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.
BioJS is a library of graphical components easy to reuse to represent biological information
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: http://www.mygoblet.org/topic-tags/protein-identification, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mass-spectrometry
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: http://www.mygoblet.org/topic-tags/next-generation-sequencing, http://www.mygoblet.org/topic-tags/qc-ngs-data, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing-data-analysis, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/cloud
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: http://www.mygoblet.org/topic-tags/teaching-aid, http://www.mygoblet.org/topic-tags/problem-based-learning, http://www.mygoblet.org/topic-tags/train-trainer
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: http://www.mygoblet.org/topic-tags/animal-pathogens, http://www.mygoblet.org/topic-tags/e-learning, http://www.mygoblet.org/topic-tags/phylogenetics
I present the points of view, the challenges and advantages of developing training materials through the cloud.
Keywords: http://www.mygoblet.org/topic-tags/cloud-computing, http://www.mygoblet.org/topic-tags/training, http://www.mygoblet.org/topic-tags/advanced-bioinformatics-training
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: http://www.mygoblet.org/topic-tags/protein-structure, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/genome-browsing, http://www.mygoblet.org/topic-tags/genomics
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
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: http://www.mygoblet.org/topic-tags/rna-seq-chip-seq-anayses, http://www.mygoblet.org/topic-tags/variant-calling, http://www.mygoblet.org/topic-tags/high-throughput-sequencing-analysis
The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry.
Keywords: http://www.mygoblet.org/topic-tags/identification, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mass-spectrometry
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...
Scientific topics: Database management
Keywords: http://www.mygoblet.org/topic-tags/genome-sequence-analysis, http://www.mygoblet.org/topic-tags/biological-databases, http://www.mygoblet.org/topic-tags/plants, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/phytopathogens, http://www.mygoblet.org/topic-tags/pathogenesis
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: http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/perl, http://www.mygoblet.org/topic-tags/python
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: http://www.mygoblet.org/topic-tags/variant-detection, http://www.mygoblet.org/topic-tags/introduction-bioinformatics, http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/protein-structure-visualisation, http://www.mygoblet.org/topic-tags/genome-browsing
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: http://www.mygoblet.org/topic-tags/differential-expression, http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/rna-seq
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
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: http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/record-parsing, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/python
Functional association networks and gene function prediction Homology based prediction Guilt-by-association: GeneMANIA
Keywords: http://www.mygoblet.org/topic-tags/functional-association-networks, http://www.mygoblet.org/topic-tags/gene-function-prediction, http://www.mygoblet.org/topic-tags/genemania
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: http://www.mygoblet.org/topic-tags/phylogenetics, http://www.mygoblet.org/topic-tags/molecular-evolution
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: http://www.mygoblet.org/topic-tags/gene-ontology, http://www.mygoblet.org/topic-tags/gene-lists
"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: http://www.mygoblet.org/topic-tags/evolutionary-biology, http://www.mygoblet.org/topic-tags/biohistory, http://www.mygoblet.org/topic-tags/evolutionary-bioinformatics
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: http://www.mygoblet.org/topic-tags/bootstrap, http://www.mygoblet.org/topic-tags/consensus-trees, http://www.mygoblet.org/topic-tags/phylogenetic-splits, http://www.mygoblet.org/topic-tags/phylogenetics
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: http://www.mygoblet.org/topic-tags/pattern-matching, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/python
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: http://www.mygoblet.org/topic-tags/plotting-data, http://www.mygoblet.org/topic-tags/microarray-data-analysis, http://www.mygoblet.org/topic-tags/r, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/visualisation
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...
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...
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: http://www.mygoblet.org/topic-tags/protein-family-characterisation, http://www.mygoblet.org/topic-tags/protein-sequence-analysis, http://www.mygoblet.org/topic-tags/integrated-diagnostic-tools
Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery
Keywords: http://www.mygoblet.org/topic-tags/transcriptional-regulation, http://www.mygoblet.org/topic-tags/pattern-discovery
Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV
Keywords: http://www.mygoblet.org/topic-tags/experimental-design-rna-seq, http://www.mygoblet.org/topic-tags/introduction-rna-seq-analysis, http://www.mygoblet.org/topic-tags/igv