1. STRATEGIC DEVELOPMENT
Bioplatforms National Initiatives aim to build new capabilities and critical data resources essential for tackling Australia’s priority scientific challenges across human health and biomedicine, nature and biodiversity, and primary industry and food sectors.
The selection and development of initiatives are initiated and overseen by Bioplatforms leadership. This process is guided by a variety of signals that reflect national priorities, such as government policies, input from state agencies and professional bodies, peak scientific organisations and communities, philanthropic investments, and industry demands, among others. By leveraging these signals, Bioplatforms ensures that initiatives are not only scientifically robust but also meet national needs, fostering a significant and enduring impact on both Australian and international research endeavours.
2. INITIATIVE LEADERSHIP AND GOVERNANCE
2.1. SCIENTIFIC AND TECHNICAL LEADERSHIP
Scientific leadership and oversight in the form of an advisory committee will be identified and sought from national leaders across the initiative domain, alongside industry and end-user representatives. It is anticipated that the National Initiatives will require a cross-disciplinary collaborative approach to achieve nationally significant outcomes, driven by both discovery and translation – and the advisory committee membership will reflect the breadth of expertise required across the initiative goals.
Therefore, the advisory committee are likely to have representation from relevant research organisations, consortia and government departments spanning the nation, including:
- State and National Herbariums
- Museums and Collections
- Statutory Rural Development Corporations (RDC’s)
- Commonwealth peak bodies and associations (e.g. CSIRO, Academy of Science)
- Federal Government Departments
- State Government Departments
- Universities and Research institutes
- Indigenous Land Councils and representatives
- Australian Research Centre investments (Centre’s of Excellence, Transformation Hubs, Training Centres)
- Co-operative Research Centres
- Private and commercial representatives (Start up, SME, and Enterprise)
- Technical and research infrastructure representatives (Australian BioCommons representatives, other NCRIS capabilities)
- Medical Research Futures Fund recipients
- National Health and Medical Research Council funding recipients
The role of the advisory committee is to provide scientific leadership and transparent governance of the initiative by:
- Providing oversight and guidance to ensure the consortium is working on the agreed scope towards the outlined objectives
- Establishing processes for decision-making and priority signalling for impact (e.g. species prioritisation)
- Production of consortium guidelines and policies, where required
- Engagement of new partners/collaborators
- Identification of external advisors for the initiative to ensure currency and engagement (nationally and internationally)
- Overall project management direction and advocacy.
2.2. GOVERNANCE STRUCTURE
The governance structure of the National Initiatives includes the advisory committee, project manager and specialist working groups to provide expert advice to the advisory committee (as required), as well as input from other external advisors, as required.
Where possible, the advisory committee will be led by a respected scientific Chair who will be determined by Bioplatforms leadership. It is the role of the Chair to provide altruistic leadership to the Initiative and provide clear direction, advocacy and leadership for the program of work.
The advisory committee will be supported by working groups that may be formed for expert sub-themes within the National Initiatives and will work through particular components of the program including defining standards, bioinformatics, impact assessment, species prioritisations, where required.
Bioplatforms will support project management at 0.3 FTE for 3 years to coordinate meetings, processes, data generation, and communications. This role will be partially funded from Bioplatforms proposed initiative investment and will be conducted by Bioplatforms project management and operations employees.
3. COMMUNITY AND COLLABORATION
Bioplatforms National Initiatives seek to build, and foster, communities of practice for data generation, and methods development, around themes of national significance. With leadership provided from the advisory committee, the Initiative will activity seek collaborative partnership and co-investment of appropriately skilled personnel to meet objectives of the initiative.
Collaborative partners across the Initiatives will be engaged and invested in working in a community of open science and sharing of knowledge to increase capability and capacity of scientific enquiries and ensure translation applications of the data assets.
Partnerships in all levels of the initiative will be set a national scale, including representatives in the advisory committee and projects supported by the initiative. This approach will provide the connective mechanism to enable enhanced collaborative opportunities seeded through these programs.
4. PROTOCOLS AND ETHICS
4.1. PROTOCOLS AND ANALYSIS
The protocols used across the Initiatives will follow the international technological and methodological best practice for omics data creation and analysis.
The technical capability including instrumentation and skilled personnel for the anticipated approaches resides in one or more Bioplatforms network laboratory facilities. The technical facilities have existing relationships with Australian life sciences researchers, as many of the potential stakeholders in Bioplatforms National Initiatives. The Initiative will work with the Bioplatforms facilities, as collaborators on the projects and where required, define new techniques and standards that are fit-for-purpose for the initiative at hand.
The assembly and analysis tools will be leveraged across the initiatives, and will include education and training components with Galaxy and Apollo, delivered through the Australian BioCommons and supported with domain expertise from within the initiative. These training forums will be designed to upskill and build bioinformatic capacity particularly targeted for new users, or to provide forums for advanced analytics of expert users.
4.2. ETHICS
National Initiative sample and data acquisition will be guided and regulated by relevant jurisdictional laws and agreements for ethical access to samples, privacy, permissions and data protection. Collaborating researchers are required to follow their State and Organisation defined laws and ethics guidelines in respect to their research projects and research domain. The Initiative project manager will ensure the declaration of the project adherence to these laws and guidelines, both at the project support step, but also when samples are processed. The data policy and metadata collected aim to ensure the recognition of sample sources, permissions and ownerships. In addition, details of the permits associated with collection of specimens, particularly in relation to Country, is required for recognition and protection of first nations rights and knowledge.
Australian biodiversity and environment initiatives will abide by sustainable access including collection authority, permission relevant to traditional knowledge and benefit sharing (for example; Queensland Biodiscovery Act 2004; Nature Conservation Act 1992; National Parks and Wildlife Act 1974; Biological Resources Regulation; Biological Resources Act 2006). Where required, each project group will be responsible for compliance with the relevant regulations.
5. INFRASTRUCTURE CAPABILITY
The Australian infrastructure capability will come in the form of Bioplatforms supported capability partners including:
- Bioplatforms facilities – genomics, proteomics, metabolomics and synthetic biology facilities will contribute to project planning, method development, data acquisition and analysis
- BioCommons Australia – methods and tool deployment, compute access and training material facilitation.
Apart from deployment of Bioplatforms national laboratories and expertise, the National Initiatives will also seek alignment to other NCRIS infrastructure partners where opportunity exists to leverage data applications, methods and technology advancements, or where the infrastructure capability provides connectivity and enhances the thematic research ecosystem.
6. BIOINFORMATICS
Bioinformatics in the National Initiatives will adhere to international standards for data generation, annotation and analysis.
Bioplatforms Australia’s role is to ensure the communities have access and are guided by domain expertise’s to achieve their research goals, while developing or using repeatable methods and tools to creating reusable data national assets.
It is anticipated that:
- The bioinformatics requirements for the National Initiatives will be a mixed approach and primarily dependant on the community needs, data types and research questions.
- The initiative will partner with domain-specific expertise to train, upskill and offer initiative-level support
- Relevant tools and learnings will be accessible from collaborators (nationally and internationally), and will leverage existing research to enhance capacity across the Initiative communities.
- The initiatives will seek co-investments for bioinformatics positions where there this is required, for example where the initiative is driven by underpinning common questions and analytics.
- The computational requirements for storage space and cloud compute will be met through the support from consortium partner institutions, ARDC and Amazon Web Services – all coordinated through the Australian BioCommons.
- The Initiative will consult Australian BioCommons early and frequently to provide initiative-level access to compute (where required) and training in point-and-click tools, or development of workflows that will be deployed across the initiative.
- Appropriate workflows and pipelines will be deployed through the Australian BioCommons Galaxy Service, and/or made available through the Australian BioCommons Australian Leadership Share (ABLeS) program.
7. METADATA
Across the national initiatives, metadata collection is consistent with international best practice respective to the research domain. In the case where Bioplatforms is the custodian of the data in the Bioplatforms Data Portal partners must use our metadata templates. These templates encompass international best practice standards with regards to omics data and related contextual information. In the case of biodiversity and agri-food samples, contextual information is based on Darwin Core international standards[1]. Human health metadata, which is not stored or maintained by Bioplatforms, is collected at the discretion of the leading researcher with the guiding principle that data needs to be findable, accessible, interoperable and reusable (FAIR).
Where required the role of National Initiative is to seek input from the consortium and ensure and test that best practice standards are fit for purpose for each initiative and will seek inclusion of new fields and correct ontologies describing the fields. Where development of new standards is required, the initiative will work in conjunction with international communities for harmonious standards generation.
8. DATA MANAGEMENT AND ACCESS
Bioplatforms are committed to ensuring that data produced in this effort are openly accessible and shared with as few restrictions as possible, including with full consideration of any sensitive information, to advance scientific discovery and maximise the value to the community from this Australian Government National Collaborative Research Infrastructure Strategy (NCRIS)-funded dataset.
Bioplatforms Australia, as the Data Sponsor, undertakes the overall duties of ownership, and is responsible for the following tasks (in consultation with various research champions):
- Defining the purpose of the data items;
- Defining access arrangements;
- Authorising any Data Users;
The Bioplatforms Data Portal team are responsible for ingesting data from the ‘Omics Facilities in to the Bioplatforms Data Portal as per the conditions outlined in Initiative ‘Data and Collaboration Agreement’[2].
Following production by one of the sequencing facilities, raw data will be uploaded to a password-secured central data repository managed by Bioplatforms Australia via the Queensland Cyber Infrastructure Foundation (QCIF, University of Queensland, Brisbane)[3]. This data is made discoverable and accessible through the Bioplatforms Australia Data Portal interface (https://data.bioplatforms.com/) and the Australian Reference Genome Atlas (ARGA)[4]. This database is held at Amazon Web Services (AWS) Sydney location and mirrored at a second site at QRIS-Cloud Brisbane to enable recovery in case of disaster.
Metadata associated with each file and files names will be made publicly available (except where information considered to be sensitive) via the web interface and associated Application Programming Interface (API). These will include metadata relating to each sample analysed and methods used for the extraction of material, preparation of sample libraries and the generation of ‘omics data. Access to the data files via the web portal and API will be restricted to authorised users and will require authentication through password use. User support guides[5] are available to facilitate access and use of the Data Portal.
All data will be licensed for use under a Creative Commons Attribution License (CC BY 4.0[6]) with the appropriate acknowledgement as defined in the respective ‘Data and Collaboration Agreement’.
Data sharing and collaborative interactions are encouraged to advance scientific discovery and maximise the value to the community from this Australian Government (NCRIS)-funded dataset. Various data types will be made available, at appropriate times, throughout the multistep process of generating, processing, assembling, annotating and dispersing of the reference datasets.
It is generally agreed that the molecular data generated by the National Initiatives is not considered to be sensitive in its own right. However, if during the course of generating this data the Project Collaborators and/or Consortium Members decide that the data, if published, would cause detriment to organisational or jurisdictional operations then the data will be held privately until mutually agreed otherwise. Likewise, metadata that is agreed to be sensitive (for example, latitude and longitude coordinates) will not be stored or published on the data portal. This metadata will be handled by the Project Leader, and requests for access will be deferred to the Project Leader to fulfil.
[2] Example Data and Collaboration Agreement for the Functional Fungi Initiative: https://bioplatforms.com/australian-fungi-data-collaboration-policy/