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Authors: Dow, Ellen (orcid: 0000-000...  or Cooke, Steele 


WEBINAR: KBase - A knowledge base for systems biology

This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.

Event description 

Developed for bench biologists and bioinformaticians, The Department of Energy Systems...

Keywords: Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology

WEBINAR: KBase - A knowledge base for systems biology https://dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology-653d9753-989d-4194-9230-6e2d90652955 This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021. Event description  Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function. This webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Q&A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources Introduction to KBase: Australian BioCommons Webinar [PDF]: Slides presented during the webinar Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tJ94i9gOJfU The slides are also available as Google slides:  https://tinyurl.com/KBase-webinar-slides Melissa Burke (melissa@biocommons.org.au) Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
WORKSHOP: Unlocking nf-core - customising workflows for your research

This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.

Event description

Processing and analysing omics datasets poses many...

Keywords: Bioinformatics, Workflows, Nextflow, nf-core

WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research-1584ff39-e007-4422-9fd5-4e407df6b6c5 This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023. Event description 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 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 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. This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).  Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).  https://sydney-informatics-hub.github.io/customising-nfcore-workshop Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, nf-core
WORKSHOP: Unlocking nf-core - customising workflows for your research

This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.

Event description

Processing and analysing omics datasets poses many...

Keywords: Bioinformatics, Workflows, Nextflow, nf-core

WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023. Event description 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 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 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. This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).  Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).  https://sydney-informatics-hub.github.io/customising-nfcore-workshop Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, nf-core
WEBINAR: KBase - A knowledge base for systems biology

This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.

Event description

Developed for bench biologists and bioinformaticians, The Department of Energy...

Keywords: Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology

WEBINAR: KBase - A knowledge base for systems biology https://dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021. **Event description** Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function. This webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. **Files and materials included in this record:** - Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. - Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. - Q&A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources - Introduction to KBase: Australian BioCommons Webinar [PDF]: Slides presented during the webinar **Materials shared elsewhere:** A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tJ94i9gOJfU The slides are also available as Google slides:  https://tinyurl.com/KBase-webinar-slides Melissa Burke (melissa@biocommons.org.au) Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology