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BLAST and multiple sequence alignment (MSA) programs

Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/materials/blast-and-multiple-sequence-alignment-msa-programs-0b2b34d0-a157-49d4-a065-3dcad67ff99d Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   Blast, E learning, Multiple sequence alignment Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
Phylogenetics of animal viral pathogens

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: Animal pathogens, E learning, Phylogenetics

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db 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 useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
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

Bioinformatics - the Power of Computers in Biology: A Practical Guide https://tess.elixir-europe.org/materials/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 humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273π variant of Linux (4273pi.org). Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to: i) search biological sequence databases using the online program BLAST, and navigate GenPept sequence records; ii) execute some basic Linux commands to perform a set of simple file-manipulation tasks; iii) perform BLAST searches via the Linux command line; and iv) evaluate the biological implications of search results, with reference to mutations and function. Sequence analysis Basic bioinformatics, Basic linux commands, Bioinformatics schools, Gene loss, Genetic mutation, Raspberry pi computers, Sequence analysis, Sequence database searching, Training materials 2019-06-08
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

A Critical Guide to the neXtProt knowledgebase: querying using SPARQL https://tess.elixir-europe.org/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 querying, and provides a means to mine the information stored in databases. This Guide illustrates the use of the SPARQL semantic query language to interrogate neXtProt and other databases that provide SPARQL endpoints. Specifically, the Guide introduces the concept of database ‘semantic triples’, and examines features of the neXtProt data model. On reading this Guide, and completing the exercises, users will be able to: i) identify key entities within the neXtProt data model; ii) explain what these entities represent, what information they contain and what the information is used for; iii) identify key SPARQL syntax elements; iv) understand SPARQL tutorial examples; and v) write a SPARQL query to retrieve entries matching specific criteria. Database management Human protein database, Introduction bioinformatics, Introduction nextprot, Nextprot data model, Rdf triples, Semantic triples, Sparql queries, Sparql syntax, Training material Beginners 2019-06-06
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

Using Bioinformatics to Understand Genetic Diseases: A Practical Guide https://tess.elixir-europe.org/materials/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 product, and how this results in disease, is explored. Specifically, this Guide introduces a range of commonly used bioinformatics tools and databases with which to analyse both DNA and protein sequences, and protein structures. On reading the Guide and completing the exercises, users will be able to: i) investigate the locations of genes on the human genome using a genome browser; ii) compare DNA sequences using an alignment tool; iii) translate a DNA sequence into its protein product; iv) search a protein structure database, and visualise the 3D structure of insulin; and v) infer whether insulin is specific to humans by using protein sequence database search tools. Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material 2019-03-18
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 the PDB https://tess.elixir-europe.org/materials/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, and issues relating to its evolution and growth are explored. Specifically, this Guide introduces the principal features of the PDB, the nature (and quality) of its contents and how these may be interrogated. On reading this Guide, users will be able to: i) explain some of the ways in which knowledge of protein structures is useful; ii) identify the constituent databases of the wwPDB; iii) explain key features of the RCSB PDB in terms of its data distribution, growth and redundancy statistics; iv) search the PDB using simple and advanced keywords and full sequences, and analyse differences between them; and v) explain various structural quality criteria, and infer the quality of individual PDB entries. Database management Introduction bioinformatics, Introduction pdb, Protein structure analysis, Protein structure databases, Protein structures Beginners 2018-09-08
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 InterPro https://tess.elixir-europe.org/materials/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 information they provide are discussed, and the role of InterPro in protein classification and function-annotation projects is outlined. Specifically, this Guide introduces the principal components of the InterPro database, the differences between them, and how their integration creates a resource whose diagnostic power is greater than the sum of its parts. On reading this Guide, users will be able to: i) explain how protein family databases are used to help annotate uncharacterised protein sequences; ii) identify InterPro’s constituent data resources and explain the main methods that underpin them; iii) search InterPro using keywords and full sequences; iv) analyse and interpret search results in terms of protein family hierarchies, their structural domains and functional features; and v) track the provenance of InterPro’s annotations. Database management Introduction bioinformatics, Introduction interpro, Protein family classification, Protein family databases, Protein family hierarchies, Protein function annotation, Protein sequence analysis Beginners 2018-09-08
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 the UniProtKB Flat-file Format https://tess.elixir-europe.org/materials/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 and mine the information they contain, so that humans and machines can get the most out of them. This Guide explores the file format that underpins one of today’s most popular protein sequence databases – UniProtKB. Specifically, this Guide introduces the concept of database ‘flat-files’, and examines features of the UniProtKB flat-file format. On reading this Guide, users will be able to: i) identify key fields within UniProtKB/Swiss-Prot and UniProtKB/TrEMBL flat-files; ii) explain what these fields mean, what information they contain and what the information is used for; iii) analyse the information in different fields and infer structural and functional features of a sequence; iv) examine and investigate the provenance of annotations; and v) compare annotations at different time-points and evaluate the likely impact of annotation changes. Database management Flat file databases, Flat files, Introduction bioinformatics, Uniprotkb flat file format Beginners 2018-09-08
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 UniProtKB https://tess.elixir-europe.org/materials/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 they provide are discussed, and issues behind the quality of their annotations are explored. Specifically, this Guide introduces the principal components of the UniProt Knowledgebase, and the differences between them. On reading this Guide, users will be able to: i) identify and explain the characteristic features of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entries; ii) distinguish annotations that are computed, and hence not experimentally validated; iii) search UniProtKB using keywords, full sequences and peptides, and interpret the results; iv) analyse and track the provenance of annotations; and v) infer which annotations are likely to be accurate and which erroneous. Database management Introduction bioinformatics, Introduction uniprot, Protein sequence databases, Uniprot knowledgebase Beginners 2018-09-08
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 BLAST https://tess.elixir-europe.org/materials/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 results are discussed. Specifically, this Guide introduces concepts and theories that underpin the BLAST search tool, and examines features of search outputs important for understanding and interpreting BLAST results. On reading this Guide, users will be able to: i) search a variety of Web-based sequence databases with different query sequences, and alter search parameters; ii) explain a range of typical search parameters, and the likely impacts on search outputs of changing them; iii) analyse the information conveyed in search outputs and infer the significance of reported matches; iv) examine and investigate the annotations of reported matches, and their provenance; and v) compare the outputs of different BLAST implementations and evaluate the implications of any differences. Introduction bioinformatics, Introduction blast, Sequence database searching, Sequence similarity searching Beginners 2018-09-08
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

A Critical Guide to Unix https://tess.elixir-europe.org/materials/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 short-cuts are also explained, which help to make the routine use of Unix commands more efficient. Specifically, this Guide showcases some of the simplest, most frequently used commands to help new users to understand and gain confidence in using the Unix Operating System. On reading the Guide, users will be able: i) to exploit a range of commands: to manipulate files, directories and processes; to navigate directory structures and explore their contents; to search for files, and search and compare file contents; and to direct command outputs into files or into other commands; and ii) to explain what many simple commands mean and how they’re used. Command line, Introduction bioinformatics, Introduction unix, Unix commands, Unix operating system Beginners 2018-09-08
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

EMBL-EBI Train Online https://tess.elixir-europe.org/materials/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. Bioinformatics Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems Beginner informatics Life sciences 2018-05-11
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

Biocuration: An Introduction https://tess.elixir-europe.org/materials/biocuration-an-introduction-bdbaa48f-b505-4b5d-affb-83328bc2fac1 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 full-screen mode. Biocuration Biologists biocurators life scientists 2018-05-11
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

BD2K Data Science Open Educational Resources (OERs) https://tess.elixir-europe.org/materials/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 (https://github.com/OHSUBD2K/BDK05-Basic-Research-Data-Standards). Standards for biomedical data, participating in communities that develop them, aiding reproducibility.BDK11 Identifiers (https://github.com/OHSUBD2K/BDK11-Identifiers). Introduction to identifiers (modeling, identifying and describing resources and objects.)BDK12 Data Annotation And Curation (https://github.com/OHSUBD2K/BDK12-Data-annotation-and-curation). Data preparation, developing standardized quality assurance processes and pipelines.BDK14 Ontologies 101 (https://github.com/OHSUBD2K/BDK14-Ontologies-101). Introduction to OWL2 and data reasoning.Authors: OHSU BD2K teamType of Material: Presentation slides, videos (in BDK12), exercises, and other resources.License: CC-BY Ontology Biocuration, Curation, Identifiers, Ontology, Standards biocurators 2018-04-02
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...

EMBER - a practical guide to bioinformatics https://tess.elixir-europe.org/materials/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 thinking about results, and end-of-chapter quizzes. A glossary of terms and further reading is also provided. The basic chapters introduce students to practical protein sequence analysis, looking at protein sequence and protein family database searching, sequence alignment and 3D structure classification. For new users, the system requires creation of an account - in the registration form, select "independent user". Once an account has been created, log in to continue (make sure you have cookies enabled in your browser before proceeding). 2018-03-15
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...

Interactive bioinformatics 'taster' for students - exploring sickle cell anaemia https://tess.elixir-europe.org/materials/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 which to introduce bioinformatics to school students. 2018-03-15
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...

