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.
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...
Scientific topics: Sequencing
Keywords: http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing
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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mooc, http://www.mygoblet.org/topic-tags/online-learning
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/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing, http://www.mygoblet.org/topic-tags/next-generation-sequencing-data-analysis, http://www.mygoblet.org/topic-tags/cloud, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/qc-ngs-data
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...
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: http://www.mygoblet.org/topic-tags/biomarker-discovery, http://www.mygoblet.org/topic-tags/flow-cytometry-data, http://www.mygoblet.org/topic-tags/flowcap
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: http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/bash, http://www.mygoblet.org/topic-tags/awk
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/integrated-diagnostic-tools, http://www.mygoblet.org/topic-tags/protein-family-characterisation, http://www.mygoblet.org/topic-tags/protein-sequence-analysis
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 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...
Scientific topics: Bioinformatics, Data quality management, Sequence assembly, Topic, Sequencing
Keywords: NGS, ChIPSeq, De novo genome assembly, RNASeq
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: http://www.mygoblet.org/topic-tags/transcript-isoforms, http://www.mygoblet.org/topic-tags/alternative-expression
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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/online-learning, http://www.mygoblet.org/topic-tags/gaming
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
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: http://www.mygoblet.org/topic-tags/structural-variations, http://www.mygoblet.org/topic-tags/ngs-bioinformatics
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: Database management, Bioinformatics, Sequence analysis, Plants
Keywords: http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/plants-bioinformatics
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
Scientific topics: Molecular interactions, pathways and networks
Keywords: http://www.mygoblet.org/topic-tags/kegg, http://www.mygoblet.org/topic-tags/pathway-analysis, http://www.mygoblet.org/topic-tags/biological-networks, http://www.mygoblet.org/topic-tags/reactome
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/bioinformatics, http://www.mygoblet.org/topic-tags/protein-structure, http://www.mygoblet.org/topic-tags/genome-browsing, http://www.mygoblet.org/topic-tags/genomics
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: http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/similarity-searching, http://www.mygoblet.org/topic-tags/hmmer, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment, http://www.mygoblet.org/topic-tags/interpro
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
Scientific topics: RNA-Seq alignment
Keywords: http://www.mygoblet.org/topic-tags/rna-seq-alignment, http://www.mygoblet.org/topic-tags/data-visualization
Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV
Keywords: http://www.mygoblet.org/topic-tags/igv, http://www.mygoblet.org/topic-tags/introduction-rna-seq-analysis, http://www.mygoblet.org/topic-tags/experimental-design-rna-seq
This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston.
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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/unixlinux
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...
Scientific topics: Transcription factors and regulatory sites
Keywords: http://www.mygoblet.org/topic-tags/farm-animals, http://www.mygoblet.org/topic-tags/transcription-factors, http://www.mygoblet.org/topic-tags/qtl, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/rnaseq
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
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/mass-spectrometry, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/identification
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...
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
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: http://www.mygoblet.org/topic-tags/trainer-skills, http://www.mygoblet.org/topic-tags/pedagogy, http://www.mygoblet.org/topic-tags/course-development
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: http://www.mygoblet.org/topic-tags/bioinformatics-history, http://www.mygoblet.org/topic-tags/biomolecular-sequences, http://www.mygoblet.org/topic-tags/european-perspective, http://www.mygoblet.org/topic-tags/biomolecular-databases