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Content provider: Australian BioCommons 

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://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) 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://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) 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://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) 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://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) 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://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) 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://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) Bioinformatics, Metabolomics, Metabolites, Data sharing
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://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) 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://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) Bioinformatics, Computational biology, Computational infrastructure
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://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) Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
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://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) 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://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) Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
WEBINAR: KBase - A knowledge base for systems biology

This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021.

Event description 

Developed for bench biologists and bioinformaticians, The Department of Energy Systems...

Keywords: Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology

WEBINAR: KBase - A knowledge base for systems biology https://dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology-653d9753-989d-4194-9230-6e2d90652955 This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021. Event description  Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function. This webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows. 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. Q&A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources Introduction to KBase: Australian BioCommons Webinar [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/tJ94i9gOJfU The slides are also available as Google slides:  https://tinyurl.com/KBase-webinar-slides Melissa Burke (melissa@biocommons.org.au) Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
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://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) 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://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) 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://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) R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating...

Keywords: Phosphoproteomics, Proteomics, Mass spectrometry

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://dresa.org.au/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics-a46784bd-7efe-4018-8893-761d1fcd32ba This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating the detailed molecular events that occur in response to cellular stimuli. Experiments can routinely detect and quantify thousands of phosphorylated peptides, and interpreting this data, and extracting biological meaning, remains challenging.  This webinar provides an overview of the phosphoproteomics data analysis website, Phosphomatics, that incorporates a suite of tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results. Phosphomatics can natively import search and quantitation results from major search engines including MaxQuant and Proteome Discoverer and employs intuitive ‘wizards’ to guide users through data preprocessing routines such as filtering, normalization and transformation. A graphical platform of interactive univariate and multivariate analysis features is provided that allow subgroups of the uploaded data containing phosphosites of statistical interest to be created and interrogated through further functional analysis. A range of databases have been integrated that, for example, provide ligand and inhibitor information for key proteins or highlight key modification sites known to be involved in functional state regulation. At each step, published literature is natively incorporated along with a ‘bibliography builder’ that allows references of interest to be assembled and exported in various formats. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis. The webinar is 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. Phosphomatics -slides  (PDF and PPTX): Slides used in the presentation   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/_WpeL5t2DSI Melissa Burke (melissa@biocommons.org.au) Phosphoproteomics, Proteomics, Mass spectrometry
WEBINAR: Getting started with deep learning

This record includes training materials associated with the Australian BioCommons webinar  ‘Getting started with deep learning’. This webinar took place on 21 July 2021.

Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep...

Keywords: Deep learning, Neural networks, Machine learning

WEBINAR: Getting started with deep learning https://dresa.org.au/materials/webinar-getting-started-with-deep-learning-986aa2d2-594a-4a7f-836c-44d6e9d5d017 This record includes training materials associated with the Australian BioCommons webinar  ‘Getting started with deep learning’. This webinar took place on 21 July 2021. Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep learning ‘in a nutshell’ and provides tips on which concepts and skills you will need to know to build a deep learning application. The presentation also provides pointers to various resources you can use to get started in deep learning. The webinar is 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 Deep Learning - 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/I1TmpnZUuiQ Melissa Burke (melissa@biocommons.org.au) Deep learning, Neural networks, Machine learning
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

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

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

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

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset-51cc7740-0da1-45f1-95de-f1a47f676053 This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Hybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Nauheimer_hybphaser_slides (PDF): Slides presented during the webinar Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/japXwTAhA5U Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

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

Multi-gene datasets used in phylogenetic...

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

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation-a6743550-b904-45e1-9635-4e481ee8f739 This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schmidt-Lebuhn - paralogy lineage sorting reticulation - slides (PDF): Slides presented during the webinar   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/1bw81q898z8 Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.   Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop   Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation
WEBINAR: 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://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) Hogg, Carolyn (type: Supervisor) Bioinformatics, Command line, Workflows, Bash, Computational biology
WORKSHOP: RNASeq: reads to differential genes and pathways

This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique...

