Register training material
19 materials found

Authors: Paul Yorke  or allegra.via Via 


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
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

Introduction to Biopython http://tess.elixir-uk.org/materials/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. Bioinformatics, Biopython, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists bioinformaticians 2013-11-04 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
Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Using R with Python http://tess.elixir-uk.org/materials/using-r-with-python This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented are also provided. Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians bioinformaticians 2013-11-04 2017-10-09
Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Searching data using Python http://tess.elixir-uk.org/materials/searching-data-using-python This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and how to use sets to find unique records in two datasets and remove redundancy.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Pattern Matching

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: Pattern matching, Programming, Python, Python biologists

Pattern Matching http://tess.elixir-uk.org/materials/pattern-matching 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 sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file. Pattern matching, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Writing functions in Python programming http://tess.elixir-uk.org/materials/writing-functions-in-python-programming This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.  Bioinformatics Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Python Programs http://tess.elixir-uk.org/materials/python-programs This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Linear Motifs and Phosphorylation Sites

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...

Keywords: Bioinformatics

Linear Motifs and Phosphorylation Sites http://tess.elixir-uk.org/materials/linear-motifs-and-phosphorylation-sites 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 P-sites Computational methods to identify them How you can represent and use them Resources and tools to deal with them Bioinformatics Biologists biocurators bioinformaticians 2013-07-16 2017-10-09
Parsing data records using Python programming

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: Bioinformatics, Programming, Python, Python biologists, Record parsing

Parsing data records using Python programming http://tess.elixir-uk.org/materials/parsing-data-records-using-python-programming 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 text of exercises is provided in a separate file.  Bioinformatics, Programming, Python, Python biologists, Record parsing Biologists beginner bioinformaticians bioinformaticians programmers 2013-07-05 2017-10-09
Introduction to Unix

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: Bioinformatics, Programming, Unixlinux

Introduction to Unix http://tess.elixir-uk.org/materials/introduction-to-unix 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     Bioinformatics, Programming, Unixlinux Anyone wants to start using the Unix/Linux OS 2013-07-04 2017-10-09