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29 materials found

Target audience: beginner bioinformaticians  or Healthcare 


Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing

This course focuses on genomic sequencing.
Topics covered:
- The changing landscape of genomics: From Sanger sequencing to Next Generation Sequencing
- Overview of Next Generation Sequencing platforms and their methodology
- Targeted resequencing
- Alignment, variant calling and...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

IBIP19 - Integrative Biological Interpretation using Proteomics (2019)

Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface...

Keywords: Proteomics

Resource type: Documentation, Exercise, Handout, Scripts

CPANG19 - Computational PANGenomics (2019)

Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation...

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

PDA19 - Proteomics Data Analysis (2019)

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification,...

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

ELB19F - Entry level Bioinformatics (First course in 2019)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELBS18 - Entry level Bioinformatics (Second course in 2018)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

PDA18 - Proteomics Data Analysis (2018)

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering peptide and protein identification, quantification,...

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ELB18F - Entry level Bioinformatics (First course in 2018)

This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is...

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

PPB18 - Programming in Python for Biologists (2018)

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and...

Operations: Data retrieval, Data handling

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are spatially close in the cell nucleus. Overall, these interaction matrices have been used to study how the genome folds within the nucleus, that is one of the most fascinating problems in modern...

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

This course is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive...

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

PSLS20 - Practical Statistics for the Life Sciences (2020)

This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data...

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

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

High-throughput sequencing training materials repository

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis.
Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Bioinformatics, Data architecture, analysis and design

Keywords: High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling

Plant and Pathogen Bioinformatics

This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an...

Keywords: Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants

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

Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Pattern Matching

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: Pattern matching, Programming, Python, Python biologists

Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Bioinformatics: Gene-protein-structure-function

This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...

Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast

InterPro: An introduction

This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose. 

Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis

PRINTS: A protein family database with a difference

A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...

Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis

Parsing data records using Python programming

This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The...

Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing