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Organiser: Australian BioCommons 

  • WEBINAR: AlphaFold: what’s in it for me?

    18 April 2023

    WEBINAR: AlphaFold: what’s in it for me? https://dresa.org.au/events/webinar-alphafold-what-s-in-it-for-me [AlphaFold](https://www.deepmind.com/research/highlighted-research/alphafold) has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research. Beyond the hype, what does this mean for structural biology as a field (and as a career)? Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases. Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis. **Speaker:** Dr Craig Morton, Principal Research Scientist and Drug Discovery Lead at the CSIRO **Who the webinar is for:** Researchers, computational biologists and bioinformaticians with an interest in structural biology or applications of deep learning and artificial intelligence to life science research. **How to join:** This webinar takes place online via Zoom Webinar. The webinar is free to join but you must register for a place in advance **[Register here](https://unimelb.zoom.us/webinar/register/WN_LwOIIh3UQemKPgcJnfAvzA)** 2023-04-18 13:00:00 UTC 2023-04-18 14:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all AlphafoldAIDeep learningStructural biologyProtein biology

  • WORKSHOP: Unlocking nf-core - customising workflows for your research

    18 - 19 May 2023

    WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/events/workshop-unlocking-nf-core-customising-workflows-for-your-research Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community. [nf-core](https://nf-co.re/) is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals. This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the[ nf-core/rnaseq](https://nf-co.re/rnaseq) workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment. **Lead Trainers** Dr Georgina Samaha, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Chris Hakkaart, Developer Advocate, Sequera Labs. **Date/Time** 18 and 19 May 2023, 1-4pm AEST/12:30-3:30pm ACST/11am -2pm AWST **Format** This online workshop will take place over two sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce the topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes** By the end of the workshop you should be able to: * Recognise how Nextflow and nf-core enable reproducible and portable bioinformatics * Write and run a basic nf-core run command * Describe nf-core code/directory structure (config, modules, submodules, workflow, main.nf) * Adjust the run command to customise the workflow * Describe Nextflow configuration hierarchy * Create and use a params file to customise workflow parameters * Create and use a custom config file to adjust resource usage * Apply external arguments not available as a workflow parameter to a process **Who the workshop is for** This workshop is for researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows. The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience running Nextflow and nf-core workflows is recommended. You must be associated with an Australian organisation for your application to be considered. If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU) or recordings of recent[ nf-core training](https://www.youtube.com/c/nf-core). **How to apply** **[Apply here](https://custom-nfcore.eventbrite.com.au/)** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Thursday 4 May 2023**. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our[ Advice on applying for Australian BioCommons workshops.](https://www.biocommons.org.au/workshop-applications) _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Sequera with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2023-05-18 13:00:00 UTC 2023-05-19 16:00:00 UTC Australian BioCommons Australian BioCommonsSydney Informatics HubSequera training@biocommons.org.au [] [] [] expression_of_interest WorkflowsNextflownf-corePipelines

  • WEBINAR: Genomic data - improving discovery and access management

    14 June 2023

    WEBINAR: Genomic data - improving discovery and access management https://dresa.org.au/events/webinar-genomic-data-improving-discovery-and-access-management Australian human genome initiatives are generating vast amounts of human genome data to understand the cause of complex diseases, improve diagnosis / early disease detection and identify tailored treatment options. To achieve this, genomic data needs to be compared between multiple individuals and cohorts, often across efforts/jurisdictions, at national or global scales, and requires the genomic data to be findable, searchable, shareable, and linkable to analytical capabilities. The[ Human Genome Platform Project](https://www.biocommons.org.au/hgpp) aims to make it as easy as possible to securely and responsibly share human genome research data nationally and internationally. The project is building a ‘services toolbox’ that combines best practice technologies in human genome data sharing. In this webinar the project team will discuss two important aspects of human genomic data sharing 1. the discovery of genomic cohorts and the GA4GH Beacon protocol that enables this functionality across multiple sites 2. the access management process whereby access to cohorts can be signed off by a responsible data access committees - and the REMS software system in place at the Garvan for doing this **Speakers:** Dr Christina Hall, Associate Director Training and Communications, Australian BioCommons Dr Andrew Patterson, Human Genomics Data Technology Lead, University of Melbourne Mustafa Syed, Bioinformatics System Integration Manager, Children’s Cancer Institute Associate Professor, Sarah Kummerfeld, Director - Data Science, Garvan Institute of Medical Research **Who the webinar is for:** This webinar is for people who are interested in implementation of a similar system for secure and responsible data sharing whether that be for genomics or other applications. **How to join:** This webinar is free to join but you must register for a place in advance. [Register here](https://unimelb.zoom.us/webinar/register/WN_dcRdDROyRquatiZhU6U7wQ) 2023-06-14 12:00:00 UTC 2023-06-14 13:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all Human genomicsAccess management sensitive dataGenomicsClinical dataGA4GH

  • WEBINAR: AlphaFold: what’s in it for me?

