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Authors: Dow, Ellen (orcid: 0000-000...  or Liffers, Matthias (orcid: 0...  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
WEBINAR: KBase - A knowledge base for systems biology

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

Event description 

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

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

WEBINAR: KBase - A knowledge base for systems biology https://dresa.org.au/materials/webinar-kbase-a-knowledge-base-for-systems-biology-653d9753-989d-4194-9230-6e2d90652955 This record includes training materials associated with the Australian BioCommons webinar ‘KBase - A knowledge base for systems biology’. This webinar took place on 22 September 2021. Event description  Developed for bench biologists and bioinformaticians, The Department of Energy Systems Biology Knowledgebase (KBase) is a free, open source, software and data science platform designed to meet the grand challenge of systems biology: predicting and designing biological function. This webinar will provide an overview of the KBase mission and user community, as well as a tour of the online platform and basic functionality. You’ll learn how KBase can support your research: Upload data, run analysis tools (Apps), share your analysis with collaborators, and publish your data and reproducible workflows. We’ll highlight a brand new feature that enables users to link environment and measurement data to sequencing data. You’ll also find out how KBase supports findable, accessible, interoperable, and reusable (FAIR) research by providing open, reproducible, shareable bioinformatics workflows. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Q&A for Australian BioCommons KBase Webinar [PDF]: Document containing answers to questions asked during the webinar and links to additional resources Introduction to KBase: Australian BioCommons Webinar [PDF]: Slides presented during the webinar Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tJ94i9gOJfU The slides are also available as Google slides:  https://tinyurl.com/KBase-webinar-slides Melissa Burke (melissa@biocommons.org.au) Systems Biology, FAIR Research, Open Source Software, Metagenomics, Microbiology
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
23 (research data) Things

23 (research data) things is a set of training materials exploring research data management. Each of the 23 things offers a variety of learning opportunities with activities at three levels of complexity:

  • Getting started
  • Learn more
  • Challenge me

All resources used in the program are online...

Keywords: research data management, training material

23 (research data) Things https://dresa.org.au/materials/23-research-data-things-793872d2-c221-4cd6-91be-11a313c74b78 23 (research data) things is a set of training materials exploring research data management. Each of the 23 things offers a variety of learning opportunities with activities at three levels of complexity: * Getting started * Learn more * Challenge me All resources used in the program are online and free to use and reuse under a Creative Commons Attribution 4.0 International licence. You could use all of them as a self-paced course, or choose components to integrate into your own course. The 23 things are designed to build knowledge as the program progresses, so if you’re new to the world of research data management, we suggest you start with things 1-3 and then decide where you want to go from there. These materials supported an international community-based training program delivered in 2016 by the Australian National Data Service. This release migrates these materials to a GitHub repository for continued maintenance. Some updates were made to material that was outdated. We welcome contributions and suggestions via GitHub Issue or Pull Request. contact@ardc.edu.au research data management, training material
Software publishing, licensing and citation

This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research...

Keywords: software, code, Repositories, code sharing, training material

Software publishing, licensing and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-49097378-f296-44aa-b724-a57d22214d99 This presentation was part of an “Orientation to ARDC services and expertise” series, specifically aimed at people involved in one of the ARDC co-investment projects commencing early 2021. In addition to co-investment of money, ARDC contributes expertise and services in a range of areas: research vocabularies, persistent identifiers, data discovery catalogues, metadata issues, licensing, governance, underpinning infrastructure (e.g. Nectar Research Cloud) and more. ARDC can also connect projects to national and international communities and initiatives trying to solve common challenges and outline best practice. This session explained why and how to publish, licence and cite software. A video recording of this session can also be found on ARDC's YouTube channel: https://youtu.be/l2acLeuF_QE contact@ardc.edu.au software, code, Repositories, code sharing, training material
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action-ffd9b4ed-b557-496b-ac35-72467c03c71b In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material
Software publishing, licensing, and citation

A short presentation for reuse includes speaker notes.

Making software citable using a code repository, an ORCID and a licence.

Keywords: Software citation, Software publishing, Software registries, Software Repositories, research Software, training material

Software publishing, licensing, and citation https://dresa.org.au/materials/software-publishing-licensing-and-citation-d222144f-380a-455d-b4aa-c56283afc23e A short presentation for reuse includes speaker notes. Making software citable using a code repository, an ORCID and a licence. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Software citation, Software publishing, Software registries, Software Repositories, research Software, training material
ARDC FAIR Data 101 self-guided

FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles

The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course.

The course structure was based on 'FAIR Data in the...

Keywords: training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management

ARDC FAIR Data 101 self-guided https://dresa.org.au/materials/ardc-fair-data-101-self-guided-2d794a84-f0ff-4e11-a39c-fa8ea481e097 FAIR Data 101 v3.0 is a self-guided course covering the FAIR Data principles The FAIR Data 101 virtual course was designed and delivered by the ARDC Skilled Workforce Program twice in 2020 and has now been reworked as a self-guided course. The course structure was based on 'FAIR Data in the Scholarly Communications Lifecycle', run by Natasha Simons at the FORCE11 Scholarly Communications Institute. These training materials are hosted on GitHub. contact@ardc.edu.au training material, FAIR data, video, webinar, activities, quiz, FAIR, research data management
ARDC Guide to making software citable

A short guide to making software citable using a code repository, an ORCID and a licence.

Keywords: Software citation, Software publishing, Software registries, Software repositories, Research software, training material

ARDC Guide to making software citable https://dresa.org.au/materials/ardc-guide-to-making-software-citable-46d0f9e4-ef55-43b9-b237-3e52a9d1e141 A short guide to making software citable using a code repository, an ORCID and a licence. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Software citation, Software publishing, Software registries, Software repositories, Research software, training material
ARDC Datacite API Jupyter notebook

This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata.

It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment

Code...

Keywords: jupyter, notebook, DataCite, api, python, metadata, DOI, training material

ARDC Datacite API Jupyter notebook https://dresa.org.au/materials/ardc-datacite-api-jupyter-notebook This Jupyter notebook presents a low-barrier entry to using the DataCite REST API to mint, update, publish, and deleted DOIs and their associated metadata. It was designed specifically to not use any third-party libraries so that it can be reused in almost any Jupyter notebook environment Code is presented alongside human readable comments that explain the use of each component of the notebook. contact@ardc.edu.au jupyter, notebook, DataCite, api, python, metadata, DOI, training material