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Keywords: Exploratory-analysis  or metagenomics  or HCI  or Programming 


Keynote on Visual Design Principles

Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure...

Keywords: Genome, HCI, Information visualisation, Communication

Resource type: Video

Keynote on Visual Design Principles https://tess.elixir-europe.org/materials/keynote-on-visual-design-principles Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure design.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Martin Krzywinski Genome, HCI, Information visualisation, Communication 2017-01-31
Infectious Disease Host/Pathogen Relationships

Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance...

Keywords: Populations, HCI

Resource type: Video

Infectious Disease Host/Pathogen Relationships https://tess.elixir-europe.org/materials/infectious-disease-host-pathogen-relationships Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance of human-computer interface professionals in the design process.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Populations, HCI 2017-01-31
Revise and Redraw—Visual Design Principles for Scientific Data

Martin Krzywinski's keynote from 1st BiVi in 2014. He discusses visual design principles and communicating effectively in pictures.This talk distills core concepts of information design into practical guidelines for creating scientific figures. We will explain how to generate visual vocabularies...

Keywords: HCI, Communication

Resource type: Video

Revise and Redraw—Visual Design Principles for Scientific Data https://tess.elixir-europe.org/materials/revise-and-redraw-visual-design-principles-for-scientific-data Martin Krzywinski's keynote from 1st BiVi in 2014. He discusses visual design principles and communicating effectively in pictures.This talk distills core concepts of information design into practical guidelines for creating scientific figures. We will explain how to generate visual vocabularies with graphical elements, combine them into phrases, and package them into a complete figure, the visual equivalent of a paragraph. We show how effective designs for this composition are underpinned by conclusions from studies in visual perception and awareness. Created at: 1st BiVi Annual Meeting. Martin Krzywinski HCI, Communication 2017-02-02
Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees

Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting.

Keywords: Genome, Populations, HCI

Resource type: Poster

Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees https://tess.elixir-europe.org/materials/evaluation-of-helium-visualisation-of-large-scale-plant-pedigrees Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting. Dr. Paul Shaw Genome, Populations, HCI 2017-02-02
RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
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://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 Problem based learning, Programming, Unix Bench biologists Clinical Scientists Graduate Students beginner bioinformaticians biocurators 2014-01-13 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
Perl 1 Training Course - For Programming Beginners

A set of slides from The Sainsbury Laboratory Perl course for absolute beginners

Keywords: Perl, Programming

Perl 1 Training Course - For Programming Beginners https://tess.elixir-europe.org/materials/perl-1-training-course-for-programming-beginners A set of slides from The Sainsbury Laboratory Perl course for absolute beginners Perl, Programming Beginners Bench biologists 2014-07-03 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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

Keywords: RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis