPAL)

● Synchrotron

ADVANCED FABRICATION &

MANUFACTURING

● Materials on a micro/nano scale

● Bioengineering, fabrication

● New classes of fabricated

devices

ADVANCED PHYSICS AND ASTRONOMY

● Optical and SKA

● International accelerators

● Precision measurement

● Nuclear (OPAL)

EARTH & ENVIRONMENTAL SYSTEMS

● Environmental prediction

● Earth monitoring, exploration

● Remote sensing

● Agriculture networks

● Marine systems

BIOSECURITY

● Prevention of exotic diseases

● Biosecurity testing facility

network

COMPLEX BIOLOGY

● Omics data translation network

● Plant phenomics

● Networked biobanks

● Bioinformatics and automation

THERAPEUTIC DEVELOPMENT

● Drug discovery, manufacturing

● Bioengineering

● Health translation

● Population, tissue, microbial,

genomics datasets

Bioscience should benefit from the ARDCNCRIS Roadmap pg 32 Table 3: Priority Areas for Digital Data and eResearch Platforms

2. Create Australian Research Data Cloud: Enhance existing capability through the integration of existing

capability – ANDS, NeCTAR and RDS to establish an integrated data-intensive infrastructure system,

incorporating physical infrastructure, policies, data, software, tools and support for researchers.

An Australian Research Data Cloud would build on existing eResearch infrastructure to create a cohesive,

seamless experience for researchers that provides a fully integrated system. It should:

● Broadly align with the European Open Science Cloud and other global initiatives.

● Support research data management from creation and discovery, through description and

provenance, integration and storage, manipulation and analysis, and preservation.

● Provide digital platforms that meet specific research requirements and integrate other data rich

research infrastructure.

● Support the sharing of informatics and software techniques to enable the deployment and wide use by

researchers.

The underpinning Australian eResearch infrastructure should include cloud computing, HPC, networks,

access, authentication and trusted data repositories. Data, collaboration and software services, skills and

knowledge provided by the Australian Research Data Cloud will be an essential part of the new system.

Timeline

Community consultations:

Brisbane 8/Aug, Perth 10-11/Oct, Cbr 30/Oct, Syd

3/Nov, Melb 8/Nov & 17/Nov, ABACBS 14/Nov, Adl 20/Nov

Phase

Period Activity

1 June - Aug 2017

Concept development and project planning

2 Sep - Dec 2017

Elaboration of requirements, options and consensus building

3 Jan - Sep 2018

Engagement with expected NCRIS planning of its investments

4 Oct 2018 - ? 2019

Steps to implement results or engage further as needed

Bioplatforms AustraliaAn NCRIS funded national research infrastructure

University of Queensland

Murdoch University

University of NSW

ANU JCSMR

University of MelbourneBioScience, Bio21

University of Queensland

The Australian Wine Research Institute

University of Adelaide

Monash University

APAF MQ

University of Queensland

Genomics Metabolomics Proteomics Bioinformatics

Murdoch University

University of Western Australia

WAIMR

AGRF

AGRF

AGRF

Ramaciotti CentreKCCG

AGRF

University of MelbourneVLSCI

NCI

EMBL Australia Bioinformatics Resource:A bioinformatics infrastructure network (supported by BPA)

HUB

• Hosted by Melbourne Bioinformatics

@ UoM (ex VLSCI)

Nodes in all states

• Expands BPA’s network into

bioinformatics

GOVERNANCE

Paul FlicekLead, Vertebrate

Genomics & ENSEMBL

Jaap HeringaHead, ELIXIR-NL

Vivien BonazziSenior Advisor Data

Science Tech & Innovation

Jason WilliamsEducation, Outreach

and Training Lead

Tony PapenfussHead, Computational Biology,

WEHI, VICMark Walker

Director, Aust Infectious Disease Res Centre, UQ, QLD

Delphine FleuryAus Centre for Plant Functional

Genomics, SA

Sean GrimmondDirector, Centre for UoM Cancer

Research, VIC

Rebecca JohnsonDirector, Australian Museum

Research Institute, NSW

International Scientific Advisory Group

National Reference Group

Prof Jacquie Batley (Plant Genetics & Breeding, UWA) Prof Dave Burt (Director Genomics, UQ)

Prof Peter Cameron (Academic Director, The Alfred Emergency and Trauma Centre/Monash U)

Prof Joanne Daly (CSIRO Honorary Fellow)

Prof Frank Gannon (Director, QIMR Berghofer) Prof Rob Henry (Director, QAAFI, UQ)

