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26 materials found

Scientific topics: Pathway or network  or Genetic variation 


Hands-on for 'From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis' tutorial

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

Hands-on for 'Exome sequencing data analysis for diagnosing a genetic disease' 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

Hands-on for 'Mapping and molecular identification of phenotype-causing mutations' 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

Hands-on for 'Identification of somatic and germline variants from tumor and normal sample pairs' 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

Hands-on for 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' 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

Hands-on for 'Trio Analysis using Synthetic Datasets from RD-Connect GPAP' 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

Hands-on for 'M. tuberculosis Variant Analysis' 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

Hands-on for 'Microbial Variant Calling' 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

Hands-on for 'Calling variants in non-diploid systems' 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

Hands-on for 'Calling very rare variants' tutorial

The questions this addresses are:
- What frequency of variants is so low that it is obscured by sequencing error rate?
- What are the different types of consensus sequences produced from duplex sequencing?

\nThe objectives are:
- Processing raw duplex sequencing data into consensus...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Hands-on for 'Calling variants in diploid systems' tutorial

The questions this addresses are:
- How to find variable sites in diploid genomes?

\nThe objectives are:
- Identification of genetic variations using variant calling

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

Introduction to 'Variant Analysis'

Slides for Variant Analysis

Scientific topics: Genetic variation

Resource type: slides

WORKSHOP: Variant calling in humans, animals and plants with Galaxy

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...

Scientific topics: Genetic variation

Keywords: Variant calling

How to use V-pipe (SARS-CoV-2 data)

This tutorial demonstrate how to use V-pipe - Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.

For the purpose of this toturial, we use the sars-cov2 branch of V-pipe and analyse SARS-CoV-2 runs downloaded from NCBI SRA.

Scientific topics: Workflows, Genetic variation, Virology

Operations: Read pre-processing, Alignment, Variant calling

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.

Scientific topics: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

Introducing Bivi.co

Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

enRoute: BioVis Best Paper

Alexander Lex (http://alexander-lex.com/) talks about enRoute, a tool for dynamic path extraction from biological pathway maps for in-depth experimental data analysis. He highlights the inherent problem with correlating real-life heterogeneous data to pathways, namely that they rarely follow the...

Scientific topics: Pathway or network

Keywords: Pathway

Resource type: Video

Biological Networks

Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction...

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Pathway

Resource type: Video

BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BioLayout Express 3D

Derek Wright discusses the BioLayout Express visualisation tool at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Genome, Pathway

Resource type: Video

BiVi theme: Pathways

Prof Tom Freeman discusses bio-visualisation within the Pathway theme at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Pathway

Resource type: Video

Reactome

Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Pathway, Databases

Resource type: Slideshow

BioJS

Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Pathway visualization in the Reactome pathway database

Reactome provides curated human biological pathways representing the consensus view of the molecular events involved. Pathway Diagrams show mechanistic details, using a style based on SBGN. A unique Overview represents all pathways in a single view. Analysis results and expression data are...

Scientific topics: Pathway or network

Keywords: Pathway

Resource type: Video

Web-based Tools for Integrative Analysis of Pancreatic Cancer Data

Poster presentation at 3rd BiVi in April 2017.Presenitng a suite of web applications, developed for the PRECISION-Parc initiative, to provide integrative analyses of genomic and transcription data from patient primary samples, cell lines and xenografts, as well as clinical data on patient...

Scientific topics: Pathway or network

Keywords: Genome, Pathway

Resource type: Poster