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17 materials found

Target audience: Bench biologists 


An introduction to MobiDB

In this course you will learn what type of information is stored in the MobiDB database (URL: https://mobidb.org/) that provides predictions and annotations for intrinsically disordered proteins. You will explore the main features of the database, its entries along with the related documentation....

Keywords: intrinsically disordered proteins, Databases, intrinsic disorder prediction, protein sequence

Resource type: Webinar, Training materials

Exploring structural and functional annotations of IDPs with DisProt

In this course you will learn how to explore a DisProt entry, along with its main features (structural and functional annotations). You will also learn how to search the database for specific annotated aspects and how to download the output of a search.

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

An introduction to DisProt

In this course you will learn what type of information is stored in DisProt, gold standard resource of manually curated Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) from the literature. You will explore the main features of the database, its entries and...

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

BLAST and multiple sequence alignment (MSA) programs

Background
The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

Resource type: e-learning

Phylogenetics of animal viral pathogens

Background
The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Resource type: e-learning

UNIX Fundamentals

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge.
The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.
At the end of...

Keywords: Problem based learning, Programming, Unix

Resource type: e-learning

RNA-seq data analysis: from raw reads to differentially expressed genes

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Bioinformatics, Data architecture, analysis and design, RNA, Sequencing

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq

Perl 1 Training Course - For Programming Beginners

A set of slides from The Sainsbury Laboratory Perl course for absolute beginners

Keywords: Perl, Programming

Training Bioinformatics in the Cloud

I present the points of view, the challenges and advantages of developing training materials through the cloud.

Keywords: Advanced bioinformatics training, Cloud computing, Training

3-day hands-on NGS workshop

This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS...

Keywords: NGS, ChIPSeq, De novo genome assembly, RNASeq

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Bioinformatics for Mass spectrometry analysis

This tutorial on Bioinformatics for Mass spectrometry analysis was part of a full series of tutorials that I have organised in 2009 while sitting in the Educational Committee of the European Proteomics Association (EuPA). Some information on bioinformatics tools would need to be verified, but the...

Keywords: Bioinformatics, Mass spectrometry, Protein identification

Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Bioinformatics

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: Introduction bioinformatics

eBioKit

Extensive teaching experience gained by conducting bioinformatics training courses in Kenya, Uganda, Mauritius (UoM), SriLanka, Sweden, Chile and Zimbabwe showed that it was difficult to successfully teach and demonstrate several bioinformatics resources, due to and often limited by slow Internet...

Keywords: Advanced bioinformatics training, Introduction bioinformatics

An Introduction to Unix, Perl and Python

This  course provides an introduction to Unix, Perl and Python. In addition to lecture material (in the form of slides), there are exercises, answers to the exercises and pointers to addition resources.

Keywords: Perl, Python, Unix