Prof Ary Hoffmann (Biosciences, Melbourne U) Prof Dean Jerry (Dep Director, JCU Centre for Tropical Fisheries and Aquaculture, JCU)

Prof Ryan Lister (Head, Epigenetics and Genomics, Harry Perkins Inst/UWA)

Prof John Mattick (Director, Garvan Institute)

Prof Kathryn North (Director, MCRI) Prof Nicki Packer (Macquarie U & Inst for Gycomics, Griffith U)

A/Prof Tony Papenfuss (President ABACBS, Computational biology WEHI & Petermac)

Dr. Maurizio Rossetto (NSW Royal Bot Gardens)

Prof Eric Stone (Director, ANU-CSIRO Centre for Genomics,

Metabolomics and Bioinformatics, ANU)

Dr Jen Taylor (Group leader Bioinformatics, CSIRO)

Prof Steve Wesselingh (Director, SAHMRI) Prof James Whisstock (Monash, EMBL-Australia)

Prof Marc Wilkins (Director, Ramaciotti Centre for Genomics, UNSW)

Dr Helen Cleugh (Director, CSIRO Climate Science Centre)

National Reference Group

What are we looking to do here?

● The prospect of an NCRIS investment in an Australian Research Data Cloud

creates a requirement for a statement of bioscience data and software

infrastructure needs

● → Setting out the biosciences framework for an Australian Bioscience Data

Capability (ABDC) has become urgent

● So, we are here proposing an approach that should lead to a

community-driven framework; and discussing the nature of the framework in

the context of local and global developments

Data infrastructure in the genomic era

NIH on the on the impact of data and informatics in 2013:

“Research in the life sciences has undergone a dramatic transformation in the past two decades. Colossal changes in biomedical research technologies and methods have shifted the bottleneck in scientific productivity from data production to data management, communication, and interpretation. Given the current and emerging needs of the biomedical research community, the NIH has a number of key opportunities to encourage and better support a research ecosystem that leverages data and tools, and to strengthen the workforce of people doing this research. The need for advances in cultivating this ecosystem is particularly evident considering the current and growing deluge of data originating from next-generation sequencing, molecular profiling, imaging, and quantitative phenotyping efforts.”

*http://www.nature.com/nature/journal/v498/n7453/pdf/498255a.pdf

Data infrastructure in the genomic era

ElixirThe ELIXIR Platforms comprise:

● Data Sustaining Europe’s life-science data infrastructure

● Tools Services and connectors to drive access and

exploitation

● Interoperability Supporting the discovery, integration and

analysis of biological data

● Compute Storage, compute and authentication/access

services

● Training Professional skills for managing and exploiting

data

Four Use Cases service domain-specific research communities:

● Human data Developing long-term strategies for managing and accessing sensitive human data

● Rare diseases Supporting the development of new therapies for rare diseases

● Marine metagenomics Developing a sustainable metagenomics infrastructure to nurture research and

innovation in marine science

● Plant science Developing an infrastructure to facilitate genotype-phenotype analyses for crop and tree

species

Although the Commons is a complex ecosystem, there are four main components, which fit together as indicated to the left.

● A computing environment, such as the cloud or HPC (High

Performance Computing) resources, which supports access,

utilization and storage of digital objects.

● Publicly available datasets that adhere to a Commons digital

object compliance model.

● Software services and tools to facilitate access to and use on

data, both the data in the Commons or elsewhere.

● A digital object compliance model that describes the

properties of digital objects that enable them to be findable,

accessible, interoperable and reproducible (FAIR).

Each of these components will require further development and

harmonization while being developed. A series of Commons pilots has

been initiated to develop and test these components in order to

understand and evaluate how well they will contribute to an

ecosystem that will effectively support and facilitate sharing and reuse

of digital objects.

de.NBI - German Network for Bioinf Infrastructure

● Provide, expand and improve a repertoire of specialized bioinformatics tools (over 100)

● Provide access to computing and storage capacities (currently 15000 cores and 5PB storage)

● Provide regular training events (~30 such events in 17/18 from 2 to 5 days in length)

● Maintain and develop specific high-quality data resources

SIB - Swiss Institute for Bioinformatics

SIB leads and coordinates the field of bioinformatics in Switzerland. Its data science experts join forces to advance biological and medical research and enhance health by:

1. Providing the national and international life science community with a state-of-the-art bioinformatics infrastructure, including resources, expertise and services

2. Federating world-class researchers and delivering training in bioinformatics.

IFB - French Institute of Bioinformatics

● Provide core bioinformatics resources to the national and international life science research community in key fields…

● Build academic cloud devoted to bioinformatics

INB - Spanish National Bioinformatics Institute

● Provide world-class core bioinformatics resources to the national

and international life science research community...

● Provide a platform of integrated core bioinformatics services to

the research community...

● Facilitate coordinated participation of bioinformatics groups in

large-scale national and international projects...

The INB consists of 10 nodes,

plus a central node that directs

and coordinates the activities.

Nodes were selected by an

international evaluation of

proposals: genomics,

proteomics, functional

genomics, structural biology,

population genomics and

genome diversity, biomedical

informatics, algorithm

development and high

performance computing.

The computational effort of the INB

is localized in the computational

node by a special agreement with the

Barcelona Supercomputing Centre.

Coordinating node

● Spanish National Cancer Research Centre (CNIO)

Specialist nodes

● Centre for Genomic Regulation, Bioinformatics

and Genomics group (CRG)

● Spanish National Cancer Research Centre,

Structural Computational Biology Group (CNIO)

● Príncipe Felipe Research Centre, Functional

genomics group (CIPF)

● Institute for Research in Biomedicine, Molecular

Recognition & Bioinformatics Group (IRB)

● University of Malaga, Bioinformatics and

Information Technologies Laboratory (UMA)

● Spanish National Center of Biotechnology,

Biocomputing Unit (CNB)

● Pompeu Fabra University, Genomic Diversity

and Population Genomics group (UPF)

● Research Programme on Biomedical Informatics

(IMIM-UPF)

● National Genome Analysis Centre (CNAG)

● Barcelona Supercomputing Centre (BSC)

Biosciences Data Capability components

Vision - Purpose and Key StepsSet out the compelling impact that the realisation of data intense biosciences can deliver

Agree critical steps and identify the key infrastructure needed to achieve those visions

Biosciences Data CommonsCommunity Resources - What and Why

Biosciences Data ConsortiumMechanisms - Who and How

Existing and expected digital bioscience resources (systems,

data, tools and skills) that are valuable to Australian bioscience:

● Be clear about supply, development and access processes.

● For off-shore resources, identify what, if any, improved means of

access or engagement with them would be possible and beneficial

and the mechanisms that could achieve that.

● For on-shore resources identify what improvements to them and

their supporting mechanisms could be made to increase their value

to Australian researchers.

● Identify how and in what way ‘on-shoring’ adds value.

Models for a cooperative structure suitable to the vision to:

● Strengthen relationships with key international data and software

resources.

● Develop agreements, desirable policies and recommended practices that

can support improved data access and data linking.

● Provide guidance to supporters, participants and users of the ABDC such as

BPA, the ARDC, Universities, MRIs, CSIRO, bioscience service providers.

● Be a vehicle for any ‘Excelerate like’ and ‘Data Commons like’ programmes

of work that may be funded to contribute to the ABDC.

● Lead to an Australian Bioinformatics Facility with a federated model such as

de.NBI or SBI or several such structures.

Biosciences Data Cloud Resources (used for Australian research)Commercial: AWS, Azure, Google Cloud, ...

Institutional and State resources

National: ANDS, NeCTAR, RDS, NCI, Pawsey, Future ARDC

INTERNATIONAL: EBI cloud (EMBASSY), Jetstream, ...

A B D C

Summary of our current understanding

30,000 health/biosciences researchers

18,000 health/biosciences RHD students

48,000 health/biosciences PG course work students

(163,000 + 40,000 =) 200,000 health/biosciences UG students

1,000 to 1,500 bioinformatician/computational biologists

ABDC users

UsersEstimated # Australian biology researchers: 30,000 (and perhaps ~ 1 million worldwide)

(In 5 years → 31,500)

Estimated #: 1,000

(In 5 years → 1,500)

bioinformaticians

research into and

application of techniques,

tool development

Eg. research generating

new tool or statistical

method; bioinformatics

core facilities applying

complex analyses

2,000

(→ 3,000)

bioinformatics-intensive

bioscience researchers

where research is fully

dependent on advanced or

novel use of bioinformatics

Eg. Genomic cancer

research, population

genomics/agricultural

genomics programs

7,000

(→ 12,000)

data-intensive

bioscience researchers

where ‘omics data analysis is

a critical contributor to, but

not definer of, the research

outcomes

Eg. RNAseq analysis to

identify upregulated genes in

broader research program

20,000

(→ 15,000)

biology-focussed bioscience

researchers

occasional users of

bioinformatics web services

where bioinformatics adds

value to research outcomes

determined by other means

Eg BLAST, Ensembl

Resources (with examples)DATA TOOLS

Data Collections

Databases Software Informatics

Services

Originating

in Australia

Global

Audience

CMRI ProCan,

ASPREE

Stemformatics,

InnateDB

UnicarbKB

edgeR, Degust,

Prokka, Snippy

Stemformatics.org

InnateDB.com

Australian

Audience

BPA Framework

datasets

WallaBase,

SpiderToxin DB

GVL Galaxy-MEL

Galaxy-QLD

Originating

elsewhere

Global (incl

Australian)

Audience

ICGC, TCGA, SRA,

1000 Genomes,

Genbank

GTex, dbGaP,

TOPMed, ENCODE,

KEGG, GO, ChEBI

TAIR, Zfin

Galaxy Ensembl, BLAST

Galaxy-Main

Initial discussions/consultations led to a ‘data complexity+scale’ layering:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

International Science Advisory Group (mid-Sept)

● The process is good (and endorsed)

● The user breakdown is realistic and valuable

● The resource categories are comparable to analogous

attempts at this

● Relating to international initiatives is critical

○ But it’s not clear how to make that work best

○ eg EBI vs ELIXIR...

Next: mapping infrastructure to users groups

This also allows impact to be mapped

Improve the quality and uptake of bioinformatics services

Enable ground breaking advances

Empower Migration

Empower Participation

Expand the scope of knowledge researchable using bioscience techniques in Australia

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

✓ Yes, but make training more explicit

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

✓ Yes, but make training more explicit

✓ ✓** Science Enabler **Investment attractor

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

Government agencies will drive this

✓ ✓** Science Enabler **Investment attractor

✓ Yes, but make training more explicit

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives ✓ May need a new entity

✓ Yes, but make training more explicit

Government agencies will drive this

✓ ✓** Science Enabler **Investment attractor

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

✓ Yes, but make training more explicit

✓ May need a new entity

Government agencies will drive this

✓ ✓** Science Enabler **Investment attractorCommon data and compute

resources?

Reference Group (3 Oct) Comments:

1. An accessible ‘service’ platform to which researchers bring

their data, tools, pipelines and research goals

2. A platform for cross-institutional data integration and

collaboration

3. A platform which can support national scale data investment

4. A mechanism for representing Australia’s interests and

participation in global initiatives

✓ Yes, but make training more explicit

✓ May need a new entity

Government agencies will drive this

✓ ✓** Science Enabler **Investment attractorCommon data and compute

resources?

Health/Clinical separate?

Non -omics?

Asia connection?

An improved investment/impact map:

An improved investment/impact map:

Efficiency + resource sustainability

An improved investment/impact map:

Accessibility domain evolution

Efficiency + resource sustainability

An improved investment/impact map:

Accessibility domain evolution

Collaboration, standards, global participation and expertise

Efficiency + resource sustainability

What else do we need to think about?

A. Imaging - where it fits

B. What not being in Europe/US means in practice

C. Relationship to Asia

D. What a data integrative omics/biology capability looks like

E. others…..?

Key National Research InfrastructureA strategy is needed to relate those in red

DIGITAL DATA AND ERESEARCH

● Tier 1 HPC (e.g. NCI, PAWSEY)

● Australian Research Data Cloud

● AREN (Network)

● AAF (Authentication)

HUMANITIES, ARTS, SOCIAL SCIENCE

● Integrated coordinated platform

● Platforms for indigenous

research

● Platforms for social sciences

CHARACTERISATION

● Microscopy network

● Biomedical imaging network

● Neutron stuff (OPAL)

● Synchrotron

ADVANCED FABRICATION &

MANUFACTURING

● Materials on a micro/nano scale

● Bioengineering, fabrication

● New classes of fabricated

devices

ADVANCED PHYSICS AND ASTRONOMY

● Optical and SKA

● International accelerators

● Precision measurement

● Nuclear (OPAL)

EARTH & ENVIRONMENTAL SYSTEMS

● Environmental prediction

● Earth monitoring, exploration

● Remote sensing

● Agriculture networks

● Marine systems

BIOSECURITY

● Prevention of exotic diseases

● Biosecurity testing facility

network

COMPLEX BIOLOGY

● Omics data translation network

● Plant phenomics

● Networked biobanks

● Bioinformatics and automation

THERAPEUTIC DEVELOPMENT

● Drug discovery, manufacturing

● Bioengineering

● Health translation

● Population, tissue, microbial,

genomics datasets