106 materials found
Content provider:
GOBLET
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/critical-guide-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/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.
Nicole Vasilevsky
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...
Biocuration: An Introduction
https://www.mygoblet.org/training-portal/materials/biocuration-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.
Nicole Vasilevsky
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://www.mygoblet.org/training-portal/materials/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
Monica Munoz-Torres
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://www.mygoblet.org/training-portal/materials/ember-practical-guide-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).
Terri Attwood
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://www.mygoblet.org/training-portal/materials/interactive-bioinformatics-taster-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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/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.
Terri Attwood
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://www.mygoblet.org/training-portal/materials/train-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.
Chris Taylor
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://www.mygoblet.org/training-portal/materials/ggplot2-pragmatic-ggplot
https://tess.elixir-europe.org/materials/ggplot2-pragmatic-ggplot
A fully contained course for GGPLOT2
Dan MacLean
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://www.mygoblet.org/training-portal/materials/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).
Donald Roy Forsdyke
Evolutionary biology
Biohistory, Evolutionary bioinformatics, Evolutionary biology
High School Students
Researchers
University and College Level Students
2017-04-04
2017-10-09
UNIX Fundamentals
This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge.
The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.
At the end of...
Keywords: Problem based learning, Programming, Unix
UNIX Fundamentals
https://www.mygoblet.org/training-portal/materials/unix-fundamentals
https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc
This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge.
The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience.
At the end of the course, participants are expected to be able to:
Have some understanding on UNIX systems
Navigate through the UNIX filesystem
Execute and understand some UNIX process commands
Correctly set file permissions
Perform basic file management
Participants are encouraged to follow the tutorial sections sequentially.
The tutorial content is sometimes an oversimplification of the Truth - yes, we know!
Due to the diversity of computer systems, we will just assume that participants do have access to a terminal.
For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics:
Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis
Patricia Palagi
Problem based learning, Programming, Unix
Bench biologists
Clinical Scientists
Graduate Students
beginner bioinformaticians
biocurators
2014-01-13
2017-10-09
BioJS
Introduction to BioJS a standard for visualisation of biological data in JavaScript
Keywords: Biojs, Javascript, Software, Standards
BioJS
https://www.mygoblet.org/training-portal/materials/biojs-0
https://tess.elixir-europe.org/materials/biojs-1ff5ad84-3b06-4997-bba6-e18a4dcf32c0
Introduction to BioJS a standard for visualisation of biological data in JavaScript
Manuel Corpas
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...
Signalling Networks: From Data to Modelling
https://www.mygoblet.org/training-portal/materials/signalling-networks-data-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.
Paul Yorke
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...
Network Analysis with Cytoscape and PSICQUIC
https://www.mygoblet.org/training-portal/materials/network-analysis-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.
Paul Yorke
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://www.mygoblet.org/training-portal/materials/statistics-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.
András Aszódi
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://www.mygoblet.org/training-portal/materials/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.
András Aszódi
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,...
R as a programming language
https://www.mygoblet.org/training-portal/materials/r-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).
András Aszódi
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://www.mygoblet.org/training-portal/materials/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.
András Aszódi
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://www.mygoblet.org/training-portal/materials/introduction-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.
allegra.via Via
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://www.mygoblet.org/training-portal/materials/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.
Gabriella Rustici
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://www.mygoblet.org/training-portal/materials/rna-seq-data-analysis-raw-reads-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
Eija Korpelainen
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
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
https://www.mygoblet.org/training-portal/materials/metagenomics-2015
https://tess.elixir-europe.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
Paul Yorke
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
https://www.mygoblet.org/training-portal/materials/introduction-linux-command-line
https://tess.elixir-europe.org/materials/introduction-to-linux-command-line
Introduction to Linux basic command line
Paul Yorke
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
https://www.mygoblet.org/training-portal/materials/embo-2015
https://tess.elixir-europe.org/materials/embo-2015
Link to the GitHub repository containing all the training materials made available for the 2015 EMBO event held at TGAC
Paul Yorke
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
GBS
https://www.mygoblet.org/training-portal/materials/gbs
https://tess.elixir-europe.org/materials/gbs
Training Materials from the 2015 GBS course run by TGAC
Paul Yorke
Genotyping
Graduate Students
post-docs
2015-09-17
2017-10-09