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Authors: Williams, Jason (orcid: 000...  or Willet, Cali (orcid: 0000-0... 

WORKSHOP: Making sense of gene and protein lists with functional enrichment analysis

This record includes training materials associated with the Australian BioCommons workshop ‘Making sense of gene and protein lists with functional enrichment analysis’. This workshop took place over two, 3 hour sessions on 20, 21 November 2024.
Event description
Omics experiments often generate...

Keywords: Bioinformatics http://edamontology.org/topic_0091, Analysis http://edamontology.org/operation_2945, Enrichment analysis http://edamontology.org/operation_3501

WORKSHOP: Making sense of gene and protein lists with functional enrichment analysis https://dresa.org.au/materials/workshop-making-sense-of-gene-and-protein-lists-with-functional-enrichment-analysis This record includes training materials associated with the Australian BioCommons workshop ‘Making sense of gene and protein lists with functional enrichment analysis’. This workshop took place over two, 3 hour sessions on 20, 21 November 2024. Event description Omics experiments often generate long lists of genes or proteins. Functional enrichment analysis identifies biological trends in the data by assessing these lists against gene ontology and pathway information. This can help interpret the experimental results in the context of larger biological systems. This workshop continues from our introductory webinar and provides a practical introduction to functional enrichment analysis. Using example data you will get hands-on with some of the most commonly used databases and tools for over representation (ORA) and gene set enrichment analysis (GSEA) and for identifying enriched biological functions in a list of genes or proteins. We’ll focus on tools available online and in R. 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 Hossein Valipour Kahrood, Bioinformatician, Monash Genomics and Bioinformatics Platform Dr Cali Willet, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney Facilitators: Georgina Samaha, Australian BioCommons Laura Perlaza-Jimenez, Monash Genomics and Bioinformatics Platform Infrastructure provision: Uwe Winter, Australian BioCommonsHost: 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. R notebooks (zip): R markdown and html rendered files, input files. Materials shared elsewhere: Training materials webpage Melissa Burke (melissa@biocommons.org.au) Bioinformatics http://edamontology.org/topic_0091, Analysis http://edamontology.org/operation_2945, Enrichment analysis http://edamontology.org/operation_3501
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: 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: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond

This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022.

Event description 

Scientists and educators...

Keywords: Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy

WEBINAR: Effective, inclusive, and scalable training in the life sciences, clinical education and beyond https://dresa.org.au/materials/webinar-effective-inclusive-and-scalable-training-in-the-life-sciences-clinical-education-and-beyond-52c113ff-573c-4ae8-a3f0-482c86f1818a This record includes training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Effective, inclusive, and scalable training in the life sciences, clinical education and beyond’. This webinar took place on 4 November 2022. Event description  Scientists and educators working in the life sciences must continuously acquire new knowledge and skills to stay up-to-date with the latest methods, technologies and research. Short-format training, such as webinars, workshops and bootcamps, are popular ways of quickly learning about new topics and gaining new skills. As trainers and educators, how can we ensure that short-format training is effective and inclusive for all? How can we ensure that our learners are equipped to continue learning and applying their new skills once they return to their day jobs? And how can we do this in a way that is scalable and sustainable? The Bicycle Principles assemble education theory and community experience into a framework for improving short-format training so that it is effective, inclusive and scalable. Over 30 international experts, including colleagues from the Australian BioCommons, Melbourne Genomics and other Australian and New Zealand organisations, helped develop the principles and an associated set of recommendations. Jason Williams, Assistant Director, DNA Learning Center, Cold Spring Harbor Laboratory - a leading genomics and bioinformatics educator and project lead, joins us to discuss the Principles and how they can be applied to achieve scalable and sustainable training in a range of Australian settings. This webinar is co-hosted by Australian BioCommons and Melbourne Genomics 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. WILLIAMS-Jason_aus-biocommons_nov-2022 (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/18dub7jGeQ8 Melissa Burke (melissa@biocommons.org.au) Short-format training, Clinical education, Continuing education, Professional development, Training, Lifelong learning, Pedagogy
Professionalizing Training - Origin Stories for the Modern Researcher

Keynote Presentation for the ARDC Skills Summit 2023

This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern...

Keywords: research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material

Professionalizing Training - Origin Stories for the Modern Researcher https://dresa.org.au/materials/professionalizing-training-origin-stories-for-the-modern-researcher-0198d9cf-9d8f-467e-8031-4d3a3536af63 Keynote Presentation for the ARDC Skills Summit 2023 This keynote presentation provides a brief outline of Jason William’s experience and an overview of the training initiatives he has been involved in. His presentation looks at what makes a good researcher and provokes thinking about modern researchers and the need for them to get serious bout career-spanning training. Jason also provides an overview of the Bike Principles and focuses on the first Bike Principles recommendation - Professionalize the training of short-format training instructors and instructional designers. contact@ardc.edu.au research, training, skills, superheroes, formal, career, change, workshops, milestones, community, principles, bicycle principles, professionalizing, training material