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Authors: Dow, Ellen (orcid: 0000-000...  or Price, Gareth (orcid: 0000-...  or Gustafsson, Johan (orcid: 0... 


WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share

This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports...

Keywords: Bioinformatics, Computational biology, Computational infrastructure

WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share https://dresa.org.au/materials/webinar-scaling-up-bioinformatics-with-ables-the-australian-biocommons-leadership-share This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024. Event description The Australian BioCommons Leadership Share (ABLeS) supports access to, and efficient use of, national computational systems for big-data bioinformatics. Designed for established life sciences projects, groups, institutes and consortia, ABLeS can be used to facilitate software optimisation and scaling, implementation of optimised software for production analyses, and creation of reference data. This webinar highlights how ABLeS is being used by life science communities across Australia to access and leverage bioinformatics at scale. We’ll explain the structure of the ABLeS program and how your life science community can get involved, as well as providing a breakdown of the program expectations and the support available from the BioCommons and our partners. Community members making use of ABLeS will share their perspective on the program, and the research outcomes that have resulted. ABLeS is supported by the Australian BioCommons in partnership with Bioplatforms Australia, the National Computational Infrastructure, and the Pawsey Supercomputing Centre. Speakers: Australian BioCommons: Dr Steven Manos Dr Johan Gustafsson Dr Ziad Al Bkhetan   ABLeS users: Dr Hardip Patel, National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University Chelsea Mayoh, Zero Childhood Cancer, Children's Cancer Institute Theodore Allnutt, Royal Botanic Gardens Victoria 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. BioCommons_ABLeS: A PDF copy of the slides presented by the BioCommons team during the webinar. Mayoh_ABLeS: A PDF copy of the slides presented by Chelsea Mayoh   Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/Eb0z2-yaJbY   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Computational biology, Computational infrastructure
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: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 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. Schedule (PDF): schedule for the workshop Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop   Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation
WEBINAR: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. 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. Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Getting started with proteomics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.

Event description 

Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...

Keywords: Bioinformatics, Proteomics, Mass spectrometry

WEBINAR: Getting started with proteomics https://dresa.org.au/materials/webinar-getting-started-with-proteomics-134c519c-0cea-4195-b444-1e73d551a20e This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023. Event description  Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases. Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.  This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps. This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities. 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. Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/RSrk2yqklQo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: Make your bioinformatics workflows findable and citable

This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.

Event description

Computational workflows are invaluable resources for research communities. They help...

Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science

WORKSHOP: Make your bioinformatics workflows findable and citable https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable-74e85d1c-d869-429e-b942-8391f4bab23d This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023. Event description Computational workflows are invaluable resources for research communities. They help us  standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community. Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily. This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.  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. 2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop Materials shared elsewhere: A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a brilliant...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia-134a8bf5-3801-421f-a454-e0f9020f4871 This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. Event description  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: Use the workflows creator in Galaxy Australia  Build a workflow based on a published method Annotate workflows so that you (and others) can understand them  Make workflows finable and citable (important and very easy to do!) 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. GalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
WORKSHOP: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

 

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.   Event description Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: Spreadsheets, organising data and first steps with R Manipulating and analysing data with dplyr Data visualisation Summarized experiments and getting started with Bioconductor   This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. 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. Schedule (PDF): A breakdown of the topics and timings for the workshop Recommended resources (PDF): A list of resources recommended by trainers and participants Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere:   This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WEBINAR: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. 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. Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WEBINAR: Getting started with proteomics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.

Event description 

Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...

Keywords: Bioinformatics, Proteomics, Mass spectrometry

WEBINAR: Getting started with proteomics https://dresa.org.au/materials/webinar-getting-started-with-proteomics This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023. Event description  Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases. Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.  This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps. This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities. 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. Getting started with proteomics_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/RSrk2yqklQo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Proteomics, Mass spectrometry
WORKSHOP: Make your bioinformatics workflows findable and citable

This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023.

Event description

Computational workflows are invaluable resources for research communities. They help...

Keywords: Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science

WORKSHOP: Make your bioinformatics workflows findable and citable https://dresa.org.au/materials/workshop-make-your-bioinformatics-workflows-findable-and-citable This record includes training materials associated with the Australian BioCommons workshop ‘Make your bioinformatics workflows findable and citable’. This workshop took place on 21 March 2023. Event description Computational workflows are invaluable resources for research communities. They help us  standardise common analyses, collaborate with other researchers, and support reproducibility. Bioinformatics workflow developers invest significant time and expertise to create, share, and maintain these resources for the benefit of the wider community and being able to easily find and access workflows is an essential factor in their uptake by the community. Increasingly, the research community is turning to workflow registries to find and access public workflows that can be applied to their research. Workflow registries support workflow findability and citation by providing a central repository and allowing users to search for and discover them easily. This workshop will introduce you to workflow registries and support attendees to register their workflows on the popular workflow registry, WorkflowHub. We’ll kick off the workshop with an introduction to the concepts underlying workflow findability, how it can benefit workflow developers, and how you can make the most of workflow registries to share your computational workflows with the research community. You will then have the opportunity to register your own workflows in WorkflowHub with support from our trainers.  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. 2023-03-21_Workflows_slides (PDF): A copy of the slides presented during the workshop Materials shared elsewhere: A recording of the first part of this workshop is available on the Australian BioCommons YouTube Channel: https://youtu.be/2kGKxaPuQN8 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, WorkflowHub, FAIR, Open Science
WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022.

Event description 

Have you discovered a...

Keywords: Bioinformatics, Workflows, FAIR, Galaxy Australia

WEBINAR: Here's one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia https://dresa.org.au/materials/webinar-here-s-one-we-prepared-earlier-re-creating-bioinformatics-methods-and-workflows-with-galaxy-australia This record includes training materials associated with the Australian BioCommons webinar ‘Here’s one we prepared earlier: (re)creating bioinformatics methods and workflows with Galaxy Australia’. This webinar took place on 26 October 2022. **Event description**  Have you discovered a brilliant bioinformatics workflow but you’re not quite sure how to use it? In this webinar we will introduce the power of Galaxy for construction and (re)use of reproducible workflows, whether building workflows from scratch, recreating them from published descriptions and/or extracting from Galaxy histories. Using an established bioinformatics method, we’ll show you how to: * Use the workflows creator in Galaxy Australia  * Build a workflow based on a published method * Annotate workflows so that you (and others) can understand them  * Make workflows finable and citable (important and very easy to do!) 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. * GalaxyWorkflows_Slides (PDF): A PDF copy of the slides presented during the webinar. **Materials shared elsewhere:** A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/IMkl6p7hkho Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, FAIR, Galaxy Australia
WORKSHOP: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022. **Event description** Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: - Spreadsheets, organising data and first steps with R - Manipulating and analysing data with dplyr - Data visualisation - Summarized experiments and getting started with Bioconductor This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. 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. - Schedule (PDF): A breakdown of the topics and timings for the workshop - Recommended resources (PDF): A list of resources recommended by trainers and participants - Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. **Materials shared elsewhere:** This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
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
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 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. - Schedule (PDF): schedule for the workshop - Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop **Materials shared elsewhere:** The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation