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Hands-on for 'Somatic Variant Discovery from WES Data Using Control-FREEC' tutorial

The questions this addresses are:
- What are the specific challenges in locating human Copy Number Variances (hCNVs)?
- How to preprocess the sequenced reads for hCNVs detection?
- How can you detect the hCNVs in/from tumor and normal tissue of the same individual?
- How can you visualise...

Scientific topics: Genetic variation

Keywords: variant-analysis

Resource type: hands-on tutorial

RDMbites: Sensitive data

The RDMbites playlist for learning how to manage sensitive data.

Keywords: sensitive data, data management

Resource type: Video

The essentials of DUO codes

The European Genome-phenome Archive (EGA) offers permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data from research projects and healthcare studies.

During this webinar, the speaker will:
- Introduce the audience to...

Scientific topics: Genomics, Bioinformatics

Keywords: bioinformatics, Genomics

Resource type: Video

Introduction to the EGA and its Ecosystem of Tools

The European Genome-phenome Archive (EGA) is a resource for archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and...

Scientific topics: Bioinformatics, Genomics

Keywords: e-learning, bioinformatics, Genomics

Resource type: Video

Hands-on for 'Trajectory Analysis using Monocle3 ' tutorial

The questions this addresses are:
- How can I prepare input files for Monocle starting from an AnnData object?
- How can I infer lineage relationships between clusters, without a time series?
- What can trajectory analysis tell us?

\nThe objectives are:
- Identify which operations to...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, trajectory-analysis, paper-replication

Resource type: hands-on tutorial

Slides for 'Trajectory analysis' tutorial

The questions this addresses are:
- What is trajectory analysis?
- What are the main methods of trajectory inference?
- How are the decisions about the trajectory analysis made?
- What to take into account when choosing the method for your data?

\nThe objectives are:
- Become familiar with...

Scientific topics: Transcriptomics

Keywords: transcriptomics

Resource type: slides

Hands-on for 'Evaluating and ranking a set of pathways based on multiple metrics' tutorial

The questions this addresses are:
- How to evaluate a set of heterologous pathways ?

\nThe objectives are:
- Calculate the production flux of the lycopene target molecule using Flux Balance Analysis tool.
- Compute thermodynamics values to optimize the yield of the reaction producing the...

Keywords: synthetic-biology

Resource type: hands-on tutorial

Hands-on for 'Teaching online' tutorial

The questions this addresses are:
- What are the different ways of teaching online?
- How Galaxy can be used to teach online?

\nThe objectives are:
- List different ways to teach online
- Use Galaxy to teach online

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Hybrid training' tutorial

The questions this addresses are:
- What is hybrid training?
- How to deliver hybrid training using Galaxy?
- What should be prepared for an hybrid training event?

\nThe objectives are:
- Describe hybrid training
- Organize an hybrid training event using Galaxy

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Motivation and Demotivation' tutorial

The questions this addresses are:
- What is motivation and demotivation?
- How do motivation and demotivation impact learning processes?
- What can instructors do to motivate learners?

\nThe objectives are:
- List factors of motivation and demotivation
- Identify what instructors can do to...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Training techniques to enhance learner participation and engagement' tutorial

The questions this addresses are:
- What does make a training effective?
- How can instructors enhance learner participation and engagement?

\nThe objectives are:
- Describe what makes training effective
- Describe what makes a trainer effective
- Identify some strategies that facilitate...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Teaching experiences' tutorial

The questions this addresses are:
- How to teach using Galaxy?
- What are the different practises?

\nThe objectives are:
- Learn how others teach using Galaxy

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Live Coding is a Skill' tutorial

The questions this addresses are:
- Why do we teach programming using participatory live coding?

\nThe objectives are:
- Explain the advantages and limitations of participatory live coding.
- Summarize the key dos and do nots of participatory live coding.
- Demonstrate participatory live...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Assessment and feedback in training and teachings' tutorial

The questions this addresses are:
- What are the different types of feedback?
- When do get and receive feedback?
- For which purpose do we need feedback?

\nThe objectives are:
- Describe the differences between formative and summative assessment
- Explain why frequent feedback is...

Keywords: teaching

Resource type: hands-on tutorial

Hands-on for 'Design and plan session, course, materials' tutorial

The questions this addresses are:
- Is the structured approach to course design?
- How to articulate learning outcomes commensurate with the cognitive complexity of the target learning?
- How to devise learning experiences and course content?
- What are the steps that can help trainers...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Principles of learning and how they apply to training and teaching' tutorial

The questions this addresses are:
- What are the main principles that drive learning?
- How can these principles be applied to training and teaching?

\nThe objectives are:
- Describe how learning works according to a few learning models
- Explain how learning models can help you improve...

Keywords: contributing

Resource type: hands-on tutorial

Slides for 'Overview of the Galaxy Training Material for Instructors' tutorial

The questions this addresses are:
- How can I use the GTN for teaching?
- What resources are available?
- Why is it a good choice?

Keywords: teaching

Resource type: slides

Hands-on for 'Deploying Tailscale/Headscale for private mesh networking' tutorial

The questions this addresses are:
- What is Tailscale?
- When is it useful?
- Is it right for me?

\nThe objectives are:
- Setup a tailnet across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

Hands-on for 'Deploying Wireguard for private mesh networking' tutorial

The questions this addresses are:
- What is wireguard?
- When is it useful?
- Is it right for me?

\nThe objectives are:
- Setup a wireguard mesh across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.

Event description 

Bioinformatics workflows can...

Keywords: Bioinformatics, Workflows, Nextflow, Containerisation

bio-tools - EDAM drop-in hackathon - discussions

bio.tools, EDAM drop-in hackathon and discussions

Data clearinghouse, validation and curation of BioSamples - ENA - Breeding API endpoints - MAR databases

 

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases
 

Prototyping the new PSICQUIC 2-0

 

Prototyping the new PSICQUIC 2.0
 

WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

  • Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

Hands-on for 'Combining datasets after pre-processing' tutorial

The questions this addresses are:
- I have some AnnData files from different samples that I want to combine into a single file. How can I combine these and label them within the object?

\nThe objectives are:
- Combine data matrices from different samples in the same experiment
- Label the...

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, español

Resource type: hands-on tutorial

Hands-on for 'Inferring Trajectories using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

\nThe objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: transcriptomics, single-cell, 10x, paper-replication, interactive-tools

Resource type: hands-on tutorial

Hands-on for 'Comparative gene analysis in unannotated genomes' tutorial

The questions this addresses are:
- I have several genomes assemblies that are not annoatated (or I do not trust annotations)
- I am interested to compare structure of a particular gene across these genome assemblies
- How do I do that?

\nThe objectives are:
- Provide a quick method for...

Keywords: genome-annotation, evolution, annotation, vgp, cookbook, eukaryote, prokaryote

Resource type: hands-on tutorial

WEBINAR: Getting started with whole genome mapping and variant calling on the command line

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.

Event description 

Life scientists are increasingly using whole genome...

Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows

Getting Started With BioMedIT

No description provided.

SPARQL endpoints at BiGCaT

Lecture discussing the SPARQL endpoints provided by the Maastricht Universty Dept. of Bioinformatics, BiGCaT.

Keywords: WikiPathways, AOP-Wiki, ChEMBL, SPARQL, chemistry, cheminformatics