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Resource type: video 

10 Reproducible Research things - Building Business Continuity

The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are...

Keywords: reproducibility, data management

Resource type: tutorial, video

10 Reproducible Research things - Building Business Continuity https://dresa.org.au/materials/9-reproducible-research-things-building-business-continuity The idea that you can duplicate an experiment and get the same conclusion is the basis for all scientific discoveries. Reproducible research is data analysis that starts with the raw data and offers a transparent workflow to arrive at the same results and conclusions. However not all studies are replicable due to lack of information on the process. Therefore, reproducibility in research is extremely important. Researchers genuinely want to make their research more reproducible, but sometimes don’t know where to start and often don’t have the available time to investigate or establish methods on how reproducible research can speed up every day work. We aim for the philosophy “Be better than you were yesterday”. Reproducibility is a process, and we highlight there is no expectation to go from beginner to expert in a single workshop. Instead, we offer some steps you can take towards the reproducibility path following our Steps to Reproducible Research self paced program. Video: https://www.youtube.com/watch?v=bANTr9RvnGg Tutorial: https://guereslib.github.io/ten-reproducible-research-things/ a.miotto@griffith.edu.au; s.stapleton@griffith.edu.au; i.jennings@griffith.edu.au; Sharron Stapleton Isaac Jennings reproducibility, data management masters phd ecr researcher support
HPC file systems and what users need to consider for appropriate and efficient usage

Three videos on miscellaneous aspects of HPC usage - useful reference for new users of HPC systems.

1 – General overview of different file systems that might be available on HPC. The video goes through shared file systems such as /home and /scratch, local compute node file systems (local...

Keywords: HPC, high performance computer, File systems

Resource type: video, presentation

HPC file systems and what users need to consider for appropriate and efficient usage https://dresa.org.au/materials/hpc-file-systems-and-what-users-need-to-consider-for-appropriate-and-efficient-usage Three videos on miscellaneous aspects of HPC usage - useful reference for new users of HPC systems. 1 – General overview of different file systems that might be available on HPC. The video goes through shared file systems such as /home and /scratch, local compute node file systems (local scratch or $TMPDIR) and storage file system. It outlines what users need to consider if they wish to use any of these in their workflows. 2 – Overview of the different directories that might be present on HPC. These could include /home, /scratch, /opt, /lib and lib64, /sw and others. 3 – Overview of the Message-of-the-day file and the message that is displayed to users every time they log in. This displays info about general help and often current problems or upcoming outages. QCIF Training (training@qcif.edu.au) HPC, high performance computer, File systems
Basic Linux/Unix commands

A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop "The Unix Shell".

Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new...

Keywords: HPC, high performance computer, Unix, Linux, Software Carpentry

Resource type: video, guide

Basic Linux/Unix commands https://dresa.org.au/materials/basic-linux-unix-commands A series of eight videos (each between 5 and 10 minutes long) following the content of the Software Carpentry workshop ["The Unix Shell"](https://swcarpentry.github.io/shell-novice/). Sessions 1, 2 and 3 provide instructions on the minimal level of Linux/Unix commands recommended for new users of HPC. 1 – An overview of how to find out where a user is in the filesystem, list the files there, and how to get help on Unix commands 2 – How to move around the file system and change into other directories 3 – Explains the difference between an absolute and relative path 4 – Overview of how to create new directories, and to create and edit new files with nano 5 – How to use the vi editor to edit files 6 – Overview of file viewers available 7 – How to copy and move files and directories 8 – How to remove files and directories Further details and exercises with solutions can be found on the Software Carpentry "The Unix Shell" page (https://swcarpentry.github.io/shell-novice/) QCIF Training (training@qcif.edu.au) HPC, high performance computer, Unix, Linux, Software Carpentry
Transferring files and data

A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer.

Keywords: sftp, file transfer, HPC, high performance computer

Resource type: video, guide

Transferring files and data https://dresa.org.au/materials/transferring-files-and-data A short video outlining the basics on how to use FileZilla to establish a secure file transfer protocol (sftp) connection to HPC to use a drag and drop interface to transfer files between the HPC and a desktop computer. QCIF Training (training@qcif.edu.au) sftp, file transfer, HPC, high performance computer
Connecting to HPC

A series of three short videos introducing how to use PuTTY to connect from a Windows PC to a secure HPC (high performance computing) cluster.

