WORKSHOP: Online data analysis for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
Workshop description
Galaxy is an online platform for biological research that allows people to use computational data...
Keywords: Bioinformatics, Analysis, Workflows, Galaxy Australia
WORKSHOP: Online data analysis for biologists
https://zenodo.org/records/5775277
https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists-08d66913-4ce3-4528-bdd6-0b0fcf234982
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
Workshop description
Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.
It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web.
This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network.
The workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators.
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
Online_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall.
Materials shared elsewhere:
The tutorial used in this workshop is available via the Galaxy Training Network.
Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Perreau, Vicky (orcid: 0000-0002-0773-7246)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Workflows, Galaxy Australia
WORKSHOP: R: fundamental skills for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to...
Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: R: fundamental skills for biologists
https://zenodo.org/records/6766951
https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.
R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.
Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R.
Topics covered in this workshop include:
Spreadsheets, organising data and first steps with R
Manipulating and analysing data with dplyr
Data visualisation
Summarized experiments and getting started with Bioconductor
This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Recommended resources (PDF): A list of resources recommended by trainers and participants
Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available.
https://saskiafreytag.github.io/biocommons-r-intro/
This is derived from material produced as part of The Carpentries Incubator project
https://carpentries-incubator.github.io/bioc-intro/
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Doyle, Maria
Ansell, Brendan (orcid: 0000-0003-0297-897X)
Varshney, Akriti
Bourke, Caitlin (orcid: 0000-0002-4466-6563)
Conradsen, Cara (orcid: 0000-0001-9797-3412)
Jung, Chol-Hee (orcid: 0000-0002-2992-3162)
Sandoval, Claudia
Chandrananda, Dineika (orcid: 0000-0002-8834-9500)
Zhang, Eden (orcid: 0000-0003-0294-3734)
Rosello, Fernando (orcid: 0000-0003-3885-8777)
Iacono, Giulia (orcid: 0000-0002-1527-0754)
Tarasova, Ilariya (orcid: 0000-0002-0895-9385)
Chung, Jessica (orcid: 0000-0002-0627-0955)
Moffet, Joel
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Ding, Ke
Feher, Kristen
Perlaza-Jimenez, Laura (orcid: 0000-0002-8511-1134)
Crowe, Mark (orcid: 0000-0002-9514-2487)
Ma, Mengyao
Kandhari, Nitika (orcid: 0000-0002-0261-727X)
Williams, Sarah
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Schreiber, Veronika (orcid: 0000-0001-6088-7828)
Pinzon Perez, William
Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: Translating workflows into Nextflow with Janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies...
Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Translating workflows into Nextflow with Janis
https://zenodo.org/records/8072678
https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis-36386c6d-f9a2-4b4d-afa9-062ce3b8ac5d
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.
Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.
This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Intro to Galaxy (PDF): Slides presented during the workshop
Intro to CWL (PDF): Slides presented during the workshop
Intro to the session & Janis (PDF): Slides presented during the workshop
Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate
A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Lupat, Richard (orcid: 0000-0002-6435-7100)
Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Hybrid de novo genome assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...
Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Hybrid de novo genome assembly
https://zenodo.org/records/5781781
https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality.
In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly.
All analyses will be performed using 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.
This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): A breakdown of the topics and timings for the workshop
Materials shared elsewhere:
This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Makunin, Igor
Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...
Keywords: Small satellites, metadata, vocabularies, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
https://zenodo.org/records/5832057
https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration-49af7d4d-f0d1-4f95-9fbe-afbd45170a6a
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets.
A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects.
Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure.
You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4
contact@ardc.edu.au
Bouquin, Daina (orcid: 0000-0003-2626-3688)
Chivvis, Daniel (orcid: 0000-0001-6656-160X)
Small satellites, metadata, vocabularies, training material
ARDC FAIR Data 101 self-guided
FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles
The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.
The course structure was based on 'FAIR Data in the...
Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
ARDC FAIR Data 101 self-guided
https://zenodo.org/records/5094034
https://dresa.org.au/materials/ardc-fair-data-101-self-guided-2d794a84-f0ff-4e11-a39c-fa8ea481e097
FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles
The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.
The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub.
contact@ardc.edu.au
Stokes, Liz (orcid: 0000-0002-2973-5647)
Liffers, Matthias (orcid: 0000-0002-3639-2080)
Burton, Nichola (orcid: 0000-0003-4470-4846)
Martinez, Paula A. (orcid: 0000-0002-8990-1985)
Simons, Natasha (orcid: 0000-0003-0635-1998)
Russell, Keith (orcid: 0000-0001-5390-2719)
McCafferty, Siobhann (orcid: 0000-0002-2491-0995)
Ferrers, Richard (orcid: 0000-0002-2923-9889)
McEachern, Steve (orcid: 0000-0001-7848-4912)
Barlow, Melanie (orcid: 0000-0002-3956-5784)
Brady, Catherine (orcid: 0000-0002-7919-7592)
Brownlee, Rowan (orcid: 0000-0002-1955-1262)
Honeyman, Tom (orcid: 0000-0001-9448-4023)
Quiroga, Maria del Mar (orcid: 0000-0002-8943-2808)
training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
WORKSHOP: Translating workflows into Nextflow with Janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies...
Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Translating workflows into Nextflow with Janis
https://zenodo.org/record/8072678
https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.
Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.
This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Intro to Galaxy (PDF): Slides presented during the workshop
Intro to CWL (PDF): Slides presented during the workshop
Intro to the session & Janis (PDF): Slides presented during the workshop
Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate
A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Lupat, Richard (orcid: 0000-0002-6435-7100)
Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: R: fundamental skills for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to...
Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: R: fundamental skills for biologists
https://zenodo.org/record/6766951
https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists
This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
**Event description**
Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.
R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.
Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R.
Topics covered in this workshop include:
- Spreadsheets, organising data and first steps with R
- Manipulating and analysing data with dplyr
- Data visualisation
- Summarized experiments and getting started with Bioconductor
This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
**Files and materials included in this record:**
- Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
- Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
- Schedule (PDF): A breakdown of the topics and timings for the workshop
- Recommended resources (PDF): A list of resources recommended by trainers and participants
- Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel.
**Materials shared elsewhere:**
This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available.
https://saskiafreytag.github.io/biocommons-r-intro/
This is derived from material produced as part of The Carpentries Incubator project
https://carpentries-incubator.github.io/bioc-intro/
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Doyle, Maria
Ansell, Brendan (orcid: 0000-0003-0297-897X)
Varshney, Akriti
Bourke, Caitlin (orcid: 0000-0002-4466-6563)
Conradsen, Cara (orcid: 0000-0001-9797-3412)
Jung, Chol-Hee (orcid: 0000-0002-2992-3162)
Sandoval, Claudia
Chandrananda, Dineika (orcid: 0000-0002-8834-9500)
Zhang, Eden (orcid: 0000-0003-0294-3734)
Rosello, Fernando (orcid: 0000-0003-3885-8777)
Iacono, Giulia (orcid: 0000-0002-1527-0754)
Tarasova, Ilariya (orcid: 0000-0002-0895-9385)
Chung, Jessica (orcid: 0000-0002-0627-0955)
Moffet, Joel
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Ding, Ke
Feher, Kristen
Perlaza-Jimenez, Laura (orcid: 0000-0002-8511-1134)
Crowe, Mark (orcid: 0000-0002-9514-2487)
Ma, Mengyao
Kandhari, Nitika (orcid: 0000-0002-0261-727X)
Williams, Sarah
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Schreiber, Veronika (orcid: 0000-0001-6088-7828)
Pinzon Perez, William
Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
WORKSHOP: Hybrid de novo genome assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly...
Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Hybrid de novo genome assembly
https://zenodo.org/record/5781781
https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
**Workshop description**
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality.
In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly.
All analyses will be performed using 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.
This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
**Files and materials included in this record:**
- Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
- Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
- Schedule (PDF): A breakdown of the topics and timings for the workshop
**Materials shared elsewhere:**
This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Makunin, Igor
Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
WORKSHOP: Online data analysis for biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
Workshop description
Galaxy is an online platform for biological research that allows people to use...
Keywords: Bioinformatics, Analysis, Workflows, Galaxy Australia
WORKSHOP: Online data analysis for biologists
https://zenodo.org/record/5775277
https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists
This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.
**Workshop description**
Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.
It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web.
This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network.
The workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators.
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
- Online_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall.
**Materials shared elsewhere:**
The tutorial used in this workshop is available via the Galaxy Training Network.
Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Perreau, Vicky (orcid: 0000-0002-0773-7246)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Workflows, Galaxy Australia
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...
Keywords: Small satellites, metadata, vocabularies, training material
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.
https://zenodo.org/record/5832057
https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration
MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets.
A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects.
Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure.
You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4
contact@ardc.edu.au
Bouquin, Daina (orcid: 0000-0003-2626-3688)
Chivvis, Daniel (orcid: 0000-0001-6656-160X)
Small satellites, metadata, vocabularies, training material
ARDC FAIR Data 101 self-guided
FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles
The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.
The course structure was based on 'FAIR Data in the...
Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
ARDC FAIR Data 101 self-guided
https://zenodo.org/record/5094034
https://dresa.org.au/materials/ardc-fair-data-101-self-guided-bba41a59-8479-4f4f-b9ee-337b9eb294bf
FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles
The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.
The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub.
contact@ardc.edu.au
Stokes, Liz (orcid: 0000-0002-2973-5647)
Liffers, Matthias (orcid: 0000-0002-3639-2080)
Burton, Nichola (orcid: 0000-0003-4470-4846)
Martinez, Paula A. (orcid: 0000-0002-8990-1985)
Simons, Natasha (orcid: 0000-0003-0635-1998)
Russell, Keith (orcid: 0000-0001-5390-2719)
McCafferty, Siobhann (orcid: 0000-0002-2491-0995)
Ferrers, Richard (orcid: 0000-0002-2923-9889)
McEachern, Steve (orcid: 0000-0001-7848-4912)
Barlow, Melanie (orcid: 0000-0002-3956-5784)
Brady, Catherine (orcid: 0000-0002-7919-7592)
Brownlee, Rowan (orcid: 0000-0002-1955-1262)
Honeyman, Tom (orcid: 0000-0001-9448-4023)
Quiroga, Maria del Mar (orcid: 0000-0002-8943-2808)
training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management