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Authors: Coddington, Paul (orcid: 00...  or Bretaudeau, Anthony (orcid:...  or Cytowski, Maciej (orcid: 00...  or Chivvis, Daniel (orcid: 000... 

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
WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description 

Genome annotation is crucial to defining the function of genomic sequences. This process...

Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation

WORKSHOP: Refining genome annotations with Apollo https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo-d8f95fb3-7dc4-40e0-87d5-e7a4b2ceaf16 This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021. Workshop description  Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort. Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations. This workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar. This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) . The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding. The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus Programme of the European Union. 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. Schedule (PDF): A breakdown of the topics and timings for the workshop 2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. Materials shared elsewhere: This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network. Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021 See also: Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012 Melissa Burke (melissa@biocommons.org.au) Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.

MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...

Keywords: Small satellites, metadata, vocabularies, training material

MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration. https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration-49af7d4d-f0d1-4f95-9fbe-afbd45170a6a MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets. A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects. Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure. You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4 contact@ardc.edu.au Small satellites, metadata, vocabularies, training material
WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description

Genome annotation is crucial to defining the function of genomic sequences. This...

Keywords: Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation

WORKSHOP: Refining genome annotations with Apollo https://dresa.org.au/materials/workshop-refining-genome-annotations-with-apollo This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021. **Workshop description** Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort. Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations. This workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar. This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) . The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding. The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus Programme of the European Union. 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. - Schedule (PDF): A breakdown of the topics and timings for the workshop - 2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service - Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. - Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia. **Materials shared elsewhere:** This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network. Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021 See also: Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012 Melissa Burke (melissa@biocommons.org.au) Apollo Software, Bioinformatics, Analysis, Workflows, Genomics, Genome annotation
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
MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration.

MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a...

Keywords: Small satellites, metadata, vocabularies, training material

MetaSat. An open, collaboratively-developed metadata toolkit to support the future of space exploration. https://dresa.org.au/materials/metasat-an-open-collaboratively-developed-metadata-toolkit-to-support-the-future-of-space-exploration MetaSat is an open metadata toolkit for describing small satellite (and even large satellite) missions in a uniform and shareable way. Optimised for small satellite missions, MetaSat fills an informatics gap. Although there have been a number of relevant metadata sets, there has been a longstanding need for a vocabulary to span these community standards. A vocabulary to annotate the data and information outputs of these satellite missions, to enable search across disparate data repositories, and provide support for application of analytical services to retrieved datasets. A common problem among small satellite teams is finding information about how other small satellites were put together, what parts worked well, what weren't compatible, what were the mission goals and outcomes. A lot of this information can be found, but it's not usually described in a consistent and searchable way across projects. MetaSat helps by building a uniform language of description which can be embedded into small satellite databases and tools to connect information across projects. Although a relatively new vocabulary initiative, MetaSat has secured early adoption by SatNOGS, a global network of ground stations that collects, manages & enables access to satellite observations. Also partnering with NASA's Small Satellite Reliability Initiative, and in discussion with NASA concerning implementation of the vocabulary in other areas of its information infrastructure. You can watch the full presentation on YouTube here: https://www.youtube.com/watch?v=uaCOzNL1eh4 contact@ardc.edu.au Small satellites, metadata, vocabularies, training material