Keywords: bioinformatics, transcriptomics, RNA-seq, RNAseq

WORKSHOP: RNASeq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rnaseq-reads-to-differential-genes-and-pathways This record includes training materials associated with the Australian BioCommons workshop 'RNASeq: reads to differential genes and pathways'. This workshop took place over two, 3 hour sessions on 11 and 12 October 2023.Event descriptionRNA sequencing (RNAseq) is a popular and powerful technique used to understand the activity of genes. Using differential gene profiling methods, we can use RNAseq data to gain valuable insights into gene activity and identify variability in gene expression between samples to understand the molecular pathways underpinning many different traits.  In this hands-on workshop, you will learn RNAseq fundamentals as you process, analyse, and interpret the results from a real RNAseq experiment on the command-line. In session one, you will convert raw sequence reads to analysis-ready count data with the nf-core/rnaseq workflow. In session two, you'll work interactively in RStudio to identify differentially expressed genes,perform functional enrichment analysis, and visualise and interpret your results using popular and best practice R packages.  This workshop was delivered as a part of the Australian BioCommons Bring Your Own Data Platforms Project and will provide you with an opportunity to explore services and infrastructure built specifically for life scientists working at the command line. By the end of the workshop, you will be familiar with Pawsey's Nimbus cloud platform and be able to process your own RNAseq datasets and perform differential expression analysis on the command-line. 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 Georgina Samaha (Sydney Informatics Hub), Dr Nandan Deshpande (Sydney Informatics Hub)Facilitators: Ching-Yu Lu and Jessica Chung.Infrastructure provision: Audrey Stott (Pawsey Supercomputing Research Centre), Alex Ip (AARNet)Host: Melissa Burke, Australian BioCommons Training materialsFiles 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.Materials shared elsewhere:This workshop follows the tutorial 'Introduction to RNAseq workshop: reads to differential gene expression' developed by the Sydney Informatics Hub.https://sydney-informatics-hub.github.io/rnaseq-workshop-2023/Additional supporting materials are available via GitHubRstudio rnaseq container: https://github.com/Sydney-Informatics-Hub/Rstudio-rnaseq-contained/tree/mainRNAseq differential expression R notebook: https://github.com/Sydney-Informatics-Hub/rna-differential-expression-Rnotebook Melissa Burke (melissa@biocommons.org.au) bioinformatics, transcriptomics, RNA-seq, RNAseq
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 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires...

Keywords: bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-6a1126cf-7105-43ec-bf55-7c492f758301 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 26 and 27 October 2023.Event descriptionAnalysis 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, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza JimenezFacilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) AntczakInfrastructure provision: Uwe WinterCoordinator: Melissa BurkeTraining materialsMaterials 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_Schedule (PDF): A breakdown of the topics and timings for the workshopMaterials shared elsewhere:This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'https://swbioinf.github.io/scRNAseqInR_Doco/index.htmlSlides used to introduce key topics are available via GitHubhttps://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slidesThis 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) bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software
WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records

This record includes training materials associated with the Australian BioCommons webinar 'BioSamples: supporting multi-omics data integration with FAIR sample records'. This webinar took place on 4 October 2023.Event description The BioSamples database at EMBL-EBI is the ELIXIR deposition...

Keywords: Bioinformatics, Metadata, Multiomics, BioSamples, Data integration

WEBINAR: BioSamples: supporting multi-omics data integration with FAIR sample records https://dresa.org.au/materials/webinar-biosamples-supporting-multi-omics-data-integration-with-fair-sample-records This record includes training materials associated with the Australian BioCommons webinar 'BioSamples: supporting multi-omics data integration with FAIR sample records'. This webinar took place on 4 October 2023.Event description The BioSamples database at EMBL-EBI is the ELIXIR deposition database and EMBL-EBI's central institutional repository for information about biological samples (metadata). BioSamples can be used to search, submit and curate sample metadata across multiple projects and contexts. BioSamples records are the key point of connection between EMBL-EBI archives (e.g ENA, ArrayExpress) and other resources.This webinar will highlight how BioSamples can be used to enable multi-omic data sharing and integration including how to submit to the database in combination with other major public repositories. We will look at how BioSamples supports Findable, Accessible, Interoperable and Reusable (FAIR) principles for sample metadata management, and examine case studies where this has been beneficial, for example for integrating data to support the COVID-19 pandemic response.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.20231004_BioSamples_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/bRQ_6zZ4ecE?si=AbU-J2FMK9qVL_JJ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Metadata, Multiomics, BioSamples, Data integration
WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023.

Event description 

RNA sequencing (RNAseq) is a powerful technique for...

Keywords: Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression

WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights https://dresa.org.au/materials/webinar-getting-started-with-rnaseq-transforming-raw-reads-into-biological-insights-1f7db385-e282-4332-a1c4-d1d73a769b1b This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023. Event description  RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multiple steps to align raw sequence reads to a reference genome, count the number of reads mapped to each gene, and perform statistical analyses to identify differentially expressed genes and functionally annotate them. RNAseq experiments have many different applications as we apply them to a variety of research questions and organisms. This diversity of applications can make it challenging to appreciate all the design considerations, processing requirements, and limitations of RNAseq experiments as they apply to you. In this webinar, you will gain an understanding of the key considerations for designing and performing your own successful experiments with bulk RNA. We’ll start at the lab bench with RNA extraction, quality control, and library preparation, then move to the sequencing machine where you will make essential decisions about sequencing platforms, optimal sequencing depth, and the importance of replicates. We’ll talk about bioinformatics workflows for RNAseq data processing and the computational requirements of transforming raw sequencing reads to analysis-ready count data. Finally, we’ll discuss how to apply differential expression and functional enrichment analyses to gain biological insights from differentially expressed genes. This webinar was developed by the Sydney Informatics Hub in collaboration with the 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. Getting started with RNAseq: 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/tITR3WR_jWI Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WEBINAR: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WORKSHOP: Translating workflows into Nextflow with Janis

This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.

