GOBLET

GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation providing a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees.

GOBLET http://tess.elixir-uk.org/content_providers/goblet GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation providing a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees. /system/content_providers/images/000/000/004/original/logo_goblet_trans.png?1469458222
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GBS

Training Materials from the 2015 GBS course run by TGAC

Keywords: Genotyping

GOBLET Poster at ISMB 2014

This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston.

Keywords: Goblet survey life scientists

Next Generation Sequencing (NGS) wikibook

Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to...

Keywords: Bioinformatics, Next generation sequencing, Ngs

Course design: Considerations for trainers – a Professional Guide

This Professional Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and...

Keywords: Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material

STAO 2014 Understanding a genetic disease thanks to Bioinformatics

This workshop allows to discover several bioinformatics tools and databases (genome browser, alignment tool, BLAST, dbSNP, UniProtKB, PDB) in the context of the discovery of a rare variant leading to the production of a non functional insulin in a Norwegian family. Additional documents are ...

Keywords: Blast, Genome browsing, Introduction bioinformatics, Protein structure visualisation, Variant detection

RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis

Basic introduction to biology of RNA-seq

        Experimental design considerations

        Commonly asked questions

        Data visualization using IGV

 

Keywords: Experimental design rna seq, Igv, Introduction rna seq analysis

Perl 1 Training Course - For Programming Beginners

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

Keywords: Perl, Programming

GGPLOT2 : Pragmatic GGPLOT

A fully contained course for GGPLOT2

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

Using Bioinformatics to Understand Genetic Diseases: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases. A rare variation in the insulin gene is discussed, and the impact of the variation on the gene...

Keywords: Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material

Biocuration: An Introduction

Claire O'Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introduction into biocuration and talks about what it is like to work as a biocurator and the skill sets you need.
This webinar was recorded on 2 March 2016 and is best viewed using Google Chrome and in...

Keywords: Biocuration

Introduction to Unix

Introductory lecture to the Unix/Linux command-line

    Description of the computer shell and the command-line interface

    Differences between graphical and command-line interfaces

    The most commond Unix/Linux commands are provided

 
 

Keywords: Bioinformatics, Programming, Unixlinux

SV-Autopilot: the new face of Structural Variant Detection

Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager...

Keywords: Ngs bioinformatics, Structural variations

Signalling Networks: From Data to Modelling

What is the course about?
Signalling pathways and networks are very important to regulate and control cellular processes, cell fate, and their malfunctions often lead to diseases, such as cancer or diabetes. This course provides an introductory overview of the most useful resources and tools to...

Keywords: Signalling

Bioinformatics - Food Detective: a Practical Guide

This Practical Guide introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help de- tect food fraud. Analyses...

Scientific topics: DNA barcoding, Sequence analysis

Keywords: Basic bioinformatics, Bioinformatics schools, Dna barcoding, Food fraud, Sequence analysis, Sequence database searching, Species identification, Training material

Problem Based Learning Guide

Problem Based Learning (PBL) is an innovative approach to learning that we used to deliver the Clinical Bioinformatics I module of the new MSc in Clinical Bioinformatics. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of...

Keywords: Problem based learning, Teaching aid, Train trainer

Flow Cytometry 2013 Module 1 - Introduction to Flow Cytometry Analysis in R

Lecture on how tools to be demonstrated have been used in research and clinical applications

    Description of data and underlying biological problem

    Summary of a typical work flow to be covered in the workshop: transformation, margin event removal, quality assurance, gating, recording and...

Keywords: Introduction flow cytometry, Review r

Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways

Over-representation analysis (ORA)

    Statistics for detecting over-representation e.g. hypergeometric test, GSEA

    Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR

    Filtering Gene Ontology e.g. using evidence codes

Keywords: Gsea, Over representation analysis

GOBLET Training portal

Presention

Keywords: Goblet

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Michael Love

MOOCs in Bioinformatics: The Online Course Model to Online Bioinformatics Education
Dr. Michael Love, edX Faculty and post-doctoral fellow in Dept. Biostatistics, Dana Farber Cancer Institute and Harvard School of Public Health.
Dr. Love teaches the Data Analysis for Genomics course offered...

