Australian BioCommons Support

What we do, and how we do it 4

• What is Australian BioCommons?
• What does BioCommons do for life science researchers?
• How is Australian BioCommons funded?
• Our team and collaborators

Background 2

• How to cite Australian BioCommons
• Cookies, data collection and privacy statements

Services 4

• What services are available?
• Who can use the services?
• What support or expertise is available when accessing BioCommons associated platforms/services?
• Where can I find technical documentation?

Activities 1

• What activities are BioCommons coordinating?

Communities 3

• What are BioCommons communities?
• How can I suggest a new community?
• What is the BioCommons community engagement strategy?

Training 6

• What is the Australian BioCommons training program?
• What is the National Bioinformatics Training Co-operative?
• Does Australian BioCommons co-host or sponsor events?
• What type of training does Australian BioCommons provide?
• Who is the training for?
• Are BioCommons training materials publicly available?

Get involved 2

• How do I stay updated?
• How can I influence what infrastructure the Australian BioCommons supports or coordinates the development of?

Getting started 5

• What is Galaxy Australia?
• Can I use Galaxy Australia for data analysis?
• Is Galaxy Australia just for genomics?
• How can I access and use Galaxy Australia?
• How can I learn more about using Galaxy?

Using Galaxy to support your research 5

• Biological data analysis using Galaxy
• Galaxy Tips and Tricks
• Using and customising workflows in Galaxy Australia
• Advanced features of Galaxy
• How to use Vertebrate Genome Project (VGP) genome assembly workflows in Galaxy Australia

Getting started 5

• What is the command line?
• What's a command line interface (CLI)?
• What’s a graphical user interface (GUI)?
• Why would I use the command line for analysis?
• How do I use the command line? How do I get started?

HPC and cloud computers 6

• What are HPC and cloud computers?
• What coding skills do I need to use HPC or cloud computers?
• How can I access HPCs and cloud compute in Australia?
• Compute systems at the BioCommons partner infrastructures
• How do I log in to HPC or cloud systems?
• Introductory Tutorials

Portable software using containers 3

• What's a container? Why are they needed?
• How do you build a customised container image?
• Scaling your research with containers

Software deployments 3

• CernVM-FS
• Spack
• Singularity HPC (SHPC)

Managing human genome data using Gen3 4

• What is Gen3?
• What groups in Australia are using Gen3?
• How do I establish/deploy a Gen3 instance?
• How do I develop a Gen3 data dictionary?

Creating Virtual Cohorts across multiple genomic repositories 4

• Background - Virtual Cohorts
• National community needs - Virtual Cohort Assembly (2022)
• The GA4GH Beacon protocol which enabled discovery of virtual cohorts across multiple sites
• GA4GH Beacon implementation guides

Helping automate the work of Data Access Committees (DACs) 4

• Background - DAC automation
• National community needs - DAC Automation (2022)
• REMS and its deployment in AWS
• Experiences using the REMS (Resource Entitlement Management System) software package

Federated Identity & Access Management (IAM) 4

• Background - Federated Identity and Access
• National community needs - Federated IAM (2022)
• CILogon and COmanage for federated access management in Australia
• CILogon and how it enables identity management

Human Genomic Data and Metadata Archiving 1

• Background - Human Genome Data Archiving