1 - The very basics on how to establish a connection to HPC.
2 - How to add more specific options for the connection to HPC.
3 - How to save the...

Keywords: HPC, high performance computer, ssh

Resource type: video, guide

Connecting to HPC https://dresa.org.au/materials/connecting-to-hpc A series of three short videos introducing how to use PuTTY to connect from a Windows PC to a secure HPC (high performance computing) cluster. 1 - The very basics on how to establish a connection to HPC. 2 - How to add more specific options for the connection to HPC. 3 - How to save the details and options for a connection for future use. QCIF Training (training@qcif.edu.au) HPC, high performance computer, ssh
Use the Trove Newspaper & Gazette Harvester (web app version)

This video shows how you can use the web app version of the Trove Newspaper & Gazette Harvester to download large quantities of digitised newspaper articles from Trove. Just give it a search from the Trove web interface, and the harvester will...

Keywords: Trove, newspapers, GLAM Workbench, HASS

Resource type: video

Use the Trove Newspaper & Gazette Harvester (web app version) https://dresa.org.au/materials/use-the-trove-newspaper-gazette-harvester-web-app-version-to-download-large-quantities-of-digitised-articles This video shows how you can use the web app version of the [Trove Newspaper & Gazette Harvester](https://glam-workbench.net/trove-harvester/) to download large quantities of digitised newspaper articles from Trove. Just give it a search from the Trove web interface, and the harvester will save the metadata of all the articles from the search results in a CSV (spreadsheet) file for further analysis. You can also save the full text of every article, as well as copies of the articles as JPG images, and even PDFs. The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: [https://glam-workbench.net/](https://glam-workbench.net/) Tim Sherratt (tim@timsherratt.org and @wragge on Twitter) Trove, newspapers, GLAM Workbench, HASS ugrad masters phd ecr researcher support
Use QueryPic to visualise searches in Trove's digitised newspapers (part 2)

This video shows how you can construct and visualise more complex searches for digitised newspaper articles in Trove using QueryPic (see part 1 for the basics). This includes limiting the date range of your query, and changing the time...

Keywords: Trove, GLAM Workbench, visualisation, newspapers, HASS

Resource type: video

Use QueryPic to visualise searches in Trove's digitised newspapers (part 2) https://dresa.org.au/materials/use-querypic-to-visualise-searches-in-trove-s-digitised-newspapers-part-2 This video shows how you can construct and visualise more complex searches for digitised newspaper articles in Trove using [QueryPic](https://glam-workbench.net/trove-newspapers/#querypic) (see part 1 for the basics). This includes limiting the date range of your query, and changing the time scale to zoom in and out of your search results. The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: https://glam-workbench.net/ Tim Sherratt (tim@timsherratt.org and @wragge on Twitter) Trove, GLAM Workbench, visualisation, newspapers, HASS ugrad masters phd ecr researcher
Use QueryPic to visualise searches in Trove's digitised newspapers (part 1)

This video demonstrates how to use the GLAM Workbench to visualise searches for digitised newspaper articles in Trove. Using the latest version of QueryPic, we can explore the complete result set, showing how the number of matching articles...

Keywords: Trove, GLAM Workbench, visualisation, newspapers, HASS

Resource type: video

Use QueryPic to visualise searches in Trove's digitised newspapers (part 1) https://dresa.org.au/materials/use-querypic-to-visualise-searches-in-trove-s-digitised-newspapers-part-1 This video demonstrates how to use the GLAM Workbench to visualise searches for digitised newspaper articles in Trove. Using the latest version of [QueryPic](https://glam-workbench.net/trove-newspapers/#querypic), we can explore the complete result set, showing how the number of matching articles changes over time. We can even compare queries to visualise changes in language or technology. It's a great way to start exploring the possibilities of GLAM data. The GLAM Workbench is a collection of tools, examples, tutorials, and apps that help you make use of collection data from GLAM organisations (Galleries, Libraries, Archives, and Museums). See: https://glam-workbench.net/ Tim Sherratt (tim@timsherratt.org & @wragge on Twitter) Trove, GLAM Workbench, visualisation, newspapers, HASS ugrad masters ecr researcher
Research Data Governance

This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders.

**Cite...

Keywords: data governance, research data

Resource type: video

Research Data Governance https://dresa.org.au/materials/research-data-governance This video contains key information for those who make research data-related decisions. It will help project leaders to start investigating ways to develop their own data governance policy, roles and responsibilities and procedures with the input of appropriate stakeholders. **Cite as** Australian Research Data Commons. (2021, June 30). Research Data Governance. Zenodo. https://doi.org/10.5281/zenodo.5044585 ARDC contact: https://ardc.edu.au/contact-us Max Wilkinson Shannon Callaghan Jo Savill Kristan Kang Kerry Levett Keith Russell Natasha Simons data governance, research data ecr researcher support
How can Software Containers help your Research?

This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility.

Software Containers in research are a solution that addresses the challenge of...

Keywords: Containers, software containers, reproducibility, replicable computational environment, software, research, reusable, cloud, standardisation

Resource type: video

How can Software Containers help your Research? https://dresa.org.au/materials/how-can-software-containers-help-your-research This video explains software containers to a research audience. It is an introduction to why containers are beneficial for research. These benefits are standardisation, portability, reliability and reproducibility. Software Containers in research are a solution that addresses the challenge of a replicable computational environment and supports reproducibility of research results. Understanding the concept of software containers enables researchers to better communicate their research needs with their colleagues and other researchers using and developing containers. **Cite as** Australian Research Data Commons. (2021, July 26). How can software containers help your research?. Zenodo. https://doi.org/10.5281/zenodo.5091260 Contact us: https://ardc.edu.au/contact-us/ Containers, software containers, reproducibility, replicable computational environment, software, research, reusable, cloud, standardisation phd ecr researcher support
Merit Allocation Training for 2022

This merit allocation training session provides critical information for researchers considering to apply for time on Pawsey’s new Setonix supercomputer in 2022.

Keywords: supercomputer, supercomputing, merit allocation, allocation

Resource type: video

Merit Allocation Training for 2022 https://dresa.org.au/materials/merit-allocation-training-for-2022 This merit allocation training session provides critical information for researchers considering to apply for time on Pawsey’s new Setonix supercomputer in 2022. training@pawsey.org.au supercomputer, supercomputing, merit allocation, allocation
WEBINAR: Getting started with deep learning

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021.

Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces...

Keywords: Deep learning, Bioinformatics, Machine learning

Resource type: video, presentation

WEBINAR: Getting started with deep learning https://dresa.org.au/materials/webinar-getting-started-with-deep-learning This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021. Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep learning ‘in a nutshell’ and provides tips on which concepts and skills you will need to know to build a deep learning application. The presentation also provides pointers to various resources you can use to get started in deep learning. The webinar is 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 Deep Learning - 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/I1TmpnZUuiQ Melissa Burke (melissa@biocommons.org.au) Deep learning, Bioinformatics, Machine learning
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: Command line, Bioinformatics

Resource type: video, presentation

WEBINAR: Getting started with command line bioinformatics https://dresa.org.au/materials/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 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 (melissa@biocommons.org.au) Command line, Bioinformatics
Australian BioCommons YouTube Channel

The Australian BioCommons YouTube channel hosts a collection of recorded webinars on a variety of bioinformatics topics from genomics, to metabolomics, containers, machine learning and more.

Keywords: Bioinformatics

Resource type: video

Australian BioCommons YouTube Channel https://dresa.org.au/materials/australian-biocommons-youtube-channel The Australian BioCommons YouTube channel hosts a collection of recorded webinars on a variety of bioinformatics topics from genomics, to metabolomics, containers, machine learning and more. Melissa (melissa@biocommons.org.au) Bioinformatics