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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

Introduction to Linux Command Line

Introduction to Linux basic command line

Scientific topics: Computer science

Keywords: Linux basics

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


Training Materials from the 2015 GBS course run by TGAC

Keywords: Genotyping

De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly

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

De Novo Assembly @ TGAC 2015

This course took place between 12-15 May 2015
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

GOBLET Training portal


Keywords: Goblet

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

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC ( 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

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

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

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

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.
Lex Nederbragt, Oslo...

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

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

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

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

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

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

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

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

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


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

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

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

GOBLET Poster at ISMB 2014

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

Keywords: Goblet survey life scientists

"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

Perl 1 Training Course - For Programming Beginners

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

Keywords: Perl, Programming

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

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

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