Astronomy Data And Computing Services - Upskilling the Australian astronomy community
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data &...
Keywords: astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material
Astronomy Data And Computing Services - Upskilling the Australian astronomy community
https://zenodo.org/records/4287748
https://dresa.org.au/materials/astronomy-data-and-computing-services-upskilling-the-australian-astronomy-community-57afa0b9-77da-4dc1-ad29-25089f19363d
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data & computing infrastructure.
During these last 3 years, we have delivered dozens of face-to-face, hands-on workshops and created several hours worth of online tutorial materials. This talk will focus on our journey to deliver this computational skills training to the community, exploring how we chose different delivery pathways and content, based both on community input as well as our professional expertise and understanding of existing skill gaps. Most importantly we will discuss our plans for the future and how we are working on actively including the community in developing new training material beyond the usual skills survey.
Come along to this talk if you would like to hear about a national effort to deliver computational skills training and would like to know more about potential new avenues to provide just-in-time training and how to collaborate with ADACS.
contact@ardc.edu.au
Lange, Rebecca (orcid: 0000-0002-9449-4384)
astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material
WEBINAR: Where to go when your bioinformatics outgrows your compute
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...
Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: Where to go when your bioinformatics outgrows your compute
https://zenodo.org/records/5240578
https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey. We also describe bioinformatics and computing support services available to Australian researchers.
This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney.
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.
Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar
Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar.
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/hNTbngSc-W0
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Sadsad, Rosemarie (orcid: 0000-0003-2488-953X)
Coddington, Paul (orcid: 0000-0003-1336-9686)
Gladman, Simon (orcid: 0000-0002-6100-4385)
Edberg, Roger
Shaikh, Javed
Cytowski, Maciej (orcid: 0000-0002-0007-0979)
Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
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://zenodo.org/records/5076668
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
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://zenodo.org/records/8185398
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Hiltemann, Saskia (orcid: 0000-0003-3803-468X)
Rasche, Helena (orcid: 0000-0001-9760-8992)
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://zenodo.org/records/7251310
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Workflows, FAIR, Galaxy Australia
Astronomy Data And Computing Services - Upskilling the Australian astronomy community
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data &...
Keywords: astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material
Astronomy Data And Computing Services - Upskilling the Australian astronomy community
https://zenodo.org/records/4287748
https://dresa.org.au/materials/astronomy-data-and-computing-services-upskilling-the-australian-astronomy-community-afea50d0-f7fe-4ad7-ad41-89fad7c14f65
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data & computing infrastructure.
During these last 3 years, we have delivered dozens of face-to-face, hands-on workshops and created several hours worth of online tutorial materials. This talk will focus on our journey to deliver this computational skills training to the community, exploring how we chose different delivery pathways and content, based both on community input as well as our professional expertise and understanding of existing skill gaps. Most importantly we will discuss our plans for the future and how we are working on actively including the community in developing new training material beyond the usual skills survey.
Come along to this talk if you would like to hear about a national effort to deliver computational skills training and would like to know more about potential new avenues to provide just-in-time training and how to collaborate with ADACS.
contact@ardc.edu.au
Lange, Rebecca (orcid: 0000-0002-9449-4384)
astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, 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://zenodo.org/records/4287858
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
Backhaus, Ann
Lange, Rebecca (orcid: 0000-0002-9449-4384)
Padmanabhan, Komathy
King, Sara (orcid: 0000-0003-3199-5592)
training inventory, training registry, national skills initiatives, 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://zenodo.org/record/8185398
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Hiltemann, Saskia (orcid: 0000-0003-3803-468X)
Rasche, Helena (orcid: 0000-0001-9760-8992)
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://zenodo.org/record/7251310
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Workflows, FAIR, Galaxy Australia
WEBINAR: Where to go when your bioinformatics outgrows your compute
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised...
Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: Where to go when your bioinformatics outgrows your compute
https://zenodo.org/record/5240578
https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey. We also describe bioinformatics and computing support services available to Australian researchers.
This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney.
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.
- Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar
- Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar.
**Materials shared elsewhere:**
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/hNTbngSc-W0
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Sadsad, Rosemarie (orcid: 0000-0003-2488-953X)
Coddington, Paul (orcid: 0000-0003-1336-9686)
Gladman, Simon (orcid: 0000-0002-6100-4385)
Edberg, Roger
Shaikh, Javed
Cytowski, Maciej (orcid: 0000-0002-0007-0979)
Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
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://zenodo.org/record/5076668
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)
Price, Gareth (orcid: 0000-0003-2439-8650)
Variant calling, Genetic Variation Analysis, SNP annotation
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://zenodo.org/record/4287858
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
Backhaus, Ann
Lange, Rebecca (orcid: 0000-0002-9449-4384)
Padmanabhan, Komathy
King, Sara (orcid: 0000-0003-3199-5592)
training inventory, training registry, national skills initiatives, training material
Astronomy Data And Computing Services - Upskilling the Australian astronomy community
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data &...
Keywords: astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material
Astronomy Data And Computing Services - Upskilling the Australian astronomy community
https://zenodo.org/record/4287748
https://dresa.org.au/materials/astronomy-data-and-computing-services-upskilling-the-australian-astronomy-community
The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data & computing infrastructure.
During these last 3 years, we have delivered dozens of face-to-face, hands-on workshops and created several hours worth of online tutorial materials. This talk will focus on our journey to deliver this computational skills training to the community, exploring how we chose different delivery pathways and content, based both on community input as well as our professional expertise and understanding of existing skill gaps. Most importantly we will discuss our plans for the future and how we are working on actively including the community in developing new training material beyond the usual skills survey.
Come along to this talk if you would like to hear about a national effort to deliver computational skills training and would like to know more about potential new avenues to provide just-in-time training and how to collaborate with ADACS.
contact@ardc.edu.au
Lange, Rebecca (orcid: 0000-0002-9449-4384)
astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material