Keywords: Bioinformatics, Mooc

A Critical Guide to the neXtProt knowledgebase: querying using SPARQL

This Critical Guide in the Introduction to Bioinformatics series briefly outlines how to explore the neXtProt human protein database using SPARQL. While text indexation has made database contents more accessible, being able to combine search criteria for specific content permits more powerful...

Scientific topics: Database management

Keywords: Human protein database, Introduction bioinformatics, Introduction nextprot, Nextprot data model, Rdf triples, Semantic triples, Sparql queries, Sparql syntax, Training material

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

Python programming primer

The purpose of this training is to teach general programming concepts using Python as an instruction tool.
Topics:
Introduction to Python: basic principles.
Python data structures: strings, tuples, lists, dictionaries, sets.
Object-oriented programming: how to model coffee machines in Python...

Scientific topics: Software engineering

Keywords: 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

Basic bioinformatics and HOPE

Many bioinformatics tools have been developed over the last decennium, most of which were meant to be used in the lab of the life scientist. Unfortunately, only a few made it, because the tools are often too non-intuitive and too much a black box to the life scientist. Therefore Hanka Venselaar...

Keywords: Disease causing mutation, Predicting effect mutation protein function, Predicting effect mutation structure

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

Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

BioJS

Introduction to BioJS a standard for visualisation of biological data in JavaScript

Keywords: Biojs, Javascript, Software, Standards

A Critical Guide to InterPro

This Critical Guide in the Introduction to Bioinformatics series provides an introduction to the InterPro database, the largest, most comprehensive, integrated protein family database in the world. The rationale for creating the resource, the nature of its contributing databases and the kinds of...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis

Bioinformatics - the Power of Computers in Biology: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in...

Scientific topics: Sequence analysis

Keywords: Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials

De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly

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

Similarity searching, multiple sequence alignment and protein families - undergraduate lab

Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...

Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching

Simple plotting in R

This quick and simple tutorial demonstrates some of the easy plotting tools in the R core software.
the data are in the "data" directory and come from an old two-colour microarray experiment where spots on the array were printed with different buffers, in different concentrations and with...

Keywords: Bioinformatics, Microarray data analysis, Plotting data, R, Visualisation

Interactive bioinformatics 'taster' for students - exploring sickle cell anaemia

Developed in collaboration with the Royal Society, this material provides a short interactive introduction to bioinformatics, and includes a bioinformatics 'game' that simulates database searching and protein sequence analysis, with a focus on sickle cell anaemia. This is a fun activity with...

Flow Cytometry 2013 Module 5 - 1D Dynamic gating

Using quantiles to set a gate based on a negative control

    Using median and standard deviation to set a gate based on a negative control

    Exploring rangeGate: an automated way to set a 1D gate for each sample individually

    Recording proportions of cells in subpopulations of interest by...

Keywords: 1d dynamic gating, Flow cytometry data

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

Understanding Multiple Sequence Alignments - Lecture Handouts & Utopia Hands-On

This presentation aims to provide a basic understanding of the range of contexts in which protein sequence alignments are used and are useful, focusing on the importance of sequence similarities and differences, and what they tell us. Overall, the objective is to offer different perspectives and...

Keywords: Multiple sequence alignment, Protein sequence analysis, Sequence analysis

"Key-terms", a learning game for conceptual consolidation

A short presentation describing a new participatory method that easily engages course participants in gamestorming and helps to consolidate new knowledge, by collectively agreeing on ways to place concepts in mind maps.
"Key-terms" is a classroom game that can be played in a variety of contexts,...

Keywords: Education, Instruction, Training

Presentation About GOBLET Portal

This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14)

Keywords: Goblet, Training portal

Metagenome data analysis Workshop, May 21-23, 2014

SciLifelab and AllBio are arranging a workshop on the analysis and interpretation of metagenomics data.
In this workshop we will combine talks by experts in the field with practical tutorials guiding the participants in the analysis of representative datasets.
Speakers:
Lex Nederbragt, Oslo...

Keywords: Allbio, Assembly, Binning, Bioinformatics, Data analysis, Metagenomics

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

RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression

Get FPKM style expression estimates using Cufflinks

        Perform differential expression analysis with Cuffdiff

        Perform summary analysis with CummeRbund

        Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)

 

Keywords: Differential expression, Transript expression

A Critical Guide to Unix

This Critical Guide in the Introduction to Bioinformatics series briefly introduces the Unix Operating System, and provides a subset of some of the most helpful and commonly used commands, including those that allow various types of search, navigation and file manipulation. Several keystroke...

Keywords: Command line, Introduction bioinformatics, Introduction unix, Unix commands, Unix operating system

A Critical Guide to UniProtKB

This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the UniProt protein sequence database, with a particular focus on the UniProt Knowledgebase – UniProtKB. The rationale for creating the resource, its contributing databases and the kinds of information...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction uniprot, Protein sequence databases, Uniprot knowledgebase

BD2K Data Science Open Educational Resources (OERs)

These Online Educational Resources (OERs) cover a variety of topics related to data science and are intended for use in courses, programs, workshops, and related activities. Modules relevant to biocuration:BDK05 Basic Research Data Standards...

Scientific topics: Ontology

Keywords: Biocuration, Curation, Identifiers, Ontology, Standards

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 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

R as a programming language

This course is aimed at colleagues who would like to learn how to use the statistical programming language "R". We will learn about the data structures and functions in R, and how to write R scripts.
Topics:
Introduction to R: general principles.
Data structures in R: vectors, matrices, arrays,...

Keywords: R programming

BioJS

BioJS is a library of graphical components easy to reuse to represent biological information

Keywords: Bioinformatics, Javascript

EMBER - a practical guide to bioinformatics

EMBER is an online practical designed to provide a brief, hands-on introduction to a range of bioinformatics databases and tools on the Web. It comprises basic and slightly more advanced 'chapters', and a number of case studies. Chapters include reflective questions, to stimulate critical...

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

Bioinformatics for MS analysis

The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry.

Keywords: Bioinformatics, Identification, Mass spectrometry

A Critical Guide to the UniProtKB Flat-file Format

This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data. Web-based interfaces have made databases more user-friendly, but knowledge of the underlying file format offers a deeper understanding of how to navigate...

Scientific topics: Database management

Keywords: Flat file databases, Flat files, Introduction bioinformatics, Uniprotkb flat file format

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

Bioinformatics approaches to Identify causative sequence variants in farm animals

ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden
The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to...

Keywords: Allbio, Farm animals, Qtl, Rnaseq, Transcription factors

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014
What is this workshop about?
The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on:
Automated and standardized data...

Scientific topics: Bioinformatics, Database management, Plant biology, Sequence analysis

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC Metagenomics: From bench to data analysis

This course took place at TGAC on 8-12 September 2014
What is the workshop about?
A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem...

Scientific topics: Metagenomics

Keywords: Metagenomics

Introduction to Linux Command Line

Introduction to Linux basic command line

Scientific topics: Computer science

Keywords: Linux basics

QuickGuides

A range of Quick Guides to commonly used bioinformatics tools and resources.

Keywords: Blast, Emboss, Mysql, Perl, Phylip, Unixlinux, Velvet

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

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

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

A Critical Guide to BLAST

This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity. Several Web-based and stand-alone implementations are reviewed, and key features of typical search...

