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WEBINAR: A practical guide to AI tools for life scientists

This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024.
Event description
The widespread availability and application of AI tools like ChatGPT have fundamentally...

Keywords: Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT

WEBINAR: A practical guide to AI tools for life scientists https://dresa.org.au/materials/webinar-a-practical-guide-to-ai-tools-for-life-scientists This record includes training materials associated with the Australian BioCommons webinar ‘A practical guide to AI tools for life scientists’. This webinar took place on 8 May 2024. Event description The widespread availability and application of AI tools like ChatGPT have fundamentally transformed our approach to work, creativity, learning, and communication. In the realm of scientific research, the impact of AI extends far beyond mere promises, already catalysing significant advances and discoveries. This talk will explore how AI is reshaping scientific exploration and innovation. We explore how AI can accelerate research processes, from data analysis and code writing to hypothesis development. We will present some of the available and emerging AI and how we might effectively leverage these tools while acknowledging their limitations. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Speaker: Dr Michael Kuiper, Principal Research Scientist in Computational Biology and acting Group Leader of the Computational Modelling (CM) group at Data61 of CSIRO.  Host: Dr Patrick Capon, 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. 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. Kuiper_May2024_b_version: A PDF copy of the slides presented during the webinar. Q_and_A_AI-life-scientists: PDF copy of questions and answers from the webinar Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/NbYvq3OLEfo   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Machine Learning, Artificial Intelligence, ChatGPT
Wildlife Insights training videos

A series of videos that provide tutorials on use of the Wildlife Insights camera trap data platform, and how to manage camera trap data in the platform

Keywords: wildlife, Camera traps, Monitoring, monitoring data management, Ecology

Wildlife Insights training videos https://dresa.org.au/materials/wildlife-insights-training-videos A series of videos that provide tutorials on use of the Wildlife Insights camera trap data platform, and how to manage camera trap data in the platform https://groups.google.com/u/0/g/wildlifeinsights?pli=1 wildlife, Camera traps, Monitoring, monitoring data management, Ecology
HeSANDA & Health Data Australia FAQ

This document provides answers to common questions about the Health Studies Australian National Data Asset (HeSANDA), and the Health Data Australia (HDA), including the usage of the health data platform, sharing, contributing and accessing clinital trails data, governance, and potential risks. 

Keywords: HeSANDA, Frequently asked Questions, Health Data Australia, training material

HeSANDA & Health Data Australia FAQ https://dresa.org.au/materials/hesanda-health-data-australia-faq This document provides answers to common questions about the Health Studies Australian National Data Asset (HeSANDA), and the Health Data Australia (HDA), including the usage of the health data platform, sharing, contributing and accessing clinital trails data, governance, and potential risks.  contact@ardc.edu.au Australian Research Data Commons (type: Editor) Australian Clinical Trials Alliance (type: Editor) Melbourne Academic Centre for Health (type: Editor) Mental Health Node (type: Editor) The Queensland Node (type: Editor) Sydney Health Partners Node (type: Editor) Western Australia Node (type: Editor) Monash University and Monash Partners Node (type: Editor) Health Translation South Australia (type: Editor) National Cancer Cooperative Trials Groups (type: Editor) Northern Australia Node (type: Editor) HeSANDA, Frequently asked Questions, Health Data Australia, training material
WEBINAR: MetaboLights: the home for metabolomics experiments and derived information

This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024.
Event description
MetaboLights is an open-access database for metabolomics studies,...

Keywords: Bioinformatics, Metabolomics, Metabolites, Data sharing

WEBINAR: MetaboLights: the home for metabolomics experiments and derived information https://dresa.org.au/materials/webinar-metabolights-the-home-for-metabolomics-experiments-and-derived-information This record includes training materials associated with the Australian BioCommons webinar ‘MetaboLights: the home for metabolomics experiments and derived information’. This webinar took place on 9 April 2024. Event description MetaboLights is an open-access database for metabolomics studies, their raw experimental data and associated metadata. It is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles and locations where available. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information. This webinar will provide an introduction to MetaboLights and how it can be used as: A repository, enabling the metabolomics community to share findings, data and protocols from metabolomics studies. A compound library of curated knowledge about metabolite structures, their reference spectra, as well as their biological roles, locations, concentrations, and raw data from metabolic experiments.  The webinar will provide details about data availability, standards and re-use, as well as guidance on submitting your own metabolomics data. Speaker: Dr Thomas Payne, Scientific Database Curator - MetaboLights, EMBL-EBI Host: Dr Patrick Capon, 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. 2024_MetaboLights_Webinar_TP: 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/aCALHhqxOiM   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Metabolomics, Metabolites, Data sharing
WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data

This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024.
Event description
Multiplexed assays of variant effect (MAVEs) are a family of...

Keywords: Bioinformatics, Genetic variation, Functional annotation, Clinical genetics

WEBINAR: MaveDB: discovery and interpretation of high-throughput functional assay data https://dresa.org.au/materials/webinar-mavedb-discovery-and-interpretation-of-high-throughput-functional-assay-data This record includes training materials associated with the Australian BioCommons webinar ‘MaveDB: discovery and interpretation of high-throughput functional assay data’. This webinar took place on 26 March 2024. Event description Multiplexed assays of variant effect (MAVEs) are a family of experimental techniques that measure all single amino acid or single nucleotide changes in a gene or other functional element. MaveDB is an international community database that enables discovery and reuse of data from these experiments. It provides a platform for integrating large-scale measurements of sequence variant impact with applications that can be used to interpret the data for basic and clinical research. In this webinar we consider:  What are MAVEs and how are the experiments performed? How much MAVE data is available in MaveDB and how is it organised? Who can submit datasets to MaveDB? What are some of the clinical applications for MAVEs and how is the data being used to understand patient variants?   Speaker: Dr Alan Rubin, Senior Research Officer, WEHI  Host: Dr Melissa Burke, Australian BioCommons   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. MAVEDB_slides: 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/BXGQ2IuDnGE   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Genetic variation, Functional annotation, Clinical genetics
WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share

This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024.
Event description
The Australian BioCommons Leadership Share (ABLeS) supports...

Keywords: Bioinformatics, Computational biology, Computational infrastructure

WEBINAR: Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share https://dresa.org.au/materials/webinar-scaling-up-bioinformatics-with-ables-the-australian-biocommons-leadership-share This record includes training materials associated with the Australian BioCommons webinar ‘Scaling up bioinformatics with ABLeS, the Australian BioCommons Leadership Share’. This webinar took place on 12 March 2024. Event description The Australian BioCommons Leadership Share (ABLeS) supports access to, and efficient use of, national computational systems for big-data bioinformatics. Designed for established life sciences projects, groups, institutes and consortia, ABLeS can be used to facilitate software optimisation and scaling, implementation of optimised software for production analyses, and creation of reference data. This webinar highlights how ABLeS is being used by life science communities across Australia to access and leverage bioinformatics at scale. We’ll explain the structure of the ABLeS program and how your life science community can get involved, as well as providing a breakdown of the program expectations and the support available from the BioCommons and our partners. Community members making use of ABLeS will share their perspective on the program, and the research outcomes that have resulted. ABLeS is supported by the Australian BioCommons in partnership with Bioplatforms Australia, the National Computational Infrastructure, and the Pawsey Supercomputing Centre. Speakers: Australian BioCommons: Dr Steven Manos Dr Johan Gustafsson Dr Ziad Al Bkhetan   ABLeS users: Dr Hardip Patel, National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University Chelsea Mayoh, Zero Childhood Cancer, Children's Cancer Institute Theodore Allnutt, Royal Botanic Gardens Victoria 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. BioCommons_ABLeS: A PDF copy of the slides presented by the BioCommons team during the webinar. Mayoh_ABLeS: A PDF copy of the slides presented by Chelsea Mayoh   Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/Eb0z2-yaJbY   Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Computational biology, Computational infrastructure
WEBINAR: Multivariate integration of multi-omics data with mixOmics

This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024.
Event description
Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of...

Keywords: Bioinformatics, Omics, Multiomics, Multi-omics, Data integration

WEBINAR: Multivariate integration of multi-omics data with mixOmics https://dresa.org.au/materials/webinar-multivariate-integration-of-multi-omics-data-with-mixomics This record includes training materials associated with the Australian BioCommons webinar ‘Multivariate integration of multi-omics data with mixOmics’. This webinar took place on 6 March 2024. Event description Multi-omics data (eg. transcriptomics, proteomics) collected from the same set of biospecimens or individuals is a powerful way to understand the underlying molecular mechanisms of a biological system.  mixOmics, a popular R package, integrates omics data from a wide range of sources into a single, unified view making it easier to explore and reveal interactions between omics layers. It overcomes many of the challenges of multi-omic data integration arising from data that are complex and large, with few samples (<50) and many molecules (>10,000), and generated using different technologies.  Prof Kim-Anh Lê Cao, head of the mixOmics team, is delivering this webinar to outline the different methods implemented in mixOmics and how statistical data integration is defined in this context. She will demonstrate how these approaches are applied to analysis of different multi-omics studies and outline the latest methodological developments in this area. From a study of human newborns, to multi-omics microbiomes, and multi-omics in single cells, these examples illustrate how mixOmics is used to perform variable selection and identify a signature of omics markers that characterise a specific phenotype or disease status. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Speaker: Prof Kim-Anh Lê Cao, Director of Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne. Host: 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. 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. Mixomics_BioCommons: 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/5XpmQ5X89lA Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Omics, Multiomics, Multi-omics, Data integration
Tutorials to learn how to use STAN

Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics.

Keywords: Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB

Tutorials to learn how to use STAN https://dresa.org.au/materials/tutorials-to-learn-how-to-use-stan Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics. https://mc-stan.org/about/team/ Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB
Open Ecoacoustics make your own recogniser

Includes the requirements and practical steps required to make your own automated call recogniser using a convolution neural network.

The "Requirements" section includes demo data and requirements for the data you should include to develop your own recogniser as well as links to Anaconda &...

Keywords: Ecoacoustics, call recogniser, convolutional neural network

Open Ecoacoustics make your own recogniser https://dresa.org.au/materials/open-ecoacoustics-make-your-own-recogniser Includes the requirements and practical steps required to make your own automated call recogniser using a convolution neural network. The "Requirements" section includes demo data and requirements for the data you should include to develop your own recogniser as well as links to Anaconda & Raven Lite software. The "Practical Steps" provides instructions to run the required Jupyter notebook to build a recogniser with CNN. * Note additional AI methods will be available soon https://openecoacoustics.org/contact/ Ecoacoustics, call recogniser, convolutional neural network
Open Ecoacoustics wrangling sound files

An introduction to slicing, dicing, chopping, resampling, compressing etc sound files with an introduction to command line and graphical tools.

A "Requirements" section with demo data, file dependencies, and required software.

A "Presentation" section with an online introduction to storing...

Keywords: Ecoacoustics, sound files, data wrangling

Open Ecoacoustics wrangling sound files https://dresa.org.au/materials/open-ecoacoustics-wrangling-sound-files An introduction to slicing, dicing, chopping, resampling, compressing etc sound files with an introduction to command line and graphical tools. A "Requirements" section with demo data, file dependencies, and required software. A "Presentation" section with an online introduction to storing data, repairing data and segmenting files. A "Practical" section inclusive of setup, Terminal use, manipulating files with FFmpeg, using the AnalysisPrograms audio cutter, run EMU software https://openecoacoustics.org/contact/ Ecoacoustics, sound files, data wrangling
Open Ecoacoustics acoustic indices

Provides an introduction to and generation of false-colour spectrograms and indices.

Includes a "Requirements" section where demo audio files, other dependencies and required software.

Includes a "Presentation" section providing an online presentation on false colour...

Keywords: Ecoacoustics, false-colour spectrograms, acoustic indices

Open Ecoacoustics acoustic indices https://dresa.org.au/materials/open-ecoacoustics-acoustic-indices Provides an introduction to and generation of false-colour spectrograms and indices. Includes a "Requirements" section where demo audio files, other dependencies and required software. Includes a "Presentation" section providing an online presentation on false colour spectrograms. Includes a "Practical" section that provides the setup, use of terminal, Analysis Programs software, and calculation of acoustic indices. https://openecoacoustics.org/contact/ Ecoacoustics, false-colour spectrograms, acoustic indices
Open Ecoacoustics recording and labelling

This module includes recommendations for deployment, recording and labelling sounds, playing those sounds and annotation using Audacity and Raven software.

The "Requirements" section includes downloads of example data, required dependencies and software.

The "Presentation" walks through an...

Keywords: Ecoacoustics, recording sound, labelling sound, spectrograms

Open Ecoacoustics recording and labelling https://dresa.org.au/materials/open-ecoacoustics-recording-and-labelling This module includes recommendations for deployment, recording and labelling sounds, playing those sounds and annotation using Audacity and Raven software. The "Requirements" section includes downloads of example data, required dependencies and software. The "Presentation" walks through an online presentation with recommendations recorder deployment recommendations, annotation, raven software, & manual validation The "Practical" includes setup, single species annotation of spectrograms, multi-species, and generating images https://openecoacoustics.org/contact/ Ecoacoustics, recording sound, labelling sound, spectrograms
Open Ecoacoustics sound basics

This online presentation provides a review of five key concepts related to ecoacoustics: 1. Decibels, 2. clipping and gain, 3. ADC: Sample rate & bit depth, 4. Fast Fourier Transform (FFT), and 5. Spectrograms: time / frequency trade off.

Keywords: Ecoacoustics, sound basics, decibels, gain, sample rate, FFT, spectrograms

Open Ecoacoustics sound basics https://dresa.org.au/materials/open-ecoacoustics-sound-basics This online presentation provides a review of five key concepts related to ecoacoustics: 1. Decibels, 2. clipping and gain, 3. ADC: Sample rate & bit depth, 4. Fast Fourier Transform (FFT), and 5. Spectrograms: time / frequency trade off. https://openecoacoustics.org/contact/ Ecoacoustics, sound basics, decibels, gain, sample rate, FFT, spectrograms
Biosecurity Commons written support material

A variety of written material describing the fundamentals of the workflows available on Biosecurity Commons as well as guides to navigating the platform.

Includes: Risk Mapping, Dispersal Modelling, Surveillance Design, Impact Analysis and Proof of Freedom.

Keywords: Biosecurity Commons, Biosecurity, risk mapping, Species Distribution Modelling, dispersal modelling, surveillance design, impact analysis, proof of freedom

Biosecurity Commons written support material https://dresa.org.au/materials/biosecurity-commons-written-support-material A variety of written material describing the fundamentals of the workflows available on Biosecurity Commons as well as guides to navigating the platform. Includes: Risk Mapping, Dispersal Modelling, Surveillance Design, Impact Analysis and Proof of Freedom. https://www.biosecuritycommons.org.au/contact-us/ Biosecurity Commons, Biosecurity, risk mapping, Species Distribution Modelling, dispersal modelling, surveillance design, impact analysis, proof of freedom professional support ugrad masters mbr phd
Biosecurity Commons YouTube instructional videos

This growing set of instructional videos teaches users how to navigate the platform and how to run the variety of workflows available on the platform. An increasing number of these videos will be embedded into the platform https://app.biosecuritycommons.org.au/

Keywords: Biosecurity, risk mapping, Species Distribution Modelling, Biosecurity Commons

Biosecurity Commons YouTube instructional videos https://dresa.org.au/materials/biosecurity-commons-youtube-instructional-videos This growing set of instructional videos teaches users how to navigate the platform and how to run the variety of workflows available on the platform. An increasing number of these videos will be embedded into the platform https://app.biosecuritycommons.org.au/ https://www.biosecuritycommons.org.au/contact-us/ Biosecurity, risk mapping, Species Distribution Modelling, Biosecurity Commons support professional masters mbr phd
EcoCommons use case estimating % of suitable habitat impacted by bushfires & utility of HCAS

We compare a variety of ways of estimating the percentage of suitable habitat impacted by the massive bushfires in eastern Australia (2019-2020), by comparing different SDM modelling algorithms, and inclusion of the Habitat Condition Assessment System (HCAS) derived variable.

Models were run...

Keywords: Species Distribution Modelling, HCAS, Fire, Ecology, EcoCommons

EcoCommons use case estimating % of suitable habitat impacted by bushfires & utility of HCAS https://dresa.org.au/materials/ecocommons-use-case-estimating-of-suitable-habitat-impacted-by-bushfires-utility-of-hcas We compare a variety of ways of estimating the percentage of suitable habitat impacted by the massive bushfires in eastern Australia (2019-2020), by comparing different SDM modelling algorithms, and inclusion of the Habitat Condition Assessment System (HCAS) derived variable. Models were run using the EcoCommons point-and-click SDM tools, and overlayed with a burnt area map https://researchdata.edu.au/google-earth-engine-map-geebam/1441550 to estimate % of suitable habitat that was impacted. HCAS data available: https://doi.org/10.25919/5j5j-4p06 https://www.ecocommons.org.au/contact/ Species Distribution Modelling, HCAS, Fire, Ecology, EcoCommons
Ecoacoustics & EcoCommons Generalised Dissimilarity Modelling (GDM) use case

This example highlights how data collected with passive acoustic monitoring (PAM) can be used to examine spatial variation in species composition.

This example draws from an R package developed to make GDM more accessible: https://github.com/EcoCommons-Australia/community-modelling

Keywords: Generalised Dissimilarity Modelling, Ecoacoustics, EcoCommons

Ecoacoustics & EcoCommons Generalised Dissimilarity Modelling (GDM) use case https://dresa.org.au/materials/ecoacoustics-ecocommons-generalised-dissimilarity-modelling-gdm-use-case This example highlights how data collected with passive acoustic monitoring (PAM) can be used to examine spatial variation in species composition. This example draws from an R package developed to make GDM more accessible: https://github.com/EcoCommons-Australia/community-modelling https://openecoacoustics.org/contact/ Generalised Dissimilarity Modelling, Ecoacoustics, EcoCommons
Astronomy Data And Computing Services - Upskilling the Australian astronomy community

The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data &...

Keywords: astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material

Astronomy Data And Computing Services - Upskilling the Australian astronomy community https://dresa.org.au/materials/astronomy-data-and-computing-services-upskilling-the-australian-astronomy-community-57afa0b9-77da-4dc1-ad29-25089f19363d The Astronomy Data And Computing Services (ADACS) initiative has been working with the Australian astronomy community for just over 3 years now. Our vision is to deliver astronomy-focused training, support and expertise to maximise the scientific return on investments in astronomical data & computing infrastructure. During these last 3 years, we have delivered dozens of face-to-face, hands-on workshops and created several hours worth of online tutorial materials. This talk will focus on our journey to deliver this computational skills training to the community, exploring how we chose different delivery pathways and content, based both on community input as well as our professional expertise and understanding of existing skill gaps. Most importantly we will discuss our plans for the future and how we are working on actively including the community in developing new training material beyond the usual skills survey. Come along to this talk if you would like to hear about a national effort to deliver computational skills training and would like to know more about potential new avenues to provide just-in-time training and how to collaborate with ADACS.  contact@ardc.edu.au astronomy, data skills, eresearch skills, skills, computational skills, training, skills gaps, astronomy-focused training, training material
HeSANDA Monash Node User Guides

This guide developed by the HeSANDA Monash node provides an overview for users of Health Data Australia (HDA).
HDA helps researchers discover and access health data. HDA is a registry and does not store the data itself but provides descriptions of the data from data owners' publishing partners....

Keywords: Health Data Australia, health data, data request, HDA, HeSANDA, data access

HeSANDA Monash Node User Guides https://dresa.org.au/materials/hesanda-monash-node-user-guides This guide developed by the HeSANDA Monash node provides an overview for users of Health Data Australia (HDA). HDA helps researchers discover and access health data. HDA is a registry and does not store the data itself but provides descriptions of the data from data owners' publishing partners. Using HDA, researchers can search these descriptions, find data of use to do their research, then request access to it. The request will be sent to the owner of the data to review. Data owners receive email notifications about new data requests and can then log into the HDA Data Request platform to review the request and determine whether access can be granted and then respond to the researcher requesting access. If the request is approved, the owner arranges for the researcher to be given access to the data. The dataset descriptions (‘metadata’) contained on HDA help researchers understand the kinds of data that exist and assess whether a dataset may be of value to their research, without the need to actually access the data. In addition to metadata, data owners provide other documentation describing the data they hold, such as study protocols and data dictionaries. Using HDA, researchers can search for data, save their searches, submit and manage data requests. Amany.Gouda-Vossos@ardc.edu.au Health Data Australia, health data, data request, HDA, HeSANDA, data access
Understanding your role as a Data Steward: the role of a Data Steward across the research data management lifecycle

This presentation provides an overview of the role and responsibilities of Data Steward at the University of Adelaide across the six key phases of the research data management lifecycle.

The resource was developed by the University of Adelaide Library in December 2023 as part of the...

Keywords: research data management, RDM, RDM Training, data stewardship, research data governance, role profiles

Resource type: presentation

Understanding your role as a Data Steward: the role of a Data Steward across the research data management lifecycle https://dresa.org.au/materials/understanding-your-role-as-a-data-steward-the-role-of-a-data-steward-across-the-research-data-management-lifecycle This presentation provides an overview of the role and responsibilities of Data Steward at the University of Adelaide across the six key phases of the research data management lifecycle. The resource was developed by the University of Adelaide Library in December 2023 as part of the Institutional Underpinnings program facilitated by the Australian Research Data Commons (ARDC). University of Adelaide Library contact: https://www.adelaide.edu.au/library/ask-library research data management, RDM, RDM Training, data stewardship, research data governance, role profiles mbr phd ecr researcher
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: Launching the new Apollo Service: collaborative genome annotation for Australian researchers

This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021.

Event description 

Genome annotation is crucial to...

Keywords: Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software

WEBINAR: Launching the new Apollo Service: collaborative genome annotation for Australian researchers https://dresa.org.au/materials/webinar-launching-the-new-apollo-service-collaborative-genome-annotation-for-australian-researchers-3d6cb4b6-50b0-4bf4-ad3a-a60c79dc04ff This record includes training materials associated with the Australian BioCommons webinar ‘Launching the new Apollo Service: collaborative genome annotation for Australian researchers’. This webinar/workshop took place on 29 September 2021. Event description  Genome annotation is crucial to defining the function of genomic sequences. Apollo is a popular tool for facilitating real-time collaborative curation and genome annotation editing. The technical obstacles faced by Australian researchers wanting to access and maintain this software have now been solved.  The new Australian Apollo Service can host your genome assembly and supporting evidence files, taking care of all the system administration so you and your team can focus on the annotation curation itself. The Australian BioCommons and partners at QCIF and Pawsey are now offering the Apollo Service free to use for Australian-based research groups and research consortia. As part of this launch, you’ll hear what’s possible from some of the early adopters who helped guide the development of the service. These Australian researchers will highlight the benefits that Apollo is bringing to their genome annotation and curation workflows. Join us to find out how you can get access to the Australian Apollo Service. 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. Degnan Lab - Apollo Launch Webinar (PDF): Slides presented by Professors Sandie and Bernie Degnan Nelson - Apollo Launch Webinar (PDF): Slides presented by Dr Tiffanie Nelson Voelker - Apollo Launch Webinar (PDF): Slides presented by Julia Voelker Rane - Apollo Launch Webinar (PDF): Slides presented by Dr Rahul Rane. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/o8jhRra-x4Y   Melissa Burke (melissa@biocommons.org.au) Genome Annotation, Genomics, Genome curation, Bioinformatics, Apollo software
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
WEBINAR: Where to go when your bioinformatics outgrows your compute

This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.

Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...

Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing

WEBINAR: Where to go when your bioinformatics outgrows your compute https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554 This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021. Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey.  We also describe bioinformatics and computing support services available to Australian researchers.  This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney. 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. Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar. Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/hNTbngSc-W0 Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: High performance bioinformatics: submitting your best NCMAS application

This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021.

Bioinformaticians are increasingly turning to specialised compute infrastructure and...

Keywords: Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS

WEBINAR: High performance bioinformatics: submitting your best NCMAS application https://dresa.org.au/materials/webinar-high-performance-bioinformatics-submitting-your-best-ncmas-application-ee80822f-74ac-41af-a5a4-e162c10e6d78 This record includes training materials associated with the Australian BioCommons webinar ‘High performance bioinformatics: submitting your best NCMAS application’. This webinar took place on 20 August 2021. Bioinformaticians are increasingly turning to specialised compute infrastructure and efficient, scalable workflows as their research becomes more data intensive. Australian researchers that require extensive compute resources to process large datasets can apply for access to national high performance computing facilities (e.g. Pawsey and NCI) to power their research through the National Computational Merit Allocation Scheme (NCMAS). NCMAS is a competitive, merit-based scheme and requires applicants to carefully consider how the compute infrastructure and workflows will be applied.  This webinar provides life science researchers with insights into what makes a strong NCMAS application, with a focus on the technical assessment, and how to design and present effective and efficient bioinformatic workflows for the various national compute facilities. It 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. High performance bioinformatics: submitting your best NCMAS application - slides (PDF and PPTX): Slides presented during the webinar   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/HeFGjguwS0Y Melissa Burke (melissa@biocommons.org.au) Computational Biology, Bioinformatics, High Performance Computing, HPC, NCMAS
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://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) R statistical software, R studio, Tidyverse, Bioinformatics, Data analysis
WEBINAR: Making sense of phosphoproteomics data with Phosphomatics

This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021.

Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating...

Keywords: Phosphoproteomics, Proteomics, Mass spectrometry

WEBINAR: Making sense of phosphoproteomics data with Phosphomatics https://dresa.org.au/materials/webinar-making-sense-of-phosphoproteomics-data-with-phosphomatics-a46784bd-7efe-4018-8893-761d1fcd32ba This record includes training materials associated with the Australian BioCommons webinar  ‘Making sense of phosphoproteomics data with Phosphomatics’. This webinar took place on 2 June 2021. Mass spectrometry-based phosphoproteomics is one of the most powerful tools available for investigating the detailed molecular events that occur in response to cellular stimuli. Experiments can routinely detect and quantify thousands of phosphorylated peptides, and interpreting this data, and extracting biological meaning, remains challenging.  This webinar provides an overview of the phosphoproteomics data analysis website, Phosphomatics, that incorporates a suite of tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results. Phosphomatics can natively import search and quantitation results from major search engines including MaxQuant and Proteome Discoverer and employs intuitive ‘wizards’ to guide users through data preprocessing routines such as filtering, normalization and transformation. A graphical platform of interactive univariate and multivariate analysis features is provided that allow subgroups of the uploaded data containing phosphosites of statistical interest to be created and interrogated through further functional analysis. A range of databases have been integrated that, for example, provide ligand and inhibitor information for key proteins or highlight key modification sites known to be involved in functional state regulation. At each step, published literature is natively incorporated along with a ‘bibliography builder’ that allows references of interest to be assembled and exported in various formats. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis. 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. Phosphomatics -slides  (PDF and PPTX): Slides used in the presentation   Materials shared elsewhere: A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/_WpeL5t2DSI Melissa Burke (melissa@biocommons.org.au) Phosphoproteomics, Proteomics, Mass spectrometry
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...

Keywords: Deep learning, Neural networks, Machine learning

WEBINAR: Getting started with deep learning https://dresa.org.au/materials/webinar-getting-started-with-deep-learning-986aa2d2-594a-4a7f-836c-44d6e9d5d017 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, Neural networks, Machine learning
WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Hybridisation plays an important role in evolution, leading to the exchange of genes...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset https://dresa.org.au/materials/webinar-detection-of-and-phasing-of-hybrid-accessions-in-a-target-capture-dataset-51cc7740-0da1-45f1-95de-f1a47f676053 This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Hybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. Nauheimer_hybphaser_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/japXwTAhA5U Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing
WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Multi-gene datasets used in phylogenetic...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation https://dresa.org.au/materials/webinar-conflict-in-multi-gene-datasets-why-it-happens-and-what-to-do-about-it-deep-coalescence-paralogy-and-reticulation-a6743550-b904-45e1-9635-4e481ee8f739 This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021. Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference. 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. Schmidt-Lebuhn - paralogy lineage sorting reticulation - 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/1bw81q898z8 Melissa Burke (melissa@biocommons.org.au) Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing