51 materials found
Keywords: Bioinformatics
WORKSHOP: Machine learning in the life sciences
This record includes training materials associated with the Australian BioCommons workshop ‘Machine Learning in the Life Sciences’. This on 11 June 2024.
Event description
Machine learning promises to revolutionise life science research by speeding up data analysis, enabling prediction of...
Keywords: Bioinformatics, Life Science, Machine Learning
WORKSHOP: Machine learning in the life sciences
https://zenodo.org/records/14676360
https://dresa.org.au/materials/workshop-machine-learning-in-the-life-sciences
This record includes training materials associated with the Australian BioCommons workshop ‘Machine Learning in the Life Sciences’. This on 11 June 2024.
Event description
Machine learning promises to revolutionise life science research by speeding up data analysis, enabling prediction of biological patterns and modelling complex biological systems.
But what exactly is machine learning and when should you use it?
This hands-on online workshop provides a high-level introduction to machine learning: what it is, its advantages and disadvantages compared to traditional modelling approaches and the types of scenarios where it may be the right tool for the job. Using example datasets and basic machine learning pipelines we contrast a few commonly used algorithms for constructing predictive models and explore some of their trade-offs. We discuss common pitfalls in how machine learning is applied and evaluated, with a focus on its application in the life sciences, to help you recognise overly optimistic results. We discuss how and why such errors arise and strategies to avoid them.
Lead trainer:
Dr Benjamin Goudey, Research Fellow, Florey Department of Neuroscience and Mental Health
Facilitators:
Dr Erin Graham, Queensland Cyber Infrastructure Foundation (QCIF) / James Cook University
William Pinzon Perez, Queensland Cyber Infrastructure Foundation (QCIF)
Dr Giorgia Mori, Sydney Informatics Hub, University of Sydney
Joseph McConnell, University of Adelaide
Jessica Chung, Melbourne Bioinformatics 0000-0002-0627-0955
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.
Schedule (PDF): Schedule describing the timing of sessions for the in person and online events
Materials shared elsewhere:
This workshop follows the Google Colab Notebook developed by Dr Benjamin Goudey: https://github.com/bwgoudey/IntroMLforLifeScienceWorkshopR
Melissa Burke (melissa@biocommons.org.au)
Goudey, Benjamin (orcid: 0000-0002-2318-985X)
Graham, Erin
Pinzon Perez, William
Mori, Giorgia (orcid: 0000-0003-3469-5632)
McConnell, Joseph
Chung, Jessica (orcid: 0000-0002-0627-0955)
Mather, Marius
Bioinformatics, Life Science, Machine Learning
WORKSHOP: Genetic Outlier Analysis
This record includes training materials associated with the Australian BioCommons workshop ‘Genetic Outlier Analysis’.
These workshops took place on:
27 - 28 February 2024: Online via Zoom
10 - 11 April 2024: In person in Melbourne
4 - 5 July 2024: In person in Sydney
Event description
There...
Keywords: Bioinformatics, Genetics
WORKSHOP: Genetic Outlier Analysis
https://zenodo.org/records/14676276
https://dresa.org.au/materials/workshop-genetic-outlier-analysis
This record includes training materials associated with the Australian BioCommons workshop ‘Genetic Outlier Analysis’.
These workshops took place on:
27 - 28 February 2024: Online via Zoom
10 - 11 April 2024: In person in Melbourne
4 - 5 July 2024: In person in Sydney
Event description
There are many interesting patterns that you can extract from genetic variant data. This can include patterns of linkage, balancing selection, or even inbreeding signals. One of the most common approaches is to find sites on the genome that are under selection.
This workshop introduces the basics of genetic selection analysis. It will step you through the process of identifying signals of selection using your own data (or an example genomic dataset) using the outlier analysis method.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
This workshop is presented by the Australian BioCommons and the Genetics Society of AustralAsia
Lead trainer:
Dr Katarina Stuart, Research Fellow, University of Auckland.
Facilitators:
Adele Barugahare, Monash Genomics and Bioinformatics Platform
Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney
Dr Ching-Yu Lu, Sydney Informatics Hub, University of Sydney
Soleille Miller, University of NSW
Dr Nandan Deshpande, Sydney Informatics Hub, University of Sydney
Infrastructure provision: Audrey Stott, Pawsey Supercomputing Research Centre
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.
Schedules describing the timing of sessions for the in person and online events
Materials shared elsewhere:
These workshops followed the materials developed by Dr Katarina Stuart
https://github.com/katarinastuart/Ev1_SelectionMetaAnalysis
Melissa Burke (melissa@biocommons.org.au)
Stuart, Katarina (orcid: 0000-0002-0386-4600)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Barugahare, Adele (orcid: 0000-0002-8976-0094)
Miller, Solleile (orcid: 0000-0002-7880-6501)
Deshpande, Nandan
Lu, Ching-Yu
Bioinformatics, Genetics
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.
Files and materials shared elsewhere:
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: 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: 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
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: 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
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
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: 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://zenodo.org/records/10005538
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)
Burdett, Tony (orcid: 0000-0002-2513-5396)
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://zenodo.org/records/8323208
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)
Deshpande, Nandan (orcid: 0000-0002-0324-8728)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
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://zenodo.org/records/8185398
https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a
This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.
Event description
Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?
Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes
This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Managing data analysis training with Galaxy_slides: A PDF copy of the slides presented during the webinar.
Materials shared elsewhere:
A recording of this webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/VNE0pF6Nqgw
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Hiltemann, Saskia (orcid: 0000-0003-3803-468X)
Rasche, Helena (orcid: 0000-0001-9760-8992)
Bioinformatics, Galaxy, Training, Training infrastructure
WORKSHOP: Translating workflows into Nextflow with Janis
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies...
Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy
WORKSHOP: Translating workflows into Nextflow with Janis
https://zenodo.org/records/8072678
https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis-36386c6d-f9a2-4b4d-afa9-062ce3b8ac5d
This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.
Event description
Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.
Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.
This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.
Materials
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Intro to Galaxy (PDF): Slides presented during the workshop
Intro to CWL (PDF): Slides presented during the workshop
Intro to the session & Janis (PDF): Slides presented during the workshop
Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate
A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY
Melissa Burke (melissa@biocommons.org.au)
Hall, Grace (orcid: 0000-0002-5105-8347)
Lupat, Richard (orcid: 0000-0002-6435-7100)
Bioinformatics, Workflows, Nextflow, CWL, Galaxy
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://zenodo.org/records/8067584
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)
Holliday, Jess (orcid: 0000-0003-2855-0066)
Patterson, Andrew (orcid: 0000-0002-1163-8558)
Syed, Mustafa
Kummerfeld, Sarah (orcid: 0000-0002-0089-2358)
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://zenodo.org/records/8026170
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)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Willet, Cali (orcid: 0000-0001-8449-1502)
Hakkaart, Chris (orcid: 0000-0001-5007-2684)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Stott, Audrey (orcid: 0000-0003-0939-3173)
Ip, Alex (orcid: 0000-0001-8937-8904)
Cooke, Steele
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://zenodo.org/records/8019318
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)
Padula, Matt (orcid: 0000-0002-8283-0643)
Carroll, Luke (orcid: 0000-0002-8600-4023)
Gustafsson, Johan (orcid: 0000-0002-2977-5032)
Bioinformatics, Proteomics, Mass spectrometry
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and...
Keywords: Bioinformatics, Workflows, HPC, High Performance Computing
WEBINAR: Pro tips for scaling bioinformatics workflows to HPC
https://zenodo.org/records/8008227
https://dresa.org.au/materials/webinar-pro-tips-for-scaling-bioinformatics-workflows-to-hpc-9f2a8b90-88da-433b-83b2-b1ab262dd9df
This record includes training materials associated with the Australian BioCommons webinar ‘Pro tips for scaling bioinformatics workflows to HPC’. This webinar took place on 31 May 2023.
Event description
High Performance Computing (HPC) infrastructures offer the computational scale and efficiency that life scientists need to handle complex biological datasets and multi-step computational workflows. But scaling workflows to HPC from smaller, more familiar computational infrastructures brings with it new jargon, expectations, and processes to learn. To make the most of HPC resources, bioinformatics workflows need to be designed for distributed computing environments and carefully manage varying resource requirements, and data scale related to biology.
In this webinar, Dr Georgina Samaha from the Sydney Informatics Hub, Dr Matthew Downton from the National Computational Infrastructure (NCI) and Dr Sarah Beecroft from the Pawsey Supercomputing Research Centre help you navigate the world of HPC for running and developing bioinformatics workflows. They explain when you should take your workflows to HPC and highlight the architectural features you should make the most of to scale your analyses once you’re there. You’ll hear pro-tips for dealing with common pain points like software installation, optimising for parallel computing and resource management, and will find out how to get access to Australia’s National HPC infrastructures at NCI and Pawsey.
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.
Pro-tips_HPC_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/YKJDRXCmGMo
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Beecroft, Sarah (orcid: 0000-0002-3935-2279)
Downton, Matthew (orcid: 0000-0002-4693-1965)
Bioinformatics, Workflows, HPC, High Performance Computing