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Keywords: fish  or reproducibility  or Galaxy 

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://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) Bioinformatics, Data analysis, Galaxy
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: Managing hands-on data analysis training with Galaxy

This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023.

Event description 

Looking for flexible, scalable, real-world solutions that enable data analysis skills to...

Keywords: Bioinformatics, Galaxy, Training, Training infrastructure

WEBINAR: Managing hands-on data analysis training with Galaxy https://dresa.org.au/materials/webinar-managing-hands-on-data-analysis-training-with-galaxy-6d3e8b36-69f2-4fec-9290-d5acd068624a This record includes training materials associated with the Australian BioCommons webinar ‘Managing hands-on data analysis training with Galaxy’. This webinar took place on 25 July 2023. Event description  Looking for flexible, scalable, real-world solutions that enable data analysis skills to be taught to anyone and anywhere?  Galaxy Australia, a national web service supporting 1000s of bioinformatics tools and workflows is a fantastic solution for training on bioinformatics concepts. Their "Training Infrastructure as a Service”, or TIaaS provides free compute and back-end support for data analysis training. It is paired with 100’s of easy-to-follow tutorials developed and maintained by the worldwide community on the Galaxy Training Network (GTN). TIaaS frees trainers from setting up and maintaining computational resources for their training events so that they can focus on student needs and learning outcomes This webinar will show you how to make the most of Galaxy Australia, TIaaS and the Galaxy Training Network for bioinformatics training. We’ll highlight all the nifty features you can use to plan, manage and deliver training to any size audience efficiently. 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. Managing data analysis training with Galaxy_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/VNE0pF6Nqgw Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Galaxy, Training, Training infrastructure
WORKSHOP: Translating workflows into Nextflow with Janis

This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023.

Event description

Bioinformatics workflows are critical for reproducibly transferring methodologies...

Keywords: Bioinformatics, Workflows, Nextflow, CWL, Galaxy

WORKSHOP: Translating workflows into Nextflow with Janis https://dresa.org.au/materials/workshop-translating-workflows-into-nextflow-with-janis-36386c6d-f9a2-4b4d-afa9-062ce3b8ac5d This record includes training materials associated with the Australian BioCommons workshop ‘Translating workflows into Nextflow with Janis’. This workshop took place online on 19 June 2023. Event description Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases.  Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use. This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows. This workshop event and accompanying materials were developed by the Melbourne Bioinformatics and the Peter MacCallum Cancer Centre. The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project funded by the Australian Research Data Commons and NCRIS via Bioplatforms Australia.    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. Intro to Galaxy (PDF): Slides presented during the workshop Intro to CWL (PDF): Slides presented during the workshop Intro to the session & Janis (PDF): Slides presented during the workshop Janis_Schedule (PDF): Schedule for the workshop providing a breakdown of topics and timings Materials shared elsewhere: This workshop follows the accompanying training materials: https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate   A recording of the workshop is available on the Australian BioCommons YouTube channel: https://youtu.be/0IiY1GEx_BY Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Workflows, Nextflow, CWL, Galaxy
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
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