    18 April 2023

    WEBINAR: AlphaFold: what’s in it for me? https://dresa.org.au/events/webinar-alphafold-what-s-in-it-for-me [AlphaFold](https://www.deepmind.com/research/highlighted-research/alphafold) has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research. Beyond the hype, what does this mean for structural biology as a field (and as a career)? Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases. Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis. **Speaker:** Dr Craig Morton, Principal Research Scientist and Drug Discovery Lead at the CSIRO **Who the webinar is for:** Researchers, computational biologists and bioinformaticians with an interest in structural biology or applications of deep learning and artificial intelligence to life science research. **How to join:** This webinar takes place online via Zoom Webinar. The webinar is free to join but you must register for a place in advance **[Register here](https://unimelb.zoom.us/webinar/register/WN_LwOIIh3UQemKPgcJnfAvzA)** 2023-04-18 13:00:00 UTC 2023-04-18 14:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all AlphafoldAIDeep learningStructural biologyProtein biology

  • WORKSHOP: Unlocking nf-core - customising workflows for your research

    18 - 19 May 2023

    WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/events/workshop-unlocking-nf-core-customising-workflows-for-your-research Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community. [nf-core](https://nf-co.re/) is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals. This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the[ nf-core/rnaseq](https://nf-co.re/rnaseq) workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment. **Lead Trainers** Dr Georgina Samaha, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney Dr Chris Hakkaart, Developer Advocate, Sequera Labs. **Date/Time** 18 and 19 May 2023, 1-4pm AEST/12:30-3:30pm ACST/11am -2pm AWST **Format** This online workshop will take place over two sessions. You must attend both sessions to get the most out of the workshop. Expert trainers will introduce the topics and guide you through hands-on activities to help you put your new skills into action. **Learning outcomes** By the end of the workshop you should be able to: * Recognise how Nextflow and nf-core enable reproducible and portable bioinformatics * Write and run a basic nf-core run command * Describe nf-core code/directory structure (config, modules, submodules, workflow, main.nf) * Adjust the run command to customise the workflow * Describe Nextflow configuration hierarchy * Create and use a params file to customise workflow parameters * Create and use a custom config file to adjust resource usage * Apply external arguments not available as a workflow parameter to a process **Who the workshop is for** This workshop is for researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows. The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience running Nextflow and nf-core workflows is recommended. You must be associated with an Australian organisation for your application to be considered. If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar[ Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU) or recordings of recent[ nf-core training](https://www.youtube.com/c/nf-core). **How to apply** **[Apply here](https://custom-nfcore.eventbrite.com.au/)** This workshop is free but participation is subject to application with selection. Applications close at **11:59pm AEST, Thursday 4 May 2023**. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our[ Advice on applying for Australian BioCommons workshops.](https://www.biocommons.org.au/workshop-applications) _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/), Sydney Informatics Hub and Sequera with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2023-05-18 13:00:00 UTC 2023-05-19 16:00:00 UTC Australian BioCommons Australian BioCommonsSydney Informatics HubSequera training@biocommons.org.au [] [] [] expression_of_interest WorkflowsNextflownf-corePipelines

  • WEBINAR: Genomic data - improving discovery and access management

    14 June 2023

    WEBINAR: Genomic data - improving discovery and access management https://dresa.org.au/events/webinar-genomic-data-improving-discovery-and-access-management Australian human genome initiatives are generating vast amounts of human genome data to understand the cause of complex diseases, improve diagnosis / early disease detection and identify tailored treatment options. To achieve this, genomic data needs to be compared between multiple individuals and cohorts, often across efforts/jurisdictions, at national or global scales, and requires the genomic data to be findable, searchable, shareable, and linkable to analytical capabilities. The[ Human Genome Platform Project](https://www.biocommons.org.au/hgpp) aims to make it as easy as possible to securely and responsibly share human genome research data nationally and internationally. The project is building a ‘services toolbox’ that combines best practice technologies in human genome data sharing. In this webinar the project team will discuss two important aspects of human genomic data sharing 1. the discovery of genomic cohorts and the GA4GH Beacon protocol that enables this functionality across multiple sites 2. the access management process whereby access to cohorts can be signed off by a responsible data access committees - and the REMS software system in place at the Garvan for doing this **Speakers:** Dr Christina Hall, Associate Director Training and Communications, Australian BioCommons Dr Andrew Patterson, Human Genomics Data Technology Lead, University of Melbourne Mustafa Syed, Bioinformatics System Integration Manager, Children’s Cancer Institute Associate Professor, Sarah Kummerfeld, Director - Data Science, Garvan Institute of Medical Research **Who the webinar is for:** This webinar is for people who are interested in implementation of a similar system for secure and responsible data sharing whether that be for genomics or other applications. **How to join:** This webinar is free to join but you must register for a place in advance. [Register here](https://unimelb.zoom.us/webinar/register/WN_dcRdDROyRquatiZhU6U7wQ) 2023-06-14 12:00:00 UTC 2023-06-14 13:00:00 UTC Australian BioCommons Australian BioCommons training@biocommons.org.au [] [] [] open_to_all Human genomicsAccess management sensitive dataGenomicsClinical dataGA4GH

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