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Keywords: fish  or reproducibility  or Data sharing 

7 Steps towards Reproducible Research

This workshop aims to take you further down your reproducibility path, by providing concepts and tools you can use in your everyday workflows. It is discipline and experience agnostic, and no coding experience is needed.

We will also examine how Reproducible Research builds business continuity...

Keywords: reproducibility, Reproducibility, reproducible workflows

Resource type: full-course, tutorial

7 Steps towards Reproducible Research https://dresa.org.au/materials/7-steps-towards-reproducible-research This workshop aims to take you further down your reproducibility path, by providing concepts and tools you can use in your everyday workflows. It is discipline and experience agnostic, and no coding experience is needed. We will also examine how Reproducible Research builds business continuity into your research group, how the culture in your institute ecosystem can affect Reproducibility and how you can identify and address risks to your knowledge. The workshop can be used as self-paced or as an instructor Amanda Miotto - a.miotto@griffith.edu.au reproducibility, Reproducibility, reproducible workflows phd support
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: Establishing Gen3 to enable better human genome data sharing in Australia

This record includes training materials associated with the Australian BioCommons webinar ‘Establishing Gen3 to enable better human genome data sharing in Australia’. This webinar took place on 16 February 2022.

Event description 

Australian human genome initiatives are generating vast amounts...

Keywords: Bioinformatics, Genomics, Human genomics, Digital infrastructure, Gen3, Data sharing, Data management

WEBINAR: Establishing Gen3 to enable better human genome data sharing in Australia https://dresa.org.au/materials/webinar-establishing-gen3-to-enable-better-human-genome-data-sharing-in-australia-d8caf8c8-d447-4218-be01-95dfd0377f3e This record includes training materials associated with the Australian BioCommons webinar ‘Establishing Gen3 to enable better human genome data sharing in Australia’. This webinar took place on 16 February 2022. Event description  Australian human genome initiatives are generating vast amounts of human genome data. There is a desire and need to share data with collaborators but researchers face significant infrastructural, technical and administrative barriers in achieving this. To efficiently share and distribute their genome data they need scalable services and infrastructure that: is easily administered; allows for the efficient data management; enables sharing and interoperability; and is aligned with global standards for human genome data sharing. Australian BioCommons has brought together a team from Zero Childhood Cancer (Zero), the University of Melbourne Centre for Cancer Research (UMCCR) and Australian Access Federation to explore the use of Gen3 technology. Establishing systems for easier management and sharing of their human genome data holdings is no simple task, and the group wants to ensure that other Australian providers and Institutions can benefit from their experience and easily deploy the same solution in the future. Gen3 is an open source software suite that makes use of private and public clouds to tackle the challenges of data management, interoperability, data sharing and analysis. It has been used in several very large NIH-funded projects that collectively house and describe data derived from hundreds of thousands of human samples (e.g. NCI Genomic Data Commons, BioData Catalyst, BloodPAC, BrainCommons, Kids First Data Commons). In this webinar you’ll hear from UMCCR and Zero about their experiences and progress towards establishing Gen3 instances to better enable better human genome data sharing in Australia. They will outline the challenges and opportunities that have arisen through this Australian BioCommons project and demonstrate the capabilities of Gen3 for human genome research. 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. Gen3_Webinar_Slides (PDF): Slides presented during the webinar   Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/1F6B03Byigk Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Genomics, Human genomics, Digital infrastructure, Gen3, Data sharing, Data management
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...

Keywords: containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material

How can software containers help your research? https://dresa.org.au/materials/how-can-software-containers-help-your-research-ca0f9d41-d83b-463b-a548-402c6c642fbf 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. Watch the video here: https://www.youtube.com/watch?v=HelrQnm3v4g If you want to share this video please use this: Australian Research Data Commons, 2021. How can software containers help your research?. [video] Available at: https://www.youtube.com/watch?v=HelrQnm3v4g DOI: http://doi.org/10.5281/zenodo.5091260 [Accessed dd Month YYYY]. contact@ardc.edu.au Martinez, Paula Andrea (type: ProjectLeader) Sam Muirhead (type: Producer) The ARDC Communications Team (type: Editor) The ARDC Skills and Workforce Development Team (type: ProjectMember) The ARDC eResearch Infrastructure & Services (type: ProjectMember) The ARDC Nectar Cloud Services team (type: ProjectMember) containers, software, research, reproducibility, RSE, standard, agility, portable, reusable, code, application, reproducible, standardisation, package, system, cloud, server, version, reliability, program, collaborator, ARDC_AU, training material
CheckEM User Guide

CheckEM is an open-source web based application which provides quality control assessments on metadata and image annotations of fish stereo-imagery. It is available at marine-ecology.shinyapps.io/CheckEM. The application can assess a range of sampling methods and annotation data formats for...

Keywords: stereo-video, fish, annotation

CheckEM User Guide https://dresa.org.au/materials/checkem-user-guide CheckEM is an open-source web based application which provides quality control assessments on metadata and image annotations of fish stereo-imagery. It is available at marine-ecology.shinyapps.io/CheckEM. The application can assess a range of sampling methods and annotation data formats for common inaccuracies made whilst annotating stereo imagery. CheckEM creates interactive plots and tables in a graphical interface, and provides summarised data and a report of potential errors to download. brooke.gibbons@uwa.edu.au stereo-video, fish, annotation
EventMeasure Annotation Guide

EventMeasure annotation guide for baited remote underwater stereo video systems (stereo-BRUVs) for count and length

Keywords: fish, stereo-video, annotation

EventMeasure Annotation Guide https://dresa.org.au/materials/eventmeasure-annotation-guide EventMeasure annotation guide for baited remote underwater stereo video systems (stereo-BRUVs) for count and length tim.langlois@uwa.edu.au fish, stereo-video, annotation
HeSANDA Queensland Node - The importance of data sharing

Hear from Professor John Prins, Health Translation Queensland's Executive Director, talk on the importance of data sharing.

Keywords: Data sharing, research data

HeSANDA Queensland Node - The importance of data sharing https://dresa.org.au/materials/hesanda-queensland-node-the-importance-of-data-sharing Hear from Professor John Prins, Health Translation Queensland's Executive Director, talk on the importance of data sharing. research@healthtranslationqld.org.au Data sharing, research data
Stereo-video workflows for fish and benthic ecologists

Stereo imagery is widely used by research institutions and management bodies around the world as a cost-effective and non-destructive method to research and monitor fish and habitats (Whitmarsh, Fairweather and Huveneers, 2017). Stereo-video can provide accurate and precise size and range...

Keywords: stereo-video, fish, sharks, habitats

Resource type: tutorial

Stereo-video workflows for fish and benthic ecologists https://dresa.org.au/materials/stereo-video-workflows-for-fish-and-benthic-ecologists Stereo imagery is widely used by research institutions and management bodies around the world as a cost-effective and non-destructive method to research and monitor fish and habitats (Whitmarsh, Fairweather and Huveneers, 2017). Stereo-video can provide accurate and precise size and range measurements and can be used to study spatial and temporal patterns in fish assemblages (McLean et al., 2016), habitat composition and complexity (Collins et al., 2017), behaviour (Goetze et al., 2017), responses to anthropogenic pressures (Bosch et al., 2022) and the recovery and growth of benthic fauna (Langlois et al. 2020). It is important that users of stereo-video collect, annotate, quality control and store their data in a consistent manner, to ensure data produced is of the highest quality possible and to enable large scale collaborations. Here we collate existing best practices and propose new tools to equip ecologists to ensure that all aspects of the stereo-video workflow are performed in a consistent way. tim.langlois@uwa.edu.au stereo-video, fish, sharks, habitats
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