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Licence: CC-BY-4.0 

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Keywords: AI  or software publishing  or RNA-seq 

WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights

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

Event description 

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

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

WEBINAR: Getting started with RNAseq: Transforming raw reads into biological insights https://dresa.org.au/materials/webinar-getting-started-with-rnaseq-transforming-raw-reads-into-biological-insights This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with RNAseq: Transforming raw reads into biological insights’. This webinar took place on 6 September 2023. Event description  RNA sequencing (RNAseq) is a powerful technique for investigating gene expression in biological samples. Processing and analysing RNAseq data involves multiple steps to align raw sequence reads to a reference genome, count the number of reads mapped to each gene, and perform statistical analyses to identify differentially expressed genes and functionally annotate them. RNAseq experiments have many different applications as we apply them to a variety of research questions and organisms. This diversity of applications can make it challenging to appreciate all the design considerations, processing requirements, and limitations of RNAseq experiments as they apply to you. In this webinar, you will gain an understanding of the key considerations for designing and performing your own successful experiments with bulk RNA. We’ll start at the lab bench with RNA extraction, quality control, and library preparation, then move to the sequencing machine where you will make essential decisions about sequencing platforms, optimal sequencing depth, and the importance of replicates. We’ll talk about bioinformatics workflows for RNAseq data processing and the computational requirements of transforming raw sequencing reads to analysis-ready count data. Finally, we’ll discuss how to apply differential expression and functional enrichment analyses to gain biological insights from differentially expressed genes. This webinar was developed by the Sydney Informatics Hub in collaboration with the Australian BioCommons. Training materials Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Getting started with RNAseq: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/tITR3WR_jWI Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Transcriptomics, RNA-seq, RNAseq, Gene expression
WEBINAR: AlphaFold: what's in it for me?

This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023.

Event description 

AlphaFold has taken the scientific world by storm with the ability to accurately predict the...

Keywords: Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning

WEBINAR: AlphaFold: what's in it for me? https://dresa.org.au/materials/webinar-alphafold-what-s-in-it-for-me This record includes training materials associated with the Australian BioCommons webinar ‘WEBINAR: AlphaFold: what’s in it for me?’. This webinar took place on 18 April 2023. Event description  AlphaFold has taken the scientific world by storm with the ability to accurately predict the structure of any protein in minutes using artificial intelligence (AI). From drug discovery to enzymes that degrade plastics, this promises to speed up and fundamentally change the way that protein structures are used in biological research.  Beyond the hype, what does this mean for structural biology as a field (and as a career)? Dr Craig Morton, Drug Discovery Lead at the CSIRO, is an early adopter of AlphaFold and has decades of expertise in protein structure / function, protein modelling, protein – ligand interactions and computational small molecule drug discovery, with particular interest in anti-infective agents for the treatment of bacterial and viral diseases. Craig joins this webinar to share his perspective on the implications of AlphaFold for science and structural biology. He will give an overview of how AlphaFold works, ways to access AlphaFold, and some examples of how it can be used for protein structure/function analysis. 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. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/4ytn2_AiH8s Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Machine Learning, Structural Biology, Proteins, Drug discovery, AlphaFold, AI, Artificial Intelligence, Deep learning
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...

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 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
Accelerating skills development in Data science and AI at scale

At the Monash Data Science and AI  platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities...

Keywords: AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material

Accelerating skills development in Data science and AI at scale https://dresa.org.au/materials/accelerating-skills-development-in-data-science-and-ai-at-scale At the Monash Data Science and AI  platform, we believe that upskilling our research community and building a workforce with data science skills are key to accelerating the application of data science in research. To achieve this, we create and leverage new and existing training capabilities within and outside Monash University. In this talk, we will discuss the principles and purpose of establishing collaborative models to accelerate skills development at scale. We will talk about our approach to identifying gaps in the existing skills and training available in data science, key areas of interest as identified by the research community and various sources of training available in the marketplace. We will provide insights into the collaborations we currently have and intend to develop in the future within the university and also nationally. The talk will also cover our approach as outlined below •        Combined survey of gaps in skills and trainings for Data science and AI •        Provide seats to partners •        Share associate instructors/helpers/volunteers •        Develop combined training materials •        Publish a repository of open source trainings •        Train the trainer activities •        Establish a network of volunteers to deliver trainings at their local regions Industry plays a significant role in making some invaluable training available to the research community either through self learning platforms like AWS Machine Learning University or Instructor led courses like NVIDIA Deep Learning Institute. We will discuss how we leverage our partnerships with Industry to bring these trainings to our research community. Finally, we will discuss how we map our training to the ARDC skills roadmap and how the ARDC platforms project “Environments to accelerate Machine Learning based Discovery” has enabled collaboration between Monash University and University of Queensland to develop and deliver training together. contact@ardc.edu.au AI, machine learning, eresearch skills, training, train the trainer, volunteer instructors, training partnerships, training material
Monash University - University of Queensland training partnership in Data science and AI

We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning,...

Keywords: data skills, training partnerships, data science, AI, training material

Monash University - University of Queensland training partnership in Data science and AI https://dresa.org.au/materials/monash-university-university-of-queensland-training-partnership-in-data-science-and-ai We describe the peer network exchange for training that has been recently created via an ARDC funded partnership between Monash University and Universities of Queensland under the umbrella of the Queensland Cyber Infrastructure Foundation (QCIF). As part of a training program in machine learning, visualisation, and computing tools, we have established a series of over 20 workshops over the year where either Monash or QCIF hosts the event for some 20-40 of their researchers and students, while some 5 places are offered to participants from the other institution. In the longer term we aim to share material developed at one institution and have trainers present it at the other. In this talk we will describe the many benefits we have found to this approach including access to a wider range of expertise in several rapidly developing fields, upskilling of trainers, faster identification of emerging training needs, and peer learning for trainers. contact@ardc.edu.au data skills, training partnerships, data science, AI, training material
Training resources for sharing and reuse

This presentation outlines the work completed during a consultancy for ARDC by Dr Paula Martinez to develop new and publish existing national skills materials for reuse by the sector. She was responsible for the work package targeted to co-develop national skills materials with a strong emphasis...

Keywords: FAIR training material, training material, guides, software citation, software publishing, containers, software licensing, training materials checklist, research data governance

Training resources for sharing and reuse https://dresa.org.au/materials/training-resources-for-sharing-and-reuse This presentation outlines the work completed during a consultancy for ARDC by Dr Paula Martinez to develop new and publish existing national skills materials for reuse by the sector. She was responsible for the work package targeted to co-develop national skills materials with a strong emphasis on sharing and reuse. This was a very collaborative project with the opportunity to work with different target audiences, topics and support expertise. To accommodate for a short timeline. We defined the scope to six topics. 1) Containers in Research 2) Data Governance 3) Software citation and Licensing 4) FAIR Data 101 5) Metadata for Training Materials 6) Machine Learning Resources. You can watch the video on YouTube here: https://youtu.be/10Yv_BFa-mw contact@ardc.edu.au FAIR training material, training material, guides, software citation, software publishing, containers, software licensing, training materials checklist, research data governance
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.

Cite as
Liffers, Matthias. (2021, July 12). Software publishing, licensing, and citation. Zenodo. https://doi.org/10.5281/zenodo.5091717

Keywords: software citation, software publishing, software registry, software repository, research software

Resource type: presentation

Software publishing, licensing, and citation https://dresa.org.au/materials/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. **Cite as** Liffers, Matthias. (2021, July 12). Software publishing, licensing, and citation. Zenodo. https://doi.org/10.5281/zenodo.5091717 ARDC Contact us: https://ardc.edu.au/contact-us/ software citation, software publishing, software registry, software repository, research software phd ecr researcher support
ARDC Guide to making Software Citable

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

Cite as
Liffers, Matthias, & Honeyman, Tom. (2021). ARDC Guide to making software citable. Zenodo. https://doi.org/10.5281/zenodo.5003989

Keywords: software citation, software publishing, software registry, software repository, research software

Resource type: guide

ARDC Guide to making Software Citable https://dresa.org.au/materials/ardc-guide-to-making-software-citable A short guide to making software citable using a code repository, an ORCID and a licence. **Cite as** Liffers, Matthias, & Honeyman, Tom. (2021). ARDC Guide to making software citable. Zenodo. https://doi.org/10.5281/zenodo.5003989 ARDC Contact us: https://ardc.edu.au/contact-us/ software citation, software publishing, software registry, software repository, research software phd ecr researcher support