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Authors: Dow, Ellen (orcid: 0000-000...  or Liffers, Matthias (orcid: 0...  or Morgan, Steven (orcid: 0000... 

WORKSHOP: Online data analysis for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021.

Workshop description

Galaxy is an online platform for biological research that allows people to use computational data...

Keywords: Bioinformatics, Analysis, Workflows, Galaxy Australia

WORKSHOP: Online data analysis for biologists https://dresa.org.au/materials/workshop-online-data-analysis-for-biologists-08d66913-4ce3-4528-bdd6-0b0fcf234982 This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 9 September 2021. Workshop description Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. It is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It also captures run information so that workflows can be saved, repeated and shared efficiently via the web. This interactive beginners workshop will provide an introduction to the Galaxy interface, histories and available tools. The material covered in this workshop is freely available through the Galaxy Training Network. The workshop will be held via Zoom and involves a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop Online_data_analysis_for_biologists_extraslides (PPTX and PDF): Slides used to introduce the data set and emphasise the importance of workflows. These slides were developed by Ms Grace Hall. Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann, 2021 Galaxy 101 for everyone (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html Online; accessed Fri Dec 10 2021 Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Workflows, Galaxy Australia
WEBINAR: 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: RNA-Seq: reads to differential genes and pathways

This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022.

Event description

RNA sequencing (RNA-seq) is a common method used to...

Keywords: Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re

WORKSHOP: RNA-Seq: reads to differential genes and pathways https://dresa.org.au/materials/workshop-rna-seq-reads-to-differential-genes-and-pathways-5a384156-d3de-4d5d-9797-e689bf6592f8 This record includes training materials associated with the Australian BioCommons workshop ‘RNA-Seq: reads to differential genes and pathways’. This workshop took place over two, 3.5 hour sessions on 27 and 28 September 2022. Event description RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.  In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq - a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis! This workshop is presented by the Australian BioCommons and Sydney Informatics Hub with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. RNAseq reads to differential genes and pathways - Additional Resources (PDF): Additional resources compiled by the Sydney Informatics Hub rnaseq_DE_analysis_Day2.html: HTML version of code used on day 2 of the workshop rnaseq_DE_analysis_Day2.Rmd: R Markdown version of code used on day 2 of the workshop RNAseq reads to differential genes and pathways_Q_and_A (PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere: This workshop follows the tutorial ‘RNA-seq: reads to differential gene expression workshop series’ developed by the Sydney Informatics Hub. https://sydney-informatics-hub.github.io/training.RNAseq.series-quarto/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, RNA-seq, Workflows, Nextflow, nf-co.re
WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945 This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022. Event description Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.  We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.   Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. scRNAseq_Slides (PDF): Slides used to introduce topics scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.   Materials shared elsewhere: This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’ https://swbioinf.github.io/scRNAseqInR_Doco/index.html This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat. It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here. Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WORKSHOP: Hybrid de novo genome assembly

This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.

Workshop description

It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...

Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly

WORKSHOP: Hybrid de novo genome assembly https://dresa.org.au/materials/workshop-hybrid-de-novo-genome-assembly-714004ba-0348-47c8-a68f-038a1f8ccfb1 This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021. Workshop description It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches which enable research on organisms for which reference genomes were not previously available. These approaches combine the strengths of short (Illumina) and long (PacBio or Nanopore) read technologies, resulting in improved assembly quality. In this workshop we will learn how to create and assess genome assemblies from Illumina and Nanopore reads using data from a Bacillus Subtilis strain. We will demonstrate two hybrid-assembly methods using the tools Flye, Pilon, and Unicycler to perform assembly and subsequent error correction. You will learn how to visualise input read sets and the assemblies produced at each stage and assess the quality of the final assembly. All analyses will be performed using Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. This workshop is presented by the Australian BioCommons and Melbourne Bioinformatics with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): A breakdown of the topics and timings for the workshop   Materials shared elsewhere: This workshop follows the tutorial ‘Hybrid genome assembly - Nanopore and Illumina’ developed by Melbourne Bioinformatics. https://www.melbournebioinformatics.org.au/tutorials/tutorials/hybrid_assembly/nanopore_assembly/ Melissa Burke (melissa@biocommons.org.au) Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
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
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 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
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
Introduction to Unix

A hands-on workshop covering the basics of the Unix command line interface.

Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing...

Keywords: Unix, Command line, Command-line, CLI

Resource type: tutorial

Introduction to Unix https://dresa.org.au/materials/introduction-to-unix A hands-on workshop covering the basics of the Unix command line interface. Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on a high-performance computing system, knowing your way around a command-line interface is highly valuable. This workshop will introduce you to Unix concepts by way of a series of hands-on exercises. This workshop is designed for participants with little or no command-line knowledge. Tools: Standard Unix commands, FileZilla Topic overview: Section 1: Getting started Section 2: Exploring your current directory Section 3: Making and changing directories Section 4: Viewing and manipulating files Section 5: Removing files and directories Section 6: Searching files Section 7: Putting it all together Section 8: Transferring files Tutorial instructions available here: https://www.melbournebioinformatics.org.au/tutorials/tutorials/unix/unix/ For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Find out when we are next running this training as an in-person workshop, by visiting the Melbourne Bioinformaitcs Eventbrite page: https://www.eventbrite.com.au/o/melbourne-bioinformatics-13058846490 For queries relating to this workshop, contact Melbourne Bioinformatics (bioinformatics-training@unimelb.edu.au). Unix, Command line, Command-line, CLI ugrad masters mbr phd ecr researcher support professional
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