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Authors: Barker, Michelle (orcid: 00...  or Price, Gareth (orcid: 0000-...  or Backhaus, Ann 

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: 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
OECD Report - Building digital workforce capacity and skills for data-intensive science (2020)

 

As a lead contributor to the OECD's Building Digital Workforce Capacity and Skills for Data-Intensive Science (2020) report, Dr Michelle Barker outlines in this presentation the goal of the report, i.e. to make recommendations to policy makers on how to facilitate the digital workforce...

Keywords: international skills initiatives, skills, training, OECD, EOSC, Capability building, Skills uplift, skills development, digital skilled workforce, training material

OECD Report - Building digital workforce capacity and skills for data-intensive science (2020) https://dresa.org.au/materials/oecd-report-building-digital-workforce-capacity-and-skills-for-data-intensive-science-2020-a456ae97-9241-4fc6-b7f9-57c201479317   As a lead contributor to the OECD's Building Digital Workforce Capacity and Skills for Data-Intensive Science (2020) report, Dr Michelle Barker outlines in this presentation the goal of the report, i.e. to make recommendations to policy makers on how to facilitate the digital workforce capacity needed for data-intensive science, based on analysis of best practice. The presentation highlights: - Digital workforce capacity and COVID19: the importance of digital skills, the need for shared access to open data, software and code, and the shortfall in skills to enable a comprehensive response to such emergencies - The ongoing need for a digital skilled workforce for data-intensive science - Five focus areas in the report include: 1. Enablers for digital workforce capacity development 2. Defining needs: digital skills, frameworks and roles 3. Provision of training 4. Community development 5. Career paths and reward structures - Recommendations for actors incl. universities, national or regional governments contact@ardc.edu.au international skills initiatives, skills, training, OECD, EOSC, Capability building, Skills uplift, skills development, digital skilled workforce, training material
Time to fill the gaps: Building out a national training inventory

 

This community discussion seeks to bring together the instructors and facilitators tasked with upskilling researchers and support staff. While this collective dialogue among instructors is not new, what is new is the traction that various groups are getting.

The newly formed group of...

Keywords: training inventory, training registry, national skills initiatives, training material

Time to fill the gaps: Building out a national training inventory https://dresa.org.au/materials/time-to-fill-the-gaps-building-out-a-national-training-inventory-cd4f10d8-83c0-4870-95e2-ee9ed4aa72c7   This community discussion seeks to bring together the instructors and facilitators tasked with upskilling researchers and support staff. While this collective dialogue among instructors is not new, what is new is the traction that various groups are getting. The newly formed group of eResearch support staff gathered by the Melbourne Data Analytics Platform (MDAP) and Sydney Informatics Hub (SIH) is one such group, as is the Lightweight Working Group (LWG): Researcher digital skills training data for enabling digital infrastructure use, spearheaded by University of Melbourne’s David Flanders during the pre-Skills Summit discussions. In this session we seek to build on the momentum, by including a hands-on working session. Participants are asked to come with information to share and questions they seek to answer. During the first half of this session, attendees will populate a public document with shareable training details. The goal is to at least double the size of the new cross-institutional national training collection started by the LWG. The second half of this session will be to ask questions to arrive at next steps. What do we need to do to continue building out this national training inventory and who will be in charge of maintaining and distributing the archive? What platforms exist and are used to capture training data and material and make it readily maintainable and findable? Can the material be reused and how do we recognise and capture re-use? Do we know about how to apply a license to our materials for appropriate reuse or do we need guidance? While there will likely be more questions than these, one question has been answered. When can we move from talking to doing? That time is now. contact@ardc.edu.au training inventory, training registry, national skills initiatives, training material
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action-ffd9b4ed-b557-496b-ac35-72467c03c71b In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material
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: 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: 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
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material
Time to fill the gaps: Building out a national training inventory

 

This community discussion seeks to bring together the instructors and facilitators tasked with upskilling researchers and support staff. While this collective dialogue among instructors is not new, what is new is the traction that various groups are getting.

The newly formed group of...

Keywords: training inventory, training registry, national skills initiatives, training material

Time to fill the gaps: Building out a national training inventory https://dresa.org.au/materials/time-to-fill-the-gaps-building-out-a-national-training-inventory   This community discussion seeks to bring together the instructors and facilitators tasked with upskilling researchers and support staff. While this collective dialogue among instructors is not new, what is new is the traction that various groups are getting. The newly formed group of eResearch support staff gathered by the Melbourne Data Analytics Platform (MDAP) and Sydney Informatics Hub (SIH) is one such group, as is the Lightweight Working Group (LWG): Researcher digital skills training data for enabling digital infrastructure use, spearheaded by University of Melbourne’s David Flanders during the pre-Skills Summit discussions. In this session we seek to build on the momentum, by including a hands-on working session. Participants are asked to come with information to share and questions they seek to answer. During the first half of this session, attendees will populate a public document with shareable training details. The goal is to at least double the size of the new cross-institutional national training collection started by the LWG. The second half of this session will be to ask questions to arrive at next steps. What do we need to do to continue building out this national training inventory and who will be in charge of maintaining and distributing the archive? What platforms exist and are used to capture training data and material and make it readily maintainable and findable? Can the material be reused and how do we recognise and capture re-use? Do we know about how to apply a license to our materials for appropriate reuse or do we need guidance? While there will likely be more questions than these, one question has been answered. When can we move from talking to doing? That time is now. contact@ardc.edu.au training inventory, training registry, national skills initiatives, training material
OECD Report - Building digital workforce capacity and skills for data-intensive science (2020)

 

As a lead contributor to the OECD's Building Digital Workforce Capacity and Skills for Data-Intensive Science (2020) report, Dr Michelle Barker outlines in this presentation the goal of the report, i.e. to make recommendations to policy makers on how to facilitate the digital workforce...

Keywords: international skills initiatives, skills, training, OECD, EOSC, Capability building, Skills uplift, skills development, digital skilled workforce, training material

OECD Report - Building digital workforce capacity and skills for data-intensive science (2020) https://dresa.org.au/materials/oecd-report-building-digital-workforce-capacity-and-skills-for-data-intensive-science-2020   As a lead contributor to the OECD's Building Digital Workforce Capacity and Skills for Data-Intensive Science (2020) report, Dr Michelle Barker outlines in this presentation the goal of the report, i.e. to make recommendations to policy makers on how to facilitate the digital workforce capacity needed for data-intensive science, based on analysis of best practice. The presentation highlights: - Digital workforce capacity and COVID19: the importance of digital skills, the need for shared access to open data, software and code, and the shortfall in skills to enable a comprehensive response to such emergencies - The ongoing need for a digital skilled workforce for data-intensive science - Five focus areas in the report include: 1. Enablers for digital workforce capacity development 2. Defining needs: digital skills, frameworks and roles 3. Provision of training 4. Community development 5. Career paths and reward structures - Recommendations for actors incl. universities, national or regional governments contact@ardc.edu.au international skills initiatives, skills, training, OECD, EOSC, Capability building, Skills uplift, skills development, digital skilled workforce, training material