49 materials found
Keywords: Workflows or Bioinformatics
WORKSHOP: Introduction to Machine Learning in R - from data to knowledge
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Machine Learning in R - from data to knowledge’. This workshop took place over one, 4 hour sessions on 09 December 2024.
Event description
With the rise in high-throughput sequencing...
Keywords: Bioinformatics, Machine Learning
WORKSHOP: Introduction to Machine Learning in R - from data to knowledge
https://zenodo.org/records/14545612
https://dresa.org.au/materials/workshop-introduction-to-machine-learning-in-r-from-data-to-knowledge
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Machine Learning in R - from data to knowledge’. This workshop took place over one, 4 hour sessions on 09 December 2024.
Event description
With the rise in high-throughput sequencing technologies, the volume of omics data has grown exponentially. A major issue is to mine useful knowledge from these heterogeneous collections of data. The analysis of complex high-volume data is not trivial and classical tools cannot be used to explore their full potential. Machine Learning (ML), a discipline in which computers perform automated learning without being programmed explicitly and assist humans to make sense of large and complex data sets, can thus be very useful in mining large omics datasets to uncover new insights that can advance the field of bioinformatics.
This hands-on workshop will introduce participants to the ML taxonomy and the applications of common ML algorithms to health data. The workshop will cover the foundational concepts and common methods being used to analyse omics data sets by providing a practical context through the use of basic but widely used R libraries. Participants will acquire an understanding of the standard ML processes, as well as the practical skills in applying them on familiar problems and publicly available real-world data sets.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Lead trainers: Dr Fotis Psomopoulos, Senior Researcher, Institute of Applied Biosciences (INAB), Center for Research and Technology Hellas (CERTH)
Facilitators:
Dr Giorgia Mori, Australian BioCommons
Dr Eden Zhang, Sydney Informatics Hub
Dr Erin Graham, Queensland Cyber Infrastructure Foundation (QCIF)
Infrastructure provision: Uwe Winter, Australian BioCommons
Host: Dr. Giorgia Mori, Australian BioCommons
Training materials
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Training materials webpage
Data and documentation
Melissa Burke (melissa@biocommons.org.au)
Psomopoulos, Fotis (orcid: 0000-0002-0222-4273)
Zhang, Eden (orcid: 0000-0003-0294-3734)
Graham, Erin
Mori, Giorgia (orcid: 0000-0003-3469-5632)
Winter, Uwe
Bioinformatics, Machine Learning
WORKSHOP: Hello Nextflow!
This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024.
Event description
The rise of big data has made it essential to be able to analyse and perform experiments on large...
Keywords: Bioinformatics, Workflows, Nextflow
WORKSHOP: Hello Nextflow!
https://zenodo.org/records/14532850
https://dresa.org.au/materials/workshop-hello-nextflow
This record includes training materials associated with the Australian BioCommons workshop ‘Hello Nextflow’. This workshop took place over two sessions on 24 - 25 September 2024.
Event description
The rise of big data has made it essential to be able to analyse and perform experiments on large datasets in a portable and reproducible manner. Nextflow is a popular bioinformatics workflow orchestrator that makes it easy to run data-intensive computational pipelines. It enables scalable and reproducible scientific workflows using software containers on any infrastructure. It allows the adaptation of workflows written in most languages and provides the ability to customise and optimise workflows for different computational environments, types and sizes of data.
This workshop will put you on the path to writing your own reproducible and scalable scientific workflows using Nextflow. You will learn how to use core Nextflow components to build, run and troubleshoot a scalable multi-step workflow.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Lead trainers:
Dr Chris Hakkaart, Developer Advocate, Seqera Labs.
Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney.
Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.
Facilitator: Dr Ziad Al Bkhetan, Australian BioCommons
Infrastructure provision: Uwe Winter, Australian BioCommons
Host: Dr Melissa Burke, Australian BioCommons
Training materials
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Materials shared elsewhere:
The materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera. The workshop was enabled through the Australian BioCommons - BioCLI Platforms Project (NCRIS via Bioplatforms Australia).
Training materials webpage:
https://sydney-informatics-hub.github.io/hello-nextflow/
Data and documentation:
https://github.com/Sydney-Informatics-Hub/hello-nextflow
Melissa Burke (melissa@biocommons.org.au)
Hakkaart, Chris (orcid: 0000-0001-5007-2684)
Jaya, Fred (orcid: 0000-0002-4019-7026)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Al Bkhetan, Ziad (orcid: 0000-0002-4032-5331)
Bioinformatics, Workflows, Nextflow
WORKSHOP: Fungal Genomics with Galaxy
This record includes training materials associated with the Bioplatforms Australia “Fungal Genomics with Galaxy Workshop”. This workshop took place over three days from 29-31 October 2024.
Event description
A three-day workshop organised by Bioplatforms Australia to introduce bioinformatics...
Keywords: Bioinformatics, Analysis, Fungi, Genome assembly, Genome annotation
WORKSHOP: Fungal Genomics with Galaxy
https://zenodo.org/records/14498677
https://dresa.org.au/materials/workshop-fungal-genomics-with-galaxy
This record includes training materials associated with the Bioplatforms Australia “Fungal Genomics with Galaxy Workshop”. This workshop took place over three days from 29-31 October 2024.
Event description
A three-day workshop organised by Bioplatforms Australia to introduce bioinformatics theory and practice to researchers, citizen scientists, and industry involved in Bioplatforms fungi-themed National Initiatives: Australian Functional Fungi Initiative, and Plant Pathogen Omics Initiative.
An in-person workshop, held over three days from ~9am-5pm.
The workshop included a series of interleaved presentations about fungal genomics theory and practical tutorials using the Galaxy Australia analysis platform, as well as discussion sessions and presentations from some of the attendees.
A breakdown of timings and topics is provided in the schedule.
Registration was open to project representatives across the Australian Functional Fungi, and Plant Pathogen Omics Initiative.
Participation was free for registrants, and was supported by Bioplatforms National Initiatives.
Number of participants = 38
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Lead trainers:
Prof. Benjamin Schwessinger (Australian National University)
Dr Alistair McTaggart (Psymbiotika Lab)
Dr Gareth Price / Dr Anna Syme (Galaxy Australia
Presenters:
Dr Mareike Moeller (Australian National University)
Rita Tam (Australian National University)
Zhenyan Luo (Australian National University)
Coordination:
Dr Kelly Scarlett (BioPlatforms Australia)
Dr Mabel Lum (BioPlatforms Australia)
Dr Sophie Mazard (BioPlatforms Australia)
Files and materials included in this record:
Event metadata (PDF): Information about the event including description, learning objectives, prerequisites, etc.
Schedule of program inlcuding links to training materials and resources (PDF)
Slide sets as PDFs (PDF)
Table of links to Galaxy workflows and example histories (PDF)
Copy of Galaxy workflows developed as examples for fungal data analysis (as .ga files)
Materials shared elsewhere:
This workshop includes tutorials from the Galaxy Training Network which are linked in the schedule document.
Melissa Burke (melissa@biocommons.org.au)
Schwessinger, Benjamin (orcid: 0000-0002-7194-2922)
McTaggart, Alistair R. (orcid: 0000-0002-0996-1313)
Price, Gareth (orcid: 0000-0003-2439-8650)
Syme, Anna (orcid: 0000-0002-9906-0673)
Möller, Mareike (orcid: 0000-0002-2146-5507)
Tam, Rita
Luo, Zhenyan (orcid: 0000-0002-4515-2556)
Bioinformatics, Analysis, Fungi, Genome assembly, Genome annotation
WEBINAR: Making sense of gene and protein lists with functional enrichment analysis
This record includes training materials associated with the Australian BioCommons webinar ‘Making sense of gene and protein lists with functional enrichment analysis’. This webinar took place on 23 October 2024.
Topic description
Do you have a long list of genes or proteins from omics experiments...
Keywords: Bioinformatics, Enrichment analysis
WEBINAR: Making sense of gene and protein lists with functional enrichment analysis
https://zenodo.org/records/14032116
https://dresa.org.au/materials/webinar-making-sense-of-gene-and-protein-lists-with-functional-enrichment-analysis
This record includes training materials associated with the Australian BioCommons webinar ‘Making sense of gene and protein lists with functional enrichment analysis’. This webinar took place on 23 October 2024.
Topic description
Do you have a long list of genes or proteins from omics experiments that you don’t know what to do with? This webinar explains how functional enrichment analysis can be used to understand what these lists mean by employing gene ontology and pathway information to highlight the underlying biology. We’ll discuss the statistics that underpin enrichment analysis methods and some of the most commonly used tools, databases and workflows.
Speakers:
Dr Hossein Valipour Kahrood, Bioinformatician, Monash Genomics and Bioinformatics Platform
Dr Cali Willet, Senior Research Bioinformatician, Sydney Informatics Hub, The University of Sydney
Host:
Dr Melissa Burke, Australian BioCommons
Training 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.
Functional_enrichment_webinar: 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://www.youtube.com/watch?v=AvpH2WMNXxA
Melissa Burke (melissa@biocommons.org.au)
Valipour Kahrood, Hossein (orcid: 0000-0003-4166-0382)
Willet, Cali (orcid: 0000-0001-8449-1502)
Bioinformatics, Enrichment analysis
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 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent...
Keywords: Bioinformatics, Data analysis, Galaxy
WORKSHOP: Online data analysis for biologists
https://zenodo.org/records/13948826
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 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent computational biological research. Widely used by researchers world wide, Galaxy gives you access to 1000’s of popular tools for analysis and processing of biological data. It is perfect for working with a wide range of big and small datasets including genome assembly, annotation, epigenetics, metabolomics, metagenomics, proteomics, statistics, transcriptomics, variant analysis and visualisation.
This workshop provides an introduction to using Galaxy and available tools. Using an example dataset, you’ll practice uploading data, choosing and running tools, and viewing the results. We’ll share our top tips for managing your experiments and speeding up your analysis with workflows.
Lead trainer: Dr Gareth Price, Galaxy Australia
Facilitator: Mike Thang, Galaxy Australia / QCIF
Infrastructure provision: Galaxy Australia
Host: Dr Melissa Burke, Australian BioCommons
Training 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_Online_data_analysis_for_biologists_210824 (PDF): Information about the event logistics including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Schedule_Online_data_analysis_for_biologists_210824 (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop is based on the Galaxy Training Network tutorial ‘Galaxy basics for everyone’: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
A recording of this workshop is available on the Australian BioCommons YouTube Channel: https://www.youtube.com/watch?v=PF39KjOvreM
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Thang, Michael
Bioinformatics, Data analysis, Galaxy
WEBINAR: Global data resources for human genomics and health
This record includes training materials associated with the Australian BioCommons webinar ‘Global data resources for human genomics and health’. This webinar took place on 20 September 2024.
Event description
Dr Mallory Freeberg takes us on a whirlwind tour of the human genomics data resources...
Keywords: Bioinformatics, Genomics
WEBINAR: Global data resources for human genomics and health
https://zenodo.org/records/13845933
https://dresa.org.au/materials/webinar-global-data-resources-for-human-genomics-and-health
This record includes training materials associated with the Australian BioCommons webinar ‘Global data resources for human genomics and health’. This webinar took place on 20 September 2024.
Event description
Dr Mallory Freeberg takes us on a whirlwind tour of the human genomics data resources available at EMBL's European Bioinformatics Institute (EMBL-EBI). Used by scientists across the world, these resources enable the discovery and exploration of genes, variants and their impact on human health and disease.
Resources that will be covered in this webinar include:
Ensembl: a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation
DECIPHER: an interactive web-based database and suite of tools that aid the clinical interpretation of genomic variants
Federated EGA: a global resource for discovery and access of sensitive human omics and associated data consented for secondary use
Perturbation Catalogue: a new project from Open Targets that is building a catalogue of harmonised and curated human gene, variant, and expression data
EMBL-EBI’s comprehensive range of freely available and up-to-date molecular data resources are used by scientists globally. The teams running these resources collaborate closely with international experts and are key partners in human genomic data sharing communities including the Global Alliance for Genomics and Health.
Speaker: Dr Mallory Freeberg, Human Genomics Team Leader, EMBL European Bioinformatics Institute
Host: Dr Melissa Burke, Australian BioCommons
Training 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.
20240920_Australian-Biocommons-Webinar_MFreeberg: 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/5FAj1KffYnY
Melissa Burke (melissa@biocommons.org.au)
Freeberg, Mallory (orcid: 0000-0003-2949-3921)
Bioinformatics, Genomics
WEBINAR: What exactly is bioinformatics?
This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024.
Event description
‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all...
Keywords: Bioinformatics
WEBINAR: What exactly is bioinformatics?
https://zenodo.org/records/13283096
https://dresa.org.au/materials/webinar-what-exactly-is-bioinformatics
This record includes training materials associated with the Australian BioCommons webinar ‘What exactly is bioinformatics?' This webinar took place on 7 August 2024.
Event description
‘Doing’ bioinformatics to extract, process, analyse, and interpret experimental results is something that all life scientists do as part of their research. But what exactly is bioinformatics? And is there a right (or a wrong) way to do it?
In this webinar, Dr Georgie Samaha welcomes you to the vast world of bioinformatics. Georgie will illuminate key concepts including:
What does a typical experiment look like?
What kind of data will I work with?
What is involved in data-preprocessing?
What’s involved in data analysis?
Where can I do bioinformatics?
We explore common experimental use cases and share essential - but easy to overlook - practical tips for accessing data, software, and computing resources you need to get your research done.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.
Host: Dr Patrick Capon, Australian BioCommons
Training materials
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.
Samaha_2024_what_is_bioinformatics_webinar: 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/wmy2C-S-rMU
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Bioinformatics
WEBINAR: A practical guide to AI tools for life scientists
This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024.
Event description
The widespread availability and application of AI tools like ChatGPT have fundamentally...
Keywords: Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT
WEBINAR: A practical guide to AI tools for life scientists
https://zenodo.org/records/11206329
https://dresa.org.au/materials/webinar-a-practical-guide-to-ai-tools-for-life-scientists
This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024.
Event description
The widespread availability and application of AI tools like ChatGPT have fundamentally transformed our approach to work, creativity, learning, and communication. In the realm of scientific research, the impact of AI extends far beyond mere promises, already catalysing significant advances and discoveries.
This talk will explore how AI is reshaping scientific exploration and innovation. We explore how AI can accelerate research processes, from data analysis and code writing to hypothesis development. We will present some of the available and emerging AI and how we might effectively leverage these tools while acknowledging their limitations.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Dr Michael Kuiper, Principal Research Scientist in Computational Biology and acting Group Leader of the Computational Modelling (CM) group at Data61 of CSIRO.
Host: Dr Patrick Capon, Australian BioCommons
Training materials
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.
Kuiper_May2024_b_version: A PDF copy of the slides presented during the webinar.
Q_and_A_AI-life-scientists: PDF copy of questions and answers from the webinar
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/NbYvq3OLEfo
Melissa Burke (melissa@biocommons.org.au)
Kuiper, Michael (orcid: 0000-0002-8213-8382)
Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT
WEBINAR: MetaboLights: the home for metabolomics experiments and derived information
This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024.
Event description
MetaboLights is an open-access database for metabolomics studies,...
Keywords: Bioinformatics, Metabolomics, Metabolites, Data sharing
WEBINAR: MetaboLights: the home for metabolomics experiments and derived information
https://zenodo.org/records/10963462
https://dresa.org.au/materials/webinar-metabolights-the-home-for-metabolomics-experiments-and-derived-information
This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024.
Event description
MetaboLights is an open-access database for metabolomics studies, their raw experimental data and associated metadata. It is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles and locations where available. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information.
This webinar will provide an introduction to MetaboLights and how it can be used as:
A repository, enabling the metabolomics community to share findings, data and protocols from metabolomics studies.
A compound library of curated knowledge about metabolite structures, their reference spectra, as well as their biological roles, locations, concentrations, and raw data from metabolic experiments.
The webinar will provide details about data availability, standards and re-use, as well as guidance on submitting your own metabolomics data.
Speaker: Dr Thomas Payne, Scientific Database Curator - MetaboLights, EMBL-EBI
Host: Dr Patrick Capon, Australian BioCommons
Training 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.
2024_MetaboLights_Webinar_TP: 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/aCALHhqxOiM
Melissa Burke (melissa@biocommons.org.au)
Payne, Thomas (orcid: 0000-0001-7522-981X)
Bioinformatics, Metabolomics, Metabolites, Data sharing
WEBINAR: Multivariate integration of multi-omics data with mixOmics
This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024.
Event description
Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of...
Keywords: Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
WEBINAR: Multivariate integration of multi-omics data with mixOmics
https://zenodo.org/records/10828246
https://dresa.org.au/materials/webinar-multivariate-integration-of-multi-omics-data-with-mixomics
This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024.
Event description
Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of biospecimens or individuals is a powerful way to understand the underlying molecular mechanisms of a biological system.
mixOmics, a popular R package, integrates omics data from a wide range of sources into a single, unified view making it easier to explore and reveal interactions between omics layers. It overcomes many of the challenges of multi-omic data integration arising from data that are complex and large, with few samples (<50) and many molecules (>10,000), and generated using different technologies.
Prof Kim-Anh Lê Cao, head of the mixOmics team, is delivering this webinar to outline the different methods implemented in mixOmics and how statistical data integration is defined in this context. She will demonstrate how these approaches are applied to analysis of different multi-omics studies and outline the latest methodological developments in this area. From a study of human newborns, to multi-omics microbiomes, and multi-omics in single cells, these examples illustrate how mixOmics is used to perform variable selection and identify a signature of omics markers that characterise a specific phenotype or disease status.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Speaker: Prof Kim-Anh Lê Cao, Director of Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne.
Host: Dr Melissa Burke, Australian BioCommons
Training materials
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.
Mixomics_BioCommons: 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/5XpmQ5X89lA
Melissa Burke (melissa@biocommons.org.au)
Lê Cao, Kim-Anh (orcid: 0000-0003-3923-1116)
Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data
This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024.
Event description
Multiplexed assays of variant effect (MAVEs) are a family of...
Keywords: Bioinformatics, Genetic variation, Functional annotation, Clinical genetics
WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data
https://zenodo.org/records/10929633
https://dresa.org.au/materials/webinar-mavedb-discovery-and-interpretation-of-high-throughput-functional-assay-data
This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024.
Event description
Multiplexed assays of variant effect (MAVEs) are a family of experimental techniques that measure all single amino acid or single nucleotide changes in a gene or other functional element. MaveDB is an international community database that enables discovery and reuse of data from these experiments. It provides a platform for integrating large-scale measurements of sequence variant impact with applications that can be used to interpret the data for basic and clinical research.
In this webinar we consider:
What are MAVEs and how are the experiments performed?
How much MAVE data is available in MaveDB and how is it organised?
Who can submit datasets to MaveDB?
What are some of the clinical applications for MAVEs and how is the data being used to understand patient variants?
Speaker: Dr Alan Rubin, Senior Research Officer, WEHI
Host: Dr Melissa Burke, Australian BioCommons
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.
MAVEDB_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/BXGQ2IuDnGE
Melissa Burke (melissa@biocommons.org.au)
Rubin, Alan (orcid: 0000-0003-1474-605X)
Bioinformatics, Genetic variation, Functional annotation, Clinical genetics
WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share
This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports...
Keywords: Bioinformatics, Computational biology, Computational infrastructure
WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share
https://zenodo.org/records/10866820
https://dresa.org.au/materials/webinar-scaling-up-bioinformatics-with-ables-the-australian-biocommons-leadership-share
This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports access to, and efficient use of, national computational systems for big-data bioinformatics. Designed for established life sciences projects, groups, institutes and consortia, ABLeS can be used to facilitate software optimisation and scaling, implementation of optimised software for production analyses, and creation of reference data.
This webinar highlights how ABLeS is being used by life science communities across Australia to access and leverage bioinformatics at scale. We’ll explain the structure of the ABLeS program and how your life science community can get involved, as well as providing a breakdown of the program expectations and the support available from the BioCommons and our partners. Community members making use of ABLeS will share their perspective on the program, and the research outcomes that have resulted.
ABLeS is supported by the Australian BioCommons in partnership with Bioplatforms Australia, the National Computational Infrastructure, and the Pawsey Supercomputing Centre.
Speakers:
Australian BioCommons:
Dr Steven Manos
Dr Johan Gustafsson
Dr Ziad Al Bkhetan
ABLeS users:
Dr Hardip Patel, National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University
Chelsea Mayoh, Zero Childhood Cancer, Children's Cancer Institute
Theodore Allnutt, Royal Botanic Gardens Victoria
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
BioCommons_ABLeS: A PDF copy of the slides presented by the BioCommons team during the webinar.
Mayoh_ABLeS: A PDF copy of the slides presented by Chelsea Mayoh
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/Eb0z2-yaJbY
Melissa Burke (melissa@biocommons.org.au)
Al Bkhetan, Ziad
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Manos, Steven (orcid: 0000-0002-3461-1307)
Patel, Hardip (orcid: 0000-0003-3169-049X)
Mayoh, Chelsea (orcid: 0000-0002-6398-3046)
Allnutt, Theodore (orcid: 0000-0002-8258-0058)
Bioinformatics, Computational biology, Computational infrastructure
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
WEBINAR: High performance bioinformatics: submitting your best NCMAS application
This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.
Bioinformaticians are increasingly turning to specialised compute infrastructure and...
Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WEBINAR: High performance bioinformatics: submitting your best NCMAS application
https://zenodo.org/records/5239883
https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application-ee80822f-74ac-41af-a5a4-e162c10e6d78
This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.
Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.
This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It will be followed by a short Q&A session.
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.
High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/HeFGjguwS0Y
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
WEBINAR: Getting started with R
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not...
Keywords: R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
WEBINAR: Getting started with R
https://zenodo.org/records/5214277
https://dresa.org.au/materials/webinar-getting-started-with-r-1c8f2b21-bc4b-4b42-9a5d-d6096a2afbe6
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not always the best choice, particularly for large and complex datasets.
R is an open-source software and programming language that enables data exploration, statistical analysis visualisation and more. While it is the tool of choice for data analysis, getting started can be a little daunting for those without a background in statistics.
In this webinar Saskia Freytag, an R user with over a decade of experience and member of the Bioconductor Community Advisory Board, will walk you through their hints and tips for getting started with R and data analysis. She’ll cover topics like R Studio and why you need it, where to get help, basic data manipulation, visualisations and extending R with libraries. The webinar will be followed by a short Q&A session
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with R - slides (PDF): Slides used in the presentation
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/JS7yZw7bnX8
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
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://zenodo.org/records/5105013
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)
Nauheimer, Lars (orcid: 0000-0002-2847-0966)
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://zenodo.org/records/5104998
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)
Schmidt-Lebuhn, Alexander (orcid: 0000-0002-7402-8941)
Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
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
WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers
This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.
Event description
Genome annotation is crucial to...
Keywords: Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers
https://zenodo.org/records/5775233
https://dresa.org.au/materials/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers-3d6cb4b6-50b0-4bf4-ad3a-a60c79dc04ff
This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.
Event description
Genome annotation is crucial to defining the function of genomic sequences. Apollo is a popular tool for facilitating real-time collaborative curation and genome annotation editing. The technical obstacles faced by Australian researchers wanting to access and maintain this software have now been solved.
The new Australian Apollo Service can host your genome assembly and supporting evidence files, taking care of all the system administration so you and your team can focus on the annotation curation itself. The Australian BioCommons and partners at QCIF and Pawsey are now offering the Apollo Service free to use for Australian-based research groups and research consortia.
As part of this launch, you’ll hear what’s possible from some of the early adopters who helped guide the development of the service. These Australian researchers will highlight the benefits that Apollo is bringing to their genome annotation and curation workflows.
Join us to find out how you can get access to the Australian Apollo Service.
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.
Degnan Lab - Apollo Launch Webinar (PDF): Slides presented by Professors Sandie and Bernie Degnan
Nelson - Apollo Launch Webinar (PDF): Slides presented by Dr Tiffanie Nelson
Voelker - Apollo Launch Webinar (PDF): Slides presented by Julia Voelker
Rane - Apollo Launch Webinar (PDF): Slides presented by Dr Rahul Rane.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/o8jhRra-x4Y
Melissa Burke (melissa@biocommons.org.au)
Nelson, Tiffanie (orcid: 0000-0002-5341-312X)
Rane, Rahul (orcid: 0000-0003-4616-6244)
Degnan, Sandie (orcid: 0000-0001-8003-0426)
Degnan, Bernie (orcid: 0000-0001-7573-8518)
Voelker, Julia (orcid: 0000-0002-7615-0553)
Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
WEBINAR: Getting started with command line bioinformatics
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.
Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of...
Keywords: Bioinformatics, Command line, Workflows, Bash, Computational biology
WEBINAR: Getting started with command line bioinformatics
https://zenodo.org/records/5068997
https://dresa.org.au/materials/webinar-getting-started-with-command-line-bioinformatics-248027d1-0773-485a-b511-831e2fd4cc64
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.
Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of learning to analyse large and ever growing datasets. Learning how to use the command line can open up many options for data analysis but getting started can be a little daunting for those without a background in computer science.
Parice Brandies and Carolyn Hogg have recently put together ten simple rules for getting started with command-line bioinformatics to help biologists begin their computational journeys. In this webinar Parice walks you through their hints and tips for getting started with the command line. She covers topics like learning tech speak, evaluating your data and workflows, assessing computational requirements, computing options, the basics of software installation, curating and testing scripts, a bit of bash and keeping good records. The webinar will be followed by a short Q&A session.
The slides were created by Parice Brandies and are based on the publication ‘Ten simple rules for getting started with command-line bioinformatics’ (https://doi.org/10.1371/journal.pcbi.1008645). The slides are shared under a Creative Commons Attribution 4.0 International unless otherwise specified and were current at the time of the webinar.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Getting started with command line bioinformatics - 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/p7pA4OLB2X4
Melissa Burke (melissa@biocommons.org.au)
Brandies, Parice (orcid: 0000-0003-1702-2938)
Hogg, Carolyn (type: Supervisor)
Bioinformatics, Command line, Workflows, Bash, Computational biology
WORKSHOP: RNA-Seq: reads to differential genes and pathways
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
Event description
RNA sequencing (RNA-seq) is a common method used to...
Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WORKSHOP: RNA-Seq: reads to differential genes and pathways
https://zenodo.org/records/7439804
https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways-5a384156-d3de-4d5d-9797-e689bf6592f8
This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.
Event description
RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.
In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis!
This workshop is presented by the Australian BioCommons and Sydney Informatics Hub 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.
RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub
rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop
rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop
RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub.
https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WEBINAR: Variant interpretation: from the clinic to the lab… and back again
This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.
Event description
The use of genomic testing is increasing rapidly as...
Keywords: Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling
WEBINAR: Variant interpretation: from the clinic to the lab… and back again
https://zenodo.org/records/7425920
https://dresa.org.au/materials/webinar-variant-interpretation-from-the-clinic-to-the-lab-and-back-again-5c6aed91-24cd-4314-9638-5e60d51e1af1
This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.
Event description
The use of genomic testing is increasing rapidly as the cost of genome sequencing decreases. Many areas of the health workforce are upskilling in genomics to help meet the increased demand. From clinicians learning how to use the right test, for the right patient, at the right time, to medical scientists learning how to interpret and classify variants, and data scientists to learning how to better create and continuously refine the pipelines and software to handle and curate big data.
In this webinar, we’ll hear from two people working at the coalface of variant interpretation – one in a diagnostic laboratory and the other in a cancer research laboratory.
Naomi Baker is Medical Scientist at Victorian Clinical Genetics Services. She helps process hundreds of genomic tests per year to find the variants that cause rare diseases. She’ll explain the clinical variant interpretation processes she uses, the pipelines, professions and people involved.
Joep Vissers is a Curation Team Leader, at the University of Melbourne Centre for Cancer Research, Department of Clinical Pathology. Joep, who also teaches cancer biology at the University, will describe how he uses variant interpretation in his work at the research/clinical interface, and the shift in mindset required when working with data for these different purposes.
Amy Nisselle, Genomics Workforce Lead at Melbourne Genomics, will then briefly outline some of the education programs available in clinical variant interpretation.
This webinar is co-presented by Australian BioCommons and Melbourne Genomics
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.
Variant interpretation from the clinic to the lab and back again.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/wLMhwIiK8Lw
Melissa Burke (melissa@biocommons.org.au)
Baker, Naomi
Vissers, Joep (orcid: 0000-0003-0435-6824)
Nisselle, Amy (orcid: 0000-0002-8908-5906)
Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling
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
WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.
Event description
Bioinformatics workflows can support...
Keywords: Bioinformatics, Workflows, Nextflow, Containerisation
WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
https://zenodo.org/records/7095271
https://dresa.org.au/materials/webinar-portable-reproducible-and-scalable-bioinformatics-workflows-using-nextflow-and-pawsey-nimbus-cloud-824bc004-4dcb-4bb5-b0dc-a207c44bbbe6
This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.
Event description
Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data.
Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level.
In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we introduce you to Nextflow concepts to get you started with building your own workflows that will save you time and support reproducible, portable and scalable analysis.
In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend.
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.
Nextflow_Nimbus_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/VnLX63yXbJU
Melissa Burke (melissa@biocommons.org.au)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Bioinformatics, Workflows, Nextflow, Containerisation
WORKSHOP: Single cell RNAseq analysis in R
This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.
Event description
Analysis and interpretation of single cell RNAseq (scRNAseq) data...
Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WORKSHOP: Single cell RNAseq analysis in R
https://zenodo.org/records/7072910
https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945
This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.
Event description
Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.
We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.
This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) 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.
scRNAseq_Slides (PDF): Slides used to introduce topics
scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop
scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants
scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.
Materials shared elsewhere:
This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’
https://swbioinf.github.io/scRNAseqInR_Doco/index.html
This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.
It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.
Melissa Burke (melissa@biocommons.org.au)
Williams, Sarah
Mehdi, Ahmed (orcid: 0000-0002-9300-2341)
Matigan, Nick
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Harrison, Paul (orcid: 0000-0002-3980-268X)
Morgan, Steven (orcid: 0000-0001-6038-6126)
Whitfield, Holly (orcid: 0000-0002-7282-387X)
Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WEBINAR: Getting started with whole genome mapping and variant calling on the command line
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.
Event description
Life scientists are increasingly using whole genome...
Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows
WEBINAR: Getting started with whole genome mapping and variant calling on the command line
https://zenodo.org/records/7024058
https://dresa.org.au/materials/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line-2046f36b-0c7a-4523-9c21-08046900d3ff
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.
Event description
Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are.
In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need
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.
WGS mapping and variant calling _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/Q2EceFyizio
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Genome mapping, Variant calling, Bioinformatics, Workflows
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software
This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.
Event description
bio.tools provides easy access to essential scientific...
Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR
WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software
https://zenodo.org/records/7024050
https://dresa.org.au/materials/webinar-bio-tools-making-it-easier-to-find-understand-and-cite-biological-tools-and-software-aea38c9e-0b40-4308-bafd-f7580563f520
This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.