Event description

Bioinformatics workflows are critical for reproducibly transferring methodologies...

Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy

WORKSHOP: Translating workflows into Nextflow with Janis https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis-36386c6d-f9a2-4b4d-afa9-062ce3b8ac5d This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023. Event description Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.  Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use. This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows. This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.    Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Intro to Galaxy (PDF): Slides presented during the workshop Intro to CWL (PDF): Slides presented during the workshop Intro to the session & Janis (PDF): Slides presented during the workshop Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings Materials shared elsewhere: This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate   A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WEBINAR:Genomic data - improving discovery and access management

This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023.

Event description 

Australian human genome initiatives are generating vast amounts of human genome data...

Keywords: Bioinformatics, Data security, Genomics, Data access management

WEBINAR:Genomic data - improving discovery and access management https://dresa.org.au/materials/webinar-genomic-data-improving-discovery-and-access-management-1b7da2fd-54b0-49b9-bd13-b1f846a5c1c4 This record includes training materials associated with the Australian BioCommons webinar ‘Genomic data - improving discovery and access management’. This webinar took place on 14 June 2023. Event description  Australian human genome initiatives are generating vast amounts of human genome data to understand the cause of complex diseases, improve diagnosis / early disease detection and identify tailored treatment options.  To achieve this, genomic data needs to be compared between multiple individuals and cohorts, often across efforts/jurisdictions, at national or global scales, and requires the genomic data to be findable, searchable, shareable, and linkable to analytical capabilities. The Human Genome Platform Project aims to make it as easy as possible to securely and responsibly share human genome research data nationally and internationally. The project is building a ‘services toolbox’ that combines best practice technologies in human genome data sharing. In this webinar the project team will discuss three important aspects of human genomic data sharing i) discovery of genomic cohorts and the GA4GH Beacon protocol that enables this functionality across multiple sites ii) streamlining of data access request management; the Garvan will share experience using the Resource Entitlement Management System (REMS) software package. iii) community management functionality of CILogon and 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. Genomic data - improving discovery and access managements - 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/9SD6gpjDGWE Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Data security, Genomics, Data access management
WORKSHOP: Unlocking nf-core - customising workflows for your research

This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023.

Event description

Processing and analysing omics datasets poses many...

Keywords: Bioinformatics, Workflows, Nextflow, nf-core

WORKSHOP: Unlocking nf-core - customising workflows for your research https://dresa.org.au/materials/workshop-unlocking-nf-core-customising-workflows-for-your-research-1584ff39-e007-4422-9fd5-4e407df6b6c5 This record includes training materials associated with the Australian BioCommons workshop Unlocking nf-core - customising workflows for your research’. This workshop took place over two, 3 hour sessions on 18-19 May 2023. Event description Processing and analysing omics datasets poses many challenges to life scientists, particularly when we need to share our methods with other researchers and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are invaluable resources for the life science community. nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data and research goals.  This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. On day 1 you will learn about the nf-core tools utility, and step through the code structure of nf-core workflows. Then on day 2, using the nf-core/rnaseq workflow as an example, you will explore the various ways to adjust the workflow parameters, customise processes, and configure the workflow for your computational environment. This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia).  Materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. nfcore_Schedule: Schedule for the workshop providing a breakdown of topics and timings nfcore_Q_and_A: Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the accompanying training materials that were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet).  https://sydney-informatics-hub.github.io/customising-nfcore-workshop Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, nf-core
WEBINAR: Getting started with proteomics

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023.

Event description 

Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is...

Keywords: Bioinformatics, Proteomics, Mass spectrometry

WEBINAR: Getting started with proteomics https://dresa.org.au/materials/webinar-getting-started-with-proteomics-134c519c-0cea-4195-b444-1e73d551a20e This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with proteomics’. This webinar took place on 7 June 2023. Event description  Proteomics aims to identify and quantify all the proteins and peptides within a sample. Mass-spectrometry is the most common tool for proteomics and the wide array of methods, techniques and specialised approaches available have made it a popular method for probing cells, tissue and organisms in response to various stimuli or diseases. Each proteomics method has unique experimental design considerations and optimum workflows for data analysis meaning that there is no one-size-fits all solution. The variety of approaches available provides flexibility but can be bewildering and a barrier to getting started.  This webinar sets you up with the foundational knowledge of what to look out for when designing and understanding proteomics experiments. It outlines what you can and can’t do with proteomics, the type of data to expect as well as common data analysis approaches and quality control steps. This webinar was developed in collaboration with the Australian Core Facilities and Australian Proteomics Communities. 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. Getting started with proteomics_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/RSrk2yqklQo Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Proteomics, Mass spectrometry