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Authors: Aidan Budd  or Paul Yorke 

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...

Ensembl Browser Workshop: Plants and Microbes http://tess.elixir-uk.org/materials/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 information about the project and resulting resources, but also to gain vital hands-on experience in the use of the Ensembl genome browser. This workshop is themed according to the target audience and is aimed at wetlab researchers, as well as being customisable to include an introduction for complete novices up to advanced usage for the more frequent users. 2016-04-14 2017-10-09
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

Signalling Networks: From Data to Modelling http://tess.elixir-uk.org/materials/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 investigate signalling pathways and networks, and also introduces basic approaches to model signalling events. The hands-on training will give a wide overview of tools and concepts related to signalling networks. What will I Learn? In this course you will learn how to use Cytoscape, where to find the most reliable signaling data, how to reconstruct, analyze and visualize a network. You will also learn how to develop your own models, mostly with logic modelling, what other modelling approaches exist, and how you can apply a model for your own research work. Signalling Grad students post-docs 2016-04-14 2017-10-09
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

Network Analysis with Cytoscape and PSICQUIC http://tess.elixir-uk.org/materials/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 PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks. Cytoscape Biologists, Genomicists, Computer Scientists 2016-04-14 2017-10-09
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

Metagenomics 2015 http://tess.elixir-uk.org/materials/metagenomics-2015 Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015 Metagenomics Metagenomics PhD post-docs 2015-11-23 2017-10-09
Introduction to Linux Command Line

Introduction to Linux basic command line

Scientific topics: Computer science

Keywords: Linux basics

Introduction to Linux Command Line http://tess.elixir-uk.org/materials/introduction-to-linux-command-line Introduction to Linux basic command line Computer science Linux basics 2015-10-28 2017-10-09
EMBO 2015

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

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

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

EMBO 2015 http://tess.elixir-uk.org/materials/embo-2015 Link to the GitHub repository containing all the training materials made available for the 2015 EMBO event held at TGAC Protein binding sites Molecular interactions, pathways and networks Bioinformatics, Multiple sequence alignment, Network visualization, Protein protein interaction networks PhD students post-docs 2015-10-08 2017-10-09
GBS

Training Materials from the 2015 GBS course run by TGAC

Keywords: Genotyping

GBS http://tess.elixir-uk.org/materials/gbs Training Materials from the 2015 GBS course run by TGAC Genotyping Graduate Students post-docs 2015-09-17 2017-10-09
De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly

De Novo http://tess.elixir-uk.org/materials/de-novo Training Materials from the 2015 De Novo course run by TGAC De novo, De novo genome assembly PhD PhD students post-docs postdoctoral researchers 2015-09-17 2017-10-09
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

Python @ TGAC - Python for Life Scientists: Managing biological data with Python http://tess.elixir-uk.org/materials/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, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover: Working with DNA and protein sequences Data retrieval from files and their manipulation Running applications, such as BLAST, locally and from a script Finding motifs in sequences Parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc. Biopython will be also introduced and applied to some of the mentioned examples. The course is meant to be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts. Unix/Linux basic skills will be provided at the beginning of the course. Biopython, Python, Python biologists PhD post-docs 2015-07-14 2017-10-09
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

De Novo Assembly @ TGAC 2015 http://tess.elixir-uk.org/materials/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 project, quality control and preprocessing of datasets, generation and evaluation of first pass assemblies, assembly improvement and finishing. Practical exercises will be performed on small-scale real datasets, including Illumina and Pacbio sequences, including best practices and tips based on TGAC’s faculty experience. The course will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities and discussions. The participants will gain first-hand experience and understanding on NGS assembly, working with the assistance of the faculty, troubleshooting small problems, and reviewing the results. De novo PhD post-docs 2015-07-14 2017-10-09
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

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies http://tess.elixir-uk.org/materials/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. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
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

Summarising sets of phylogenies http://tess.elixir-uk.org/materials/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 examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
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

Introduction to Multiple Sequence Alignment http://tess.elixir-uk.org/materials/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 alignmetns (structural and evolutionary), and ways of building manual and automatic alignments, and an introduction to JalView Multiple sequence analysis, Protein structure, Sequence analysis Bench biologists 2013-10-23 2017-10-09
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

Introduction to Bioinformatics http://tess.elixir-uk.org/materials/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 be wrong, and what we can do to spot it. Introduction bioinformatics Bench biologists 2013-10-23 2017-10-09
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

Interpreting Phylogenies http://tess.elixir-uk.org/materials/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 trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09