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7 materials found

Keywords: fish  or NCMAS 


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
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
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...

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 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 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