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109 materials found

Content provider: GOBLET 

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

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

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

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

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

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

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

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

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 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

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

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

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

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...

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...

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...

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

GGPLOT2 : Pragmatic GGPLOT

A fully contained course for GGPLOT2

Evolutionary Bioinformatics Videos

"Evolution Academy" videos ( 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


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

Keywords: Biojs, Javascript, Software, Standards

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...

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

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

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

Python programming primer

The purpose of this training is to teach general programming concepts using Python as an instruction tool.
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

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.
Introduction to R: general principles.
Data structures in R: vectors, matrices, arrays,...

Keywords: R programming

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

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

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: Data architecture, analysis and design, Bioinformatics

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

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: Sequencing, RNA, Data architecture, analysis and design, Bioinformatics

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq