This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.
Event description
Biologists need data analysis skills to be able to...
Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.
Event description
bio.tools provides easy access to essential scientific...
Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR
This record includes training materials associated with the Australian BioCommons webinar ‘Protection of genomic data and the Australian Privacy Act: when is genomic data ‘personal information’?’. This webinar took place on 6 April 2022.
Event description
It is easy to assume that genomic data...
Keywords: Bioinformatics, Genomics, Genetic data, Personal information, Health information, Privacy
This record includes training materials associated with the Australian BioCommons workshop ‘Introduction to Metabarcoding using QIIME2’. This workshop took place on 22 February 2022.
Event description
Metabarcoding has revolutionised the study of biodiversity science. By combining DNA taxonomy...
Keywords: Bioinformatics, Analysis, Workflows, Microbial ecology, Metabarcoding, Microbiome
This record includes training materials associated with the Australian BioCommons webinar ‘Conservation genomics in the age of extinction’. This webinar took place on 8 March 2022.
Event description
Biodiversity is crashing and millions of plant and animal species are at the edge of...
Keywords: Conservation genomics, Genomics, Bioinformatics, Sequencing, Threatened Species Initiative, Galaxy 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
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
This record includes training materials associated with the Australian BioCommons workshop ‘Hybrid de novo genome assembly’. This workshop took place on 7 October 2021.
Workshop description
It’s now easier than ever to assemble new reference genomes thanks to hybrid genome assembly approaches...
Keywords: Galaxy Australia, Bioinformatics, Analysis, Workflows, Genomics, Genome assembly, De novo assembly
This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021.
Workshop description
Explore the many useful functions that the Bioconductor...
Keywords: R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
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
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
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
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
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
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
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
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
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
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
This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.
Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...
Keywords: Variant calling, Genetic Variation Analysis, SNP annotation
This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with command line bioinformatics’. This webinar took place on 22 June 2021.
Bioinformatics skills are in demand like never before and biologists are stepping up to the challenge of...
Keywords: Bioinformatics, Command line, Workflows, Bash, Computational biology
The questions this addresses are:
- Learn how to get and use data from the Sequence Read Archive in Galaxy.
\nThe objectives are:
- Understand how Galaxy and the Sequence Read Archive interact.
- Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to...
Scientific topics: Genetic variation
Keywords: variant-analysis, covid19
Resource type: hands-on tutorial
The questions this addresses are:
- How do you identify genetic variants in samples based on exome sequencing data?
- How do you, among the set of detected variants, identify candidate causative variants for a given phenotype/disease?
\nThe objectives are:
- Jointly call variants and...
Scientific topics: Genetic variation
Keywords: variant-analysis
Resource type: hands-on tutorial
The questions this addresses are:
- What is mapping-by-sequencing?
- How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?
\nThe objectives are:
- Use joint variant calling and extraction to facilitate variant comparison across samples
-...
Scientific topics: Genetic variation
Keywords: variant-analysis
Resource type: hands-on tutorial
The questions this addresses are:
- What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?
- How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?
-...
Scientific topics: Genetic variation
Keywords: variant-analysis
Resource type: hands-on tutorial
The questions this addresses are:
- How can we extract annotated allelic variants in SARS-Cov-2 sequences in Galaxy?
- Which tools and workflows can we use to identify SARS-CoV-2 lineages in Galaxy?
\nThe objectives are:
- Repeat SARS-CoV-2 data preparation
- Select and run workflow to...
Scientific topics: Genetic variation
Keywords: variant-analysis, covid19
Resource type: hands-on tutorial
The questions this addresses are:
- How do you import data from the EGA?
- How to download files with HTSGET in Galaxy?
- How do you pre-process VCFs?
- How do you identify causative variants?
\nThe objectives are:
- Requesting DAC access and importing data from the EGA.
- Pre-process...
Scientific topics: Genetic variation
Keywords: variant-analysis, cancer, cyoa
Resource type: hands-on tutorial
The questions this addresses are:
- How do we detect differences between a set of reads from M. tuberculosis (Mtb) and the Mtb reference genome
\nThe objectives are:
- How should we filter those variants
- How can we predict drug resistance from those variants
- How do we annotate those...
Scientific topics: Genetic variation
Keywords: variant-analysis, prokaryote
Resource type: hands-on tutorial
The questions this addresses are:
- How do we detect differences between a set of reads from a microorganism and a reference genome
\nThe objectives are:
- Find variants between a reference genome and a set of reads
- Visualise the SNP in context of the reads aligned to the genome
-...
Scientific topics: Genetic variation
Keywords: variant-analysis, prokaryote
Resource type: hands-on tutorial
The questions this addresses are:
- How does frequency of mitochondrial polymorphisms change from mother to child?
\nThe objectives are:
- Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
Scientific topics: Genetic variation
Keywords: variant-analysis, prokaryote
Resource type: hands-on tutorial