| title | toc |
|---|---|
ABLeS processes |
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If you are new to the ABLeS program, please read the processes below to get started using ABLeS resources. You may also contact us for more information and assistance.
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|---|---|---|---|---|
| Reference Data | Production Bioinformatics | Software Accelerator | ||
| Data centric outcomes | Production of reference and derived data assets that will be published to enable use / reuse by others outside the group. | Yes | Yes | |
| Research centric outcomes | Production of data assets and outputs that are critical to research projects and consortia making use of best practice, production level bioinformatics approaches. | Yes | ||
| Software centric outcomes | Creation, development, installation, testing and/or optimisation of software that will be made available for use / reuse by others in the life sciences community. | Yes | ||
| Common research theme | A defined cross-institutional collaboration, project, community, consortium, or some other collaborative construct, that is focused on a common research theme. | Yes | ||
| Development & optimisation | Groups work to understand their software, methods and the optimal approaches to solving the bioinformatics problems at hand. ABLeS will facilitate both the experimental / testing and production phases of computational analyses. | Yes | ||
| Planned usage of ABLeS resources | The use of ABLeS resources is planned and approached with a level of care appropriate to their status as limited and consumable resources. | Yes | ||
| Sharing | Appropriate mechanisms are used to share outputs that support and assist other groups, with examples provided in the ABLeS publication. Outputs include software, methods, training, resource usage and quality assessments for derived reference data sets, submissions to data international repositories and research publications. | Yes | ||
ABLeS users will follow one of the paths illustrated below as per the three allocation schemes supported by ABLeS (Creation of reference data assets, Production bioinformatics, and Software accelerator).
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The Australian BioCommons and the bioinformatics leads for each group have different roles during an ABLeS project's initiation, operation and closing phases.
ABLeS projects are led and maintained by their users with the support of the ABLeS team to facilitate access to ABLeS resources.
Project bioinformatics lead's role:
- Familarise themselves with ABLeS schemes, expectations, and responsibilities.
- Submit a project plan that contains the details of the project (link). The community’s steering committee (or bioinformatics leads) should approve the plan.
- Identify known challenges that BioCommons, NCI, or Pawsey may be able to address and / or support as part of ABLeS. You can use the GoogleForm to let us know about these challenges.
- Create of a project allocation (at NCI or Pawsey) for a group
- Invite the group bioinformatics leads to a project allocation as Chief Investigators
- Provide information on how to utilise ABLeS resources and contribute to the shared tool and software repository.
- Manage the resources available to the ABLeS programme across all active projects.
Project bioinformatics lead's role:
- Request additional resources when the project needs more resources than are available. Each project gets default resources automatically at the beginning of each quarter without the need to request them.
- Attend a quarterly meeting with BioCommons to discuss and report the outcomes of the project (data, methods, publications etc.) in the previous quarter.
- Manage the resources provided by ABLeS including:
- Adding members to the project(s).
- Educating / onboarding new project members.
- Contributing and / or coordinating contributions to the shared tool and software repository (if89), as well as encouraging community contribution.
- Utilise ABLeS resources efficiently and use the resource for the project purposes.
- Help to deploy and install software, tools and workflows to the shared repository (this activity may be coordinated by the project bioinformatics leads, as needed)
- Installing tools, software, pipelines when special support is needed.
- Optimising workflows and software to be used by all projects.
- Developing and improving cross-cutting tools and workflows.
- Managing the allocation of resources for projects and adding default resources at the beginning of each quarter.
Project bioinformatics lead's role:
- Notify Australian BioCommons when you are ready to close your project.
- Make sure all project data is archived as the project storage will be released.
- Make sure all workflows are registered with WorkflowHub and well documented so they are findable.
- Report the project outcomes to the Australian BioCommons.
- Finalise the closing process with the infrastrucure provider.
| Principle | Description |
|---|---|
| Project leadership | A project lead is responsible for all use of resources provided, which will need to adhere to relevant facility processes and policies. The lead will also monitor and manage reasonable usage of their project computational infrastructure allocations. |
| Group-level decision making | A collaborative decision making mechanism to prioritise the bioinformatics work using relevant computational resources must exist. This can be a formalised steering committee, a working group, or some other forum which is representative of the collaboration. Resources used must be agreed upon / in line with the community’s decision making mechanism and align with community priorities. |
| Group-level expertise | The community has expertise which will drive and execute its bioinformatics agenda. This expertise offers a strong collaboration link with the expertise and support available through ABLeS, NCI and Pawsey. |
| Collaboration & consultation | ABLeS is collaborative and involves BioCommons, the research community, and the computational facilities. It is also a standing item for discussion and forums play a strong role in managing the use of ABLeS: groups will thus engage with BioCommons in an open and collaborative manner, with regular meetups. |
| Follow compute facility access policies | All users must abide by the relevant access policies of Pawsey and NCI. NCI Terms and Conditions of Access; NCI Data Collections Management; and Pawsey Conditions of Access. |
| Time frame / duration of allocations | Each project is reviewed at the 6 month mark, to ensure resources are being used as efficiently as practical and so challenges can be identified / addressed by the ABLeS team. Reference data and production projects are ongoing by definition, while software accelerator projects need to be renewed at 6 months if the work originally described for the project has not been completed. |