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Keywords: digital research training  or Phylogeny  or software 

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Hybridisation plays an important role in evolution, leading to the exchange of genes...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset-51cc7740-0da1-45f1-95de-f1a47f676053 This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Hybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. Nauheimer_hybphaser_slides (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/japXwTAhA5U Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Multi-gene datasets used in phylogenetic...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation-a6743550-b904-45e1-9635-4e481ee8f739 This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. Schmidt-Lebuhn - paralogy lineage sorting reticulation - slides (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/1bw81q898z8 Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
DReSA: Project team reflections

This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual...

Keywords: training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training

DReSA: Project team reflections https://dresa.org.au/materials/dresa-project-team-reflections-9dcb8538-6b7c-4822-b0ee-fbe57085dc70 This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual reflections on collaboration and working together on the project so far. You can watch the video on YouTube here: https://youtu.be/qqH92itI8SI   contact@ardc.edu.au training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training
How can software containers help your research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. 

Software Containers in research are a solution that addresses the challenge of a...

Keywords: containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material

How can software containers help your research? https://dresa.org.au/materials/how-can-software-containers-help-your-research-ca0f9d41-d83b-463b-a548-402c6c642fbf This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.  Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. Watch the video here: https://www.youtube.com/watch?v=HelrQnm3v4g If you want to share this video please use this: Australian Research Data Commons, 2021. How can software containers help your research?. [video] Available at: https://www.youtube.com/watch?v=HelrQnm3v4g DOI: http://doi.org/10.5281/zenodo.5091260 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Sam Muirhead (type: Producer) The ARDC Communications Team (type: Editor) The ARDC Skills and Workforce Development Team (type: ProjectMember) The ARDC eResearch Infrastructure & Services (type: ProjectMember) The ARDC Nectar Cloud Services team (type: ProjectMember) containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning

This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are...

Keywords: coding, software, training impact, culture change, community, skills training, training material

Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning https://dresa.org.au/materials/coding-and-software-club-at-the-burnet-institute-a-sisyphean-story-of-normalising-peer-to-peer-learning-665e90f8-6fd5-49e7-9476-e16b6ffe17c6 This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are the challenges, opportunities and lessons learnt - valuable insights into what it tkaes to keep a community focused and enduring. You can watch the video on YouTube here: https://youtu.be/c2syM1Dfqbo contact@ardc.edu.au coding, software, training impact, culture change, community, skills training, training material
Software publishing, licensing and citation

This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research...

Keywords: software, code, Repositories, code sharing, training material

Software publishing, licensing and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-49097378-f296-44aa-b724-a57d22214d99 This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research vocabularies, persistent identifiers, data discovery catalogues, metadata issues, licensing, governance, underpinning infrastructure (e.g. Nectar Research Cloud) and more. ARDC can also connect projects to national and international communities and initiatives trying to solve common challenges and outline best practice. This session explained why and how to publish, licence and cite software. A video recording of this session can also be found on ARDC's YouTube channel: https://youtu.be/l2acLeuF_QE contact@ardc.edu.au software, code, Repositories, code sharing, training material
"How To" Video Guide for the Australian Child and Youth Wellbeing Atlas

This "How To" Video Guide for the Australian Child and Youth Wellbeing Atlas covers key features, step-by-step instructions, and screen shots. It assists users in navigating the data platform with 400+ data sets on children and young people's health and wellbeing. The platform offers geospatial...

Keywords: research data, digital research skills, health data, digital research training, Community Connect, ARDC

"How To" Video Guide for the Australian Child and Youth Wellbeing Atlas https://dresa.org.au/materials/how-to-video-guide-for-the-australian-child-and-youth-wellbeing-atlas This "How To" Video Guide for the Australian Child and Youth Wellbeing Atlas covers key features, step-by-step instructions, and screen shots. It assists users in navigating the data platform with 400+ data sets on children and young people's health and wellbeing. The platform offers geospatial visualisations and maps at various geographic levels. A/Prof Rebecca Glauert, UWA, Marketa Reeves, UWA research data, digital research skills, health data, digital research training, Community Connect, ARDC
User Manual for the Australian Child and Youth Wellbeing Atlas

This user manual for the Australian Child and Youth Wellbeing Atlas covers key features of the platform, step-by-step instructions, and screen shots. It assists users in navigating the data platform with 400+ data sets on children and young people's health and wellbeing. The platform offers...

Keywords: research data, health data, digital research skills, digital research training, Community Connect, ARDC

User Manual for the Australian Child and Youth Wellbeing Atlas https://dresa.org.au/materials/user-manual-for-the-australian-child-and-youth-wellbeing-atlas This user manual for the Australian Child and Youth Wellbeing Atlas covers key features of the platform, step-by-step instructions, and screen shots. It assists users in navigating the data platform with 400+ data sets on children and young people's health and wellbeing. The platform offers geospatial visualisations and maps at various geographic levels. A/Prof Rebecca Glauert, UWA, Marketa Reeves, UWA research data, health data, digital research skills, digital research training, Community Connect, ARDC
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Hybridisation plays an important role in evolution, leading to the exchange of genes...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Hybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. - Nauheimer_hybphaser_slides (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/japXwTAhA5U Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Multi-gene datasets used in phylogenetic...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. - Schmidt-Lebuhn - paralogy lineage sorting reticulation - slides (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/1bw81q898z8 Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning

This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are...

Keywords: coding, software, training impact, culture change, community, skills training, training material

Coding and Software Club at the Burnet Institute: a Sisyphean story of normalising peer-to-peer learning https://dresa.org.au/materials/coding-and-software-club-at-the-burnet-institute-a-sisyphean-story-of-normalising-peer-to-peer-learning This presentation outlines the Burnet Institute and its Coding and Software Club. What motivated the establishment of the Club and what keeps it going, the tools used to engage, teach and learn and finally, how the Club has impacted people at various levels of the organisation. Also explored are the challenges, opportunities and lessons learnt - valuable insights into what it tkaes to keep a community focused and enduring. You can watch the video on YouTube here: https://youtu.be/c2syM1Dfqbo contact@ardc.edu.au coding, software, training impact, culture change, community, skills training, training material
DReSA: Project team reflections

This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual...

Keywords: training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training

DReSA: Project team reflections https://dresa.org.au/materials/dresa-project-team-reflections This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual reflections on collaboration and working together on the project so far. You can watch the video on YouTube here: https://youtu.be/qqH92itI8SI   contact@ardc.edu.au training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training
Software publishing, licensing and citation

This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research...

Keywords: software, code, Repositories, code sharing, training material

Software publishing, licensing and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-432694d3-0366-45bb-ad49-84ffd7587dcb This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research vocabularies, persistent identifiers, data discovery catalogues, metadata issues, licensing, governance, underpinning infrastructure (e.g. Nectar Research Cloud) and more. ARDC can also connect projects to national and international communities and initiatives trying to solve common challenges and outline best practice. This session explained why and how to publish, licence and cite software. A video recording of this session can also be found on ARDC's YouTube channel: https://youtu.be/l2acLeuF_QE contact@ardc.edu.au software, code, Repositories, code sharing, training material
How can software containers help your research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. 

Software Containers in research are a solution that addresses the challenge of a...

Keywords: containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material

How can software containers help your research? https://dresa.org.au/materials/how-can-software-containers-help-your-research-5bc99ea4-58dd-413d-a04b-230ff14873f1 This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.  Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. Watch the video here: https://www.youtube.com/watch?v=HelrQnm3v4g If you want to share this video please use this: Australian Research Data Commons, 2021. How can software containers help your research?. [video] Available at: https://www.youtube.com/watch?v=HelrQnm3v4g DOI: http://doi.org/10.5281/zenodo.5091260 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Sam Muirhead (type: Producer) The ARDC Communications Team (type: Editor) The ARDC Skills and Workforce Development Team (type: ProjectMember) The ARDC eResearch Infrastructure & Services (type: ProjectMember) The ARDC Nectar Cloud Services team (type: ProjectMember) containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material
How can Software Containers help your Research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.

Software Containers in research are a solution that addresses the challenge of...

Keywords: Containers, software containers, reproducibility, replicable computational environment, software, research, reusable, cloud, standardisation

Resource type: video

How can Software Containers help your Research? https://dresa.org.au/materials/how-can-software-containers-help-your-research This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. **Cite as** Australian Research Data Commons. (2021, July 26). How can software containers help your research?. Zenodo. https://doi.org/10.5281/zenodo.5091260 Contact us: https://ardc.edu.au/contact-us/ Containers, software containers, reproducibility, replicable computational environment, software, research, reusable, cloud, standardisation phd ecr researcher support