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 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent...
Keywords: Bioinformatics, Data analysis, Galaxy
WORKSHOP: Online data analysis for biologists
https://zenodo.org/records/13948826
https://dresa.org.au/materials/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 21 August 2024.
Topic description
Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent computational biological research. Widely used by researchers world wide, Galaxy gives you access to 1000’s of popular tools for analysis and processing of biological data. It is perfect for working with a wide range of big and small datasets including genome assembly, annotation, epigenetics, metabolomics, metagenomics, proteomics, statistics, transcriptomics, variant analysis and visualisation.
This workshop provides an introduction to using Galaxy and available tools. Using an example dataset, you’ll practice uploading data, choosing and running tools, and viewing the results. We’ll share our top tips for managing your experiments and speeding up your analysis with workflows.
Lead trainer: Dr Gareth Price, Galaxy Australia
Facilitator: Mike Thang, Galaxy Australia / QCIF
Infrastructure provision: Galaxy Australia
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_Online_data_analysis_for_biologists_210824 (PDF): Information about the event logistics including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Schedule_Online_data_analysis_for_biologists_210824 (PDF): Schedule for the workshop providing a breakdown of topics and timings
Materials shared elsewhere:
This workshop is based on the Galaxy Training Network tutorial ‘Galaxy basics for everyone’: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
A recording of this workshop is available on the Australian BioCommons YouTube Channel: https://www.youtube.com/watch?v=PF39KjOvreM
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Thang, Michael
Bioinformatics, Data analysis, Galaxy
WEBINAR: Getting started with R
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not...
Keywords: R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
WEBINAR: Getting started with R
https://zenodo.org/records/5214277
https://dresa.org.au/materials/webinar-getting-started-with-r-1c8f2b21-bc4b-4b42-9a5d-d6096a2afbe6
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with R’. This webinar took place on 16 August 2021.
Data analysis skills are now central to most biological experiments. While Excel can cover some of your data analysis needs, it is not always the best choice, particularly for large and complex datasets.
R is an open-source software and programming language that enables data exploration, statistical analysis visualisation and more. While it is the tool of choice for data analysis, getting started can be a little daunting for those without a background in statistics.
In this webinar Saskia Freytag, an R user with over a decade of experience and member of the Bioconductor Community Advisory Board, will walk you through their hints and tips for getting started with R and data analysis. She’ll cover topics like R Studio and why you need it, where to get help, basic data manipulation, visualisations and extending R with libraries. The webinar will be 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 R - 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/JS7yZw7bnX8
Melissa Burke (melissa@biocommons.org.au)
Freytag, Saskia (orcid: 0000-0002-2185-7068)
R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
Exploratory Data Analysis
This is the second of three modules in our exciting new machine learning workshop series by the Sydney Informatics Hub (SIH).
Module 1: https://youtu.be/dMwHFhKWRRI
Module 3:...
Keywords: Data analysis, training material
Exploratory Data Analysis
https://youtu.be/HVAFflj2PS0
https://dresa.org.au/materials/exploratory-data-analysis
This is the second of three modules in our exciting new machine learning workshop series by the Sydney Informatics Hub (SIH).
**Module 1**: [https://youtu.be/dMwHFhKWRRI](https://youtu.be/dMwHFhKWRRI)
**Module 3**: [https://github.com/Sydney-Informatics-Hub/Module3R](https://github.com/Sydney-Informatics-Hub/Module3R)
*The Sydney Informatics Hub is a Core Research Facility at The University of Sydney, enabling excellence in research* [https://sydney.edu.au/informatics-hub](https://sydney.edu.au/informatics-hub)
sih.training@sydney.edu.au
Zhang, Eden (orcid: 0000-0003-0294-3734)
Mori, Giorgia (orcid: 0000-0003-3469-5632)
Data analysis, training material
National Transfusion Dataset Secure eResearch Platform (SeRP)/SafeHaven Training
A short training video for NTD users on how to access and use the SeRP once data access is granted.