Intended Learning Outcome Advisor https://tess.elixir-europe.org/materials/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 appropriateness of the verbs used; where verbs appear ambiguous, the tool offers guidance to help improve the description of the respective ILO. 2018-02-15
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

Train the Trainer course materials https://tess.elixir-europe.org/materials/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 Training hub. The five slide decks cover pedagogical theory, trainer skills and course development. The Excel workbook implements a version of Honey and Mumford's Learning Styles Questionnaire. Course development, Pedagogy, Trainer skills Prospective and existing trainers 2017-06-30 2017-10-09
GGPLOT2 : Pragmatic GGPLOT

A fully contained course for GGPLOT2

GGPLOT2 : Pragmatic GGPLOT https://tess.elixir-europe.org/materials/ggplot2-pragmatic-ggplot A fully contained course for GGPLOT2 2017-06-12 2017-10-09
Evolutionary Bioinformatics Videos

"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: Biohistory, Evolutionary bioinformatics, Evolutionary biology

Evolutionary Bioinformatics Videos https://tess.elixir-europe.org/materials/evolutionary-bioinformatics-videos "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 h) conference presentations that bring together various themes. These are backed by several webpages (accessible by way of http://post.queensu.ca/~forsdyke/homepage.htm ), and a textbook, now in its third edition (2016; for Introduction see Materials File). Evolutionary biology Biohistory, Evolutionary bioinformatics, Evolutionary biology High School Students Researchers University and College Level Students 2017-04-04 2017-10-09
BioJS

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

Keywords: Biojs, Javascript, Software, Standards

BioJS https://tess.elixir-europe.org/materials/biojs-1ff5ad84-3b06-4997-bba6-e18a4dcf32c0 Introduction to BioJS a standard for visualisation of biological data in JavaScript Biojs, Javascript, Software, Standards software developers, bioinformaticians 2014-02-27 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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
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

Statistics with R https://tess.elixir-europe.org/materials/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. Topics: Sampling theory: obtaining information about a population via sampling. Sample characteristics (location, dispersion, skewness), estimation of the mean, standard error of the mean. Discrete and continuous probability distributions. Central limit theorem. Hypothesis testing. Basic principles, one- and two-sided testing, types of errors, power calculations. "Cookbook of tests": location testing, normality, variance comparisons, counting statistics, contingency tables, regression tests. Statistics and probability Biostatistics, R 2016-04-21 2017-10-09
Python programming primer

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

Python programming primer https://tess.elixir-europe.org/materials/python-programming-primer The purpose of this training is to teach general programming concepts using Python as an instruction tool. Topics: Introduction to Python: basic principles. Python data structures: strings, tuples, lists, dictionaries, sets. Object-oriented programming: how to model coffee machines in Python :-). Inheritance (base and derived classes), polymorphism. Write your own script to convert BED files to GFF. Command-line option processing, file I/O, error handling. Software engineering Python biologists 2016-04-21 2017-10-09
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. Topics: Introduction to R: general principles. Data structures in R: vectors, matrices, arrays,...

Keywords: R programming

R as a programming language https://tess.elixir-europe.org/materials/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. Topics: Introduction to R: general principles. Data structures in R: vectors, matrices, arrays, lists, data frames. Data import/export. Functions in R: how to write your own functions and scripts. Visualization in R: various plot types (built-in graphics only). R programming 2016-04-21 2017-10-09
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

UNIX command line and scripting https://tess.elixir-europe.org/materials/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. Awk, Bash, Unix 2016-04-21 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 https://tess.elixir-europe.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
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

High-throughput sequencing training materials repository https://tess.elixir-europe.org/materials/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 in next-generation sequencing data analysis” workshop which took place at the University of Cambridge, UK, on 13-14 January 2015. Following this workshop, a Git repository has been set up for sharing annotated materials. This repository uses Git, hence it is decentralized and self-managed by the community and can be forked/built-upon by all users. Data architecture, analysis and design Bioinformatics High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling Life Science Researchers PhD students Trainers beginner bioinformaticians post-docs 2015-12-17 2017-10-09
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

RNA-seq data analysis: from raw reads to differentially expressed genes https://tess.elixir-europe.org/materials/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 10-30 minute lectures intertwined with hands-on exercises, and it can be accomplished in a day. As the user-friendly Chipster software is used in the exercises, no prior knowledge of R/Bioconductor or Unix ir required, and the course is thus suitable for everybody. Our book RNA-seq data analysis: A practical approach (CRC Press) can be used as background reading. The following topics and analysis tools are covered: 1. Introduction to the Chipster analysis platform 2. Quality control of raw reads (FastQC, PRINSEQ) 3. Preprocessing (Trimmomatic, PRINSEQ) 4. Alignment to reference genome (TopHat2) 5. Alignment level quality control (RseQC) 6. Quantitation (HTSeq) 7. Experiment level quality control with PCA and MDS plots 8. Differential expression analysis (DESeq2, edgeR) -normalization -dispersion estimation -statistical testing -controlling for batch effects, multifactor designs -filtering -multiple testing correction 9. Visualization of reads and results -genome browser -Venn diagram -volcano plot -plotting normalized counts for a gene -expression profiles 10. Experimental design Sequencing RNA Data architecture, analysis and design Bioinformatics Bioinformatics, Differential expression, Ngs, Rna seq Bench biologists Life Science Researchers 2015-12-04 2017-10-09