Keywords: Introduction bioinformatics, Introduction blast, Sequence database searching, Sequence similarity searching

A Critical Guide to the PDB

This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures. The rationale for creating the resource and the kinds of information it provides are discussed,...

Scientific topics: Database management

Keywords: Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures

RNA-seq analysis

I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund.

Evolutionary Bioinformatics Videos

"Evolution Academy" videos (http://post.queensu.ca/~forsdyke/videolectures.htm). The latter are a course of 54 short (15 min) videos that follow the style of Salman Khan's "Khan Academy," and are addressed primarily to High School and beginning College students. There are also several longer (1...

Scientific topics: Evolutionary biology

Keywords: Biohistory, Evolutionary bioinformatics, Evolutionary biology

Ensembl Browser Workshop: Plants and Microbes

Ensembl is a joint project between European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute to provide a source of thorough, integrated annotation data across a variety of genomes.
This one-day workshop not only offers participants the opportunity to glean background...

RNA-seq Analysis 2014 Module 2 - Alignment and Visualization

Use of Bowtie/TopHat

        ‘Regular mode’ vs. ‘Fusion mode’

        Introduction to the BAM format

        Basic manipulation of BAMs with samtools, etc.

        Visualization of RNA-seq alignments - IGV

        BAM read counting and determination of variant allele expression status
 

 

Keywords: Data visualization, Rna seq alignment

Quality Control of Illumina Sequencing data in the cloud

This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data...

Keywords: Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data

Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis

Overview of transcription

    Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data

    Basics of processing data

    Pattern discovery

Keywords: Pattern discovery, Transcriptional regulation

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

Introduction to Biopython

This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.

Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists

Metagenomics 2015

Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015

Scientific topics: Metagenomics

Keywords: Metagenomics

RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression

Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.
 

Scientific topics: RNA

Keywords: Alternative expression, Transcript isoforms

Concepts, historical milestones & the central place of bioinformatics in modern biology: a European perspective

Short history of the emergence of bioinformatics as a discipline in Europe, following the near simultaneous advent of high-throughput sequencing techniques and the World Wide Web, which made dissemination of the rapidly accumulating sequence data both simple and feasible on a large scale.

Keywords: Bioinformatics history, Biomolecular databases, Biomolecular sequences, European perspective

Pathway and Network Analysis 2014 Module 5 - Network Visualization

Introduction to network visualization

    Visualizing omics data on a network or pathway

    Active modules in Cytoscape

Keywords: Cytoscape, Network visualization

Working with Affymetrix CEL files in R

This tutorial shows how to download some public Affymetrix microarray data, load the data into R, calculate expression values and do some very simple plotting

Keywords: Affymetrix, Microarrays, R

De Novo Assembly @ TGAC 2015

This course took place between 12-15 May 2015
Overview:
The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing...

Keywords: De novo

A mind map is a nice visual way of describing the content of a training course

A Mind Map can be built by arranging boxes with subject titles in a variety of ways. In this example, the objective was to create a visual aid to better understand the relationship between the subjects that had been covered.
The diagram is centered in the core subject, and other subjects occupy...

Keywords: Mind map, Training technique, Visual aid

Intended Learning Outcome Advisor

This tool allows trainers to evaluate Intended Learning Outcomes (ILOs) they've written to accompany their training resources. The tool is able to assess sets of ILOs against representative verbs for each level of Bloom's Taxonomy, verifying both the Bloom's level to which they correspond and the...

Network Analysis with Cytoscape and PSICQUIC

This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the...

Keywords: Cytoscape

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

UPGMA Worked Example

A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI...

Keywords: Molecular phylogeny, Phylogenetics, Upgma

Bioinformatics Introductory Module

This Bioinformatics Introductory Module for self-study was designed for future students of the  Molecular Mechanisms of Disease (MMD) master’s program at Radboud University Medical Centre. To level out the starting differences in bioinformatics knowledge between this incoming heterogeneous group...

Keywords: Bioinformatics, Genome browsing, Genomics, Protein structure

Multiple sequence alignment and phylogeny - undergraduate lab

This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab...

Keywords: Clustalw, Multiple sequence alignment, Phylip, Phylogeny

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - David Searls

Self-directed Learning: Does online learning in bioinformatics work?
Proposed Speaker: (CONFIRMED) David Searls, Adjunct Associate Professor, Perleman School of Medicine, University of Pennsylvania.
Dr. Searls is an independent consultant in bioinformatics and former Senior VP of Bioinformatics...

Keywords: Bioinformatics, Mooc, Online learning

Clinical Bioinformatics I - Tutor notes

Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work...

Keywords: Clinical bioinformatics, Genomics, Introduction bioinformatics

Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists

Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis

    Where do gene lists come from?

    Working with gene function information

Keywords: Gene lists, Gene ontology

Pathway and Network Analysis 2014 Module 6 - Gene Function Prediction

Functional association networks and gene function prediction

    Homology based prediction

    Guilt-by-association: GeneMANIA

Keywords: Functional association networks, Gene function prediction, Genemania

Flow Cytometry 2013 Module 2 - Exploring FCM data in R

Loading a single or groups of FCS files into R

    flowFrame and flowSet objects and their attributes

    Exploring sample annotation and keywords stored within the FCS file format, searching for specic samples (such as controls) using grep, highlighting the importance of correct sample annotation...

Keywords: Fcs files, Plotting data, R

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

Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data

Preprocessing

            Removing margin events

            Data transformation: log vs. biexponential

            Data normalization


    Quality Assurance

            Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common...

Keywords: Flow cytometry data, Preprocessing, Quality assurance

EMBL-EBI Train Online

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently.

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems

Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday.
Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics

Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis

Introduction to pathway and network analysis

    Basic network concepts

    Types of pathway and network information

    Pathway Databases: Reactome, KEGG, etc.

    Pathway analysis of large scale genomics data sets, including cancer genomics

Keywords: Biological networks, Kegg, Pathway analysis, Reactome

Linear Motifs and Phosphorylation Sites

This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused.
The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites.
Here you can find:

    A definition of linear motifs and...

Keywords: Bioinformatics

EMBO 2015

Link to the GitHub repository containing all the training materials made available for the 2015 EMBO event held at TGAC

Scientific topics: Molecular interactions, pathways and networks, Protein binding sites

Keywords: Bioinformatics, Multiple sequence alignment, Network visualization, Protein protein interaction networks

Flow Cytometry 2013 Module 4 - 1D Static gating

How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set

    How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate

    Visualizing the proportions using a density...

Keywords: 1d static gating, Flow cytometry data

UNIX command line and scripting

The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH.

Keywords: Awk, Bash, Unix

Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools

Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project

    K-means explained

    flowMeans: smart k-means for FCM data

    flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering

    Biomarker discovery: flowType and RchyOptimyx, advanced tools used...

Keywords: Biomarker discovery, Flow cytometry data, Flowcap

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

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

Train the Trainer course materials

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor (with contributions from Emily Angiolini, Jamie Edwards and Paul Yorke) while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics...

Keywords: Course development, Pedagogy, Trainer skills

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

Python @ TGAC - Python for Life Scientists: Managing biological data with Python

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input,...

Keywords: Biopython, Python, Python biologists

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

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good

Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education
Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute.
Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge....

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Gaming, Online learning

GOBLET Talk at INCoB 2014

Supporting Trainers to Improve Bioinformatics Education Globally
Speaker: Dr. Michelle Brazas
A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not...

Keywords: Goblet

Statistics with R

The aim of this course is to teach you how to perform basic statistical analysis using R. First we review the foundations (sampling theory, discrete and continuous distributions), then we focus on classical hypothesis testing. This course will improve your generic statistics knowledge....

Scientific topics: Statistics and probability

Keywords: Biostatistics, R

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