Keywords: research data, Data analysis, research data management
National Transfusion Dataset Secure eResearch Platform (SeRP)/SafeHaven Training
https://www.transfusiondataset.com/training-and-user-guides
https://dresa.org.au/materials/national-transfusion-dataset-secure-eresearch-platform-serp-safehaven-training
A short training video for NTD users on how to access and use the SeRP once data access is granted.
sphpm.ntd@monash.edu
research data, Data analysis, research data management
Introduction to Data Cleaning with OpenRefine
Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data...
Keywords: data skills, Data analysis
Resource type: tutorial
Introduction to Data Cleaning with OpenRefine
https://griffithunilibrary.github.io/data-cleaning-intro/
https://dresa.org.au/materials/introduction-to-data-cleaning-with-openrefine
Learn basic data cleaning techniques in this self-paced online workshop using open data from data.qld.gov.au and open source tool OpenRefine openrefine.org. Learn techniques to prepare messy tabular data for comupational analysis. Of most relevance to HASS disciplines, working with textual data in a structured or semi-structured format.
s.stapleton@griffith.edu.au;
Sharron Stapleton
data skills, Data analysis
mbr
phd
ecr
researcher
support
professional
VOSON Lab Code Blog
The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages.
Keywords: visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics
Resource type: tutorial, other
VOSON Lab Code Blog
https://vosonlab.github.io/
https://dresa.org.au/materials/voson-lab-code-blog
The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages.
robert.ackland@anu.edu.au
visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics
researcher
support
phd
masters
Embracing new solutions for in-situ visualisation
This PPT was used by Jean Favre, senior visualisation software engineer at CSCS, the Swiss National Supercomputing Centre during his presentation at P'Con '21 (Pawsey's first PaCER Conference).
This material discusses the upcoming release of ParaView v5.10, a leading scientific visualisation...
Keywords: ParaView, GPUs, supercomputer, supercomputing, visualisation, data visualisation
Resource type: presentation
Embracing new solutions for in-situ visualisation
https://github.com/jfavre/InSitu/blob/master/InSitu-Revisited.pdf
https://dresa.org.au/materials/embracing-new-solutions-for-in-situ-visualisation
This PPT was used by Jean Favre, senior visualisation software engineer at CSCS, the Swiss National Supercomputing Centre during his presentation at P'Con '21 (Pawsey's first PaCER Conference).
This material discusses the upcoming release of ParaView v5.10, a leading scientific visualisation application. In this release ParaView consolidates its implementation of the Catalyst API, a specification developed for simulations and scientific data producers to analyse and visualise data in situ.
The material reviews some of the terminology and issues of different in-situ visualisation scenarios, then reviews early Data Adaptors for tight-coupling of simulations and visualisation solutions. This is followed by an introduction of Conduit, an intuitive model for describing hierarchical scientific data. Both ParaView-Catalyst and Ascent use Conduit’s Mesh Blueprint, a set of conventions to describe computational simulation meshes.
Finally, the materials present CSCS’ early experience in adopting ParaView-Catalyst and Ascent via two concrete examples of instrumentation of some proxy numerical applications.
training@pawsey.org.au
Jean Favre
ParaView, GPUs, supercomputer, supercomputing, visualisation, data visualisation
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://youtu.be/J_LgNL2EM4M
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://youtu.be/vdyKNowv9gw
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
Galaxy Training
Galaxy is a hosted web-accessible platform that lets you conduct accessible, reproducible, and transparent computational biological research. It is an international, community driven effort to make it easy for life scientists to analyse their data for free and without the need for programmatic...
Keywords: Galaxy Australia, Galaxy Project, Bioinformatics, Data analysis
Galaxy Training
https://training.galaxyproject.org/training-material/
https://dresa.org.au/materials/galaxy-training
Galaxy is a hosted web-accessible platform that lets you conduct accessible, reproducible, and transparent computational biological research. It is an international, community driven effort to make it easy for life scientists to analyse their data for free and without the need for programmatic skills.
This is a collection of tutorials developed and maintained by the worldwide Galaxy community that show you how to analyse a variety of biological data using Galaxy.
Melissa (melissa@biocommons.org.au)
Galaxy Australia, Galaxy Project, Bioinformatics, Data analysis