Event description
bio.tools provides easy access to essential scientific and technical information about software, command-line tools, databases and services. It’s backed by ELIXIR, the European Infrastructure for Biological Information, and is being used in Australia to register software (e.g. Galaxy Australia, prokka). It underpins the information provided in the Australian BioCommons discovery service ToolFinder.
Hans Ienasescu and Matúš Kalaš join us to explain how bio.tools uses a community driven, open science model to create this collection of resources and how it makes it easier to find, understand, utilise and cite them. They’ll delve into how bio.tools is using standard semantics (e.g. the EDAM ontology) and syntax (e.g. biotoolsSchema) to enrich the annotation and description of tools and resources. Finally, we’ll see how the community can contribute to bio.tools and take advantage of its key features to share and promote their own research software.
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.
biotools_EDAM_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/K0J4_bAUG3Y
Melissa Burke (melissa@biocommons.org.au)
Ienasescu, Hans
Kalaš, Matúš (orcid: 0000-0002-1509-4981)
Bioinformatics, Research software, EDAM, Workflows, FAIR
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
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?
This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.
Event description
It is easy to assume that genomic data...
Keywords: Bioinformatics, Genomics, Genetic data, Personal information, Health information, Privacy
WEBINAR: Protection of genomic data and the Australian Privacy Act: when is genomic data 'personal information'?
https://zenodo.org/records/6423621
https://dresa.org.au/materials/webinar-protection-of-genomic-data-and-the-australian-privacy-act-when-is-genomic-data-personal-information-1f7194f9-4034-468f-8a78-614f83ef67b0
This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.
Event description
It is easy to assume that genomic data will be captured by legal definitions of ‘health information’ and ‘genetic information’, but the legal meaning of ‘genetic information’ need not align with scientific categories.
There are many different types of genomic data, with varied characteristics, uses and applications. Clarifying when genomic data is covered by the Privacy Act 1988 (Cth) is an ongoing evaluative exercise but is important for at least 3 reasons:
those subject to the Privacy Act need to be able to confidently navigate their responsibilities
understanding current controls is a prerequisite for meaningful external critique (and this is particularly important at a time when the Privacy Act is under review), and
while legislation that applies to state public sector agencies is generally distinct from the Privacy Act there are similarities that extend the relevance of the question when is genomic data ‘personal information’ under the Privacy Act?
In this presentation, Mark will explore the relationship between the legal concept of genetic information and the concept of genomic data relevant to health and medical research, reflect on the characteristics of each, and the possibility
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.
Taylor_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/Iaei-9Gu-AI
Melissa Burke (melissa@biocommons.org.au)
Taylor, Mark (orcid: 0000-0003-2009-6284)
Bioinformatics, Genomics, Genetic data, Personal information, Health information, Privacy
WORKSHOP: Introduction to Metabarcoding using QIIME2
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.
Event description
Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy...
Keywords: Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
WORKSHOP: Introduction to Metabarcoding using QIIME2
https://zenodo.org/records/6350808
https://dresa.org.au/materials/workshop-introduction-to-metabarcoding-using-qiime2-d3a7ac82-63aa-47e6-9d8e-5126419f9982
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.
Event description
Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy with high-throughput DNA sequencing, it offers the potential to observe a larger diversity in the taxa within a single sample, rapidly expanding the scope of microbial analysis and generating high-quality biodiversity data.
This workshop will introduce the topic of metabarcoding and how you can use Qiime2 to analyse 16S data and gain simultaneous identification of all taxa within a sample. Qiime2 is a popular tool used to perform powerful microbiome analysis that can transform your raw data into publication quality visuals and statistics. In this workshop, using example 16S data from the shallow-water marine anemone E. diaphana, you will learn how to use this pipeline to run essential steps in microbial analysis including generating taxonomic assignments and phylogenic trees, and performing both alpha- and beta- diversity analysis.
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 ‘Introduction to metabarcoding with QIIME2’ which has been made publicly available by Melbourne Bioinformatics.
https://www.melbournebioinformatics.org.au/tutorials/tutorials/qiime2/qiime2/
Melissa Burke (melissa@biocommons.org.au)
Dungan, Ashley (orcid: 0000-0003-0958-2177)
Philip, Gayle (orcid: 0000-0002-2671-5093)
Perry, Andrew (orcid: 0000-0001-9256-6068)
Ismail, Rania
Geissler, Laura
Tandon, Kshitij (orcid: 0000-0003-3022-0808)
Makunin, Igor
Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome