ELIXIR TtR course: Basic genomics using advanced analysis tools
Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
Scientific topics: Genomics
Keywords: Galaxy, training, Genomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
ELIXIR TtR course: Basic genomics using advanced analysis tools
https://elixir.mf.uni-lj.si/course/view.php?id=42
http://tess.elixir-uk.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools
Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
Christophe Antoniewski
Olivier Inizan
Christophe Antoniewski
Olivier Inizan
Genomics
Galaxy, training, Genomics, eLearning, EeLP
life scientists
beginner bioinformaticians
Postgraduate students
Probabilistic programming with (R)Stan
Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be...
Scientific topics: Statistics and probability
Probabilistic programming with (R)Stan
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/358-probabilistic-programming-with-r-stan
http://tess.elixir-uk.org/materials/probabilistic-programming-with-r-stan
Probabilistic models describe how the observed data was generated, and what structure the signal and noise from potentially multiple sources may have. Many classical statistical models are special cases of probabilistic models with special modeling assumptions. Probabilistic models can be implemented, improved, and critizised in a flexible, explicit and transparent manner, and the analysis can be supported with prior information about the data.
This 1-day course provides an introduction to Bayesian/probabilistic models. We will implement standard linear models based on the rstanarm package of the R statistical programming environment and readily available example data sets. The workshop is an ideal opportunity to familiarize yourself with the basic ideas in probabilistic modeling such as prior information, likelihood, model criticism and validation, as well as some of the available tools. At the end, you should be able to implement basic probabilistic models yourself, and understand their relative advantages and pitfalls compared to their classical alternatives.
Leo Lahti
Statistics and probability
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
Image Ethics and Poster Design
The image ethics part handles on the theoretical aspects of image manipulation, the mistakes people make and how to avoid image fraud. VIB has guidelines for acceptable scientific image manipulations. Not all manipulations are scientifically correct. There are manipulations that fall within the...
Image Ethics and Poster Design
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/360-image-ethics-and-poster-design
http://tess.elixir-uk.org/materials/image-ethics-and-poster-design
The image ethics part handles on the theoretical aspects of image manipulation, the mistakes people make and how to avoid image fraud. VIB has guidelines for acceptable scientific image manipulations. Not all manipulations are scientifically correct. There are manipulations that fall within the scope of scientific misconduct, because they result in misrepresentation of the data. Such misrepresentation makes it impossible for others to interpret the data correctly, or worse, leads to conclusions that are not correct. The second part of this course deals with poster design. Scientific posters are a resume of a piece or timespan of research on one square meter of paper. They are best compared to slides for oral presentations, not a written document. Posters can’t convey detailed evidence like scientific articles, it must visualize a message on its own. When standing a meter away from a poster you hardly feel like reading much text, especially when the author/designer stands next to it. A poster must bring that message without requiring oral explanation, but with as little text as possible.
Prerequisites
Participants must have experience with GIMP and Inkscape.
Schedule
See the TRAINING AT VIB website for a detailed schedule of this training.
Training material
Not available
Links
Not available
Scientific topics
Image data
Target audience
Life Science Researchers, PhD students, post-docs, beginner bioinformaticians
Christof De Bo
Image
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
Analysis of metabolome data
This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of...
Scientific topics: Metabolomics
Analysis of metabolome data
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/356-analysis-of-metabolome-data
http://tess.elixir-uk.org/materials/analysis-of-metabolome-data
This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of differential metabolites will be introduced. Afterwards, the trainee should be able to perform independently a comparative analysis of raw metabolome data and to pinpoint the well-known metabolites in the chromatogram.
Kris Morreel
Metabolomics
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
Advanced FlowJo training
The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high...
Advanced FlowJo training
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/359-advanced-flowjo-training
http://tess.elixir-uk.org/materials/advanced-flowjo-training
The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high dimensionality.
Prerequisites
Participants must have experience with FlowJo.
Schedule
See the TRAINING AT VIB website for a detailed schedule of this training.
Training material
Not available
Links
Not available
Scientific topics
FlowJo
Target audience
Life Science Researchers, PhD students, post-docs, beginner bioinformaticians
Christoph Freier (FlowJo)
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
A tour of machine learning - classification
Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses,...
Scientific topics: Machine learning
A tour of machine learning - classification
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/357-a-tour-of-machine-learning-classification
http://tess.elixir-uk.org/materials/a-tour-of-machine-learning-classification
Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses, gene/protein annotation, drug design, image recognition, text mining and many others. However, building successful machine learning models requires a substantial amount of “black art” that is hard to find in textbooks. This course is an interactive Jupyter Notebook (Python) that will teach you how to build successful machine learning models. No background in machine learning is assumed, just a keen interest.
Sven Degroeve
Machine learning
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
Introduction to Biopython
Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient.
The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the...
Scientific topics: Software engineering
Introduction to Biopython
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/176-biopython
http://tess.elixir-uk.org/materials/introduction-to-biopython-8ccf2441-bd7d-46f2-84f8-c2b123844a23
Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient.
The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the command line. Afterwards you will take a tour of the most important components: sequences, NCBI queries, BLAST, trees, and 3D structures. You will try each of these modules on practical examples. Please don't hesitate to ask questions about Python basics or particular data formats (e.g. XML or NGS data).
The second day of the training is to broaden your perspective: What other features does the library have? How can you use the documentation effectively? What is Biopython not capable of? What can I do to visualize my data? Are there alternatives? If you have your own data that you would like to work on with Biopython in more detail, there is room for that.
For us, the most important thing is to identify concrete Python modules and functions that help you to get your research done.
Participants are encouraged to submit a description of their research topic and/or the questions they would like to answer with Biopython. Additionally, participants can bring their own data that they would like to process in Python to the training.
Kristian Rother
Software engineering
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
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
Resource type: e-learning
UNIX Fundamentals
https://www.mygoblet.org/training-portal/materials/unix-fundamentals
http://tess.elixir-uk.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
Vassilios Ioannidis
Grégoire Rossier
Volker Flegel
Heinz Stockinger
Frédéric Schütz
Problem based learning, Programming, Unix
Bench biologists
Clinical Scientists
Graduate Students
beginner bioinformaticians
biocurators
2014-01-13
2017-10-09
Metagenomics
This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees.
The 2nd part of the...
Metagenomics
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/329-metagenomics
http://tess.elixir-uk.org/materials/metagenomics
This training will start with the presentation of a 16S pipeline (psbweb05.psb.ugent.be/lotus/) in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees.
The 2nd part of the training will give an overview of numerical ecology and takes part entierly in R.
Falk Hildebrand (EMBL)
post-docs
PhD students
beginner bioinformaticians
Life Science Researchers
2016-04-22
2016-08-31
RNA-Seq analysis for differential expression in GenePattern
We will investigate the following items:
Quality control of the sequence reads to detect biases or contaminating adapters
Mapping of the reads to the reference genome with use of a transcript database model
Quality control of the mapping results
Adjusting the mapping data to...
RNA-Seq analysis for differential expression in GenePattern
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/328-rna-seq-analysis-genepattern
http://tess.elixir-uk.org/materials/rna-seq-analysis-for-differential-expression-in-genepattern
We will investigate the following items:
Quality control of the sequence reads to detect biases or contaminating adapters
Mapping of the reads to the reference genome with use of a transcript database model
Quality control of the mapping results
Adjusting the mapping data to compensate for artefacts like duplicates
Calculate transcript counts usable for differential expression and merging of count tables
Computing differential expression using EdgeR and DESeq2
The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training.
Janick Mathys and Guy Bottu
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
Introduction to Linux for bioinformatics
This training is intended for all Linux novices who want to learn the basics of Linux without getting too much technical details.
This hands-on training will show you how to effectively use Linux, a free operating system. Bioinformatics depends heavily on Linux-based computers and software. A lot...
Introduction to Linux for bioinformatics
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/124-linux-for-bioinformatics
http://tess.elixir-uk.org/materials/introduction-to-linux-for-bioinformatics
This training is intended for all Linux novices who want to learn the basics of Linux without getting too much technical details.
This hands-on training will show you how to effectively use Linux, a free operating system. Bioinformatics depends heavily on Linux-based computers and software. A lot of good scientific software is written specifically for Linux/Unix. Additionally, Linux has most popular programming languages (e.g.Python, Perl, C) already installed and ready to use! Data management happens swiftly with the dedicated text manipulation tools and file system properties. This training will teach you all you need to know to swiftly start using Linux, be it on the server of your department, or on your own computer (even if you're already running Windows or Mac OS).
Prior to the training session, you will receive a poll to ask you your personal goals by following this training sesion. Depending on the outcome, the schedule will be adjusted.
Christof De Bo
Life Science Researchers
PhD students
beginner bioinformaticians
2016-04-22
2017-10-09
Hands-on introduction to ChIP-Seq analysis
This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to...
Scientific topics: Mapping, ChIP-seq
Hands-on introduction to ChIP-Seq analysis
https://www.bits.vib.be/training-list/112-bits/training/upcoming-trainings/211-chip-seq
http://tess.elixir-uk.org/materials/hands-on-introduction-to-chip-seq-analysis
This training gives an introduction to ChIP-seq data analysis, covering the processing steps starting from the reads to the peaks. Among all possible downstream analyses, the practical aspect will focus on motif analyses. A particular emphasis will be put on deciding which downstream analyses to perform depending on the biological question.
This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs.
Morgane Thomas-Chollier
Mapping
ChIP-seq
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
RNA-Seq analysis for differential expression
We first perform quality control of the sequence reads to detect biases or leftover adaptors.
We then map the reads to the reference genome with use of a transcript database model.
We perform a detailed QC analysis of the mapping results to again detect potential problems.
The mapping data is...
Scientific topics: RNA-Seq, Gene expression, Differential gene expression profiling
RNA-Seq analysis for differential expression
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/202-rna-seq-analysis
http://tess.elixir-uk.org/materials/rna-seq-analysis-for-differential-expression
We first perform quality control of the sequence reads to detect biases or leftover adaptors.
We then map the reads to the reference genome with use of a transcript database model.
We perform a detailed QC analysis of the mapping results to again detect potential problems.
The mapping data is adjusted to compensate for artifacts like duplicates.
The mappings are used to obtain transcript counts usable for differential expression.
The count tables are merged and used to compute differential expression using several programs.
We START a typical functional analysis of the obtained results similar to what is done for microarray data in order to exemplify handy tools and commercial alternatives.
The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training.
St├®phane Plaisance
RNA-Seq
Gene expression
Differential gene expression profiling
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
Introductory session on programming with Bioperl
On the first day, we will refresh Perl syntax and types of variables. This basic knowledge will serve as a starting point to explain the use of subroutines, and how to make a module of your subroutine.
On the second day we will prepare for Bioperl by explaining how you can reuse Perl code....
Introductory session on programming with Bioperl
https://www.bits.vib.be/training-overview/programming-with-bioperl
http://tess.elixir-uk.org/materials/introductory-session-on-programming-with-bioperl
On the first day, we will refresh Perl syntax and types of variables. This basic knowledge will serve as a starting point to explain the use of subroutines, and how to make a module of your subroutine.
On the second day we will prepare for Bioperl by explaining how you can reuse Perl code. Object-oriented programming will only be explained to the extent necessary for using Bioperl. We will write our first simple program in Bioperl and explore places where you can find information on the Bioperl modules.
On the third day we will practice Bioperl further in real-life examples like sequence processing and applications that are defined by the participants.
By the end of the session, you will understand Bioperl, and have already some first programming skills in Bioperl, which will allow you to practice further at an accelerated speed in order to becoming proficient in Bioperl.
Marc Logghe
Life Science Researchers
PhD students
post-docs
beginner bioinformaticians
2016-04-22
2016-06-15
Gentle hands-on introduction to Python programming
This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing...
Scientific topics: Software engineering
Gentle hands-on introduction to Python programming
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/92-python
http://tess.elixir-uk.org/materials/gentle-hands-on-introduction-to-python-programming
This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing programming skills in Python.
Tuur Muyldermans / Alexander Botzki
Software engineering
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
GATK Best practices for variant discovery
ÔÇïIn the course of this workshop, we highlight key functionalities such as
GVCF workflow for joint variant discovery in cohorts
RNAseq-specific processing
somatic variant discovery using MuTect2.
capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery
the use...
Scientific topics: RNA-Seq
GATK Best practices for variant discovery
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/286-gatk-best-practices-for-variant-discovery
http://tess.elixir-uk.org/materials/gatk-best-practices-for-variant-discovery
ÔÇïIn the course of this workshop, we highlight key functionalities such as
GVCF workflow for joint variant discovery in cohorts
RNAseq-specific processing
somatic variant discovery using MuTect2.
capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery
the use of pipelining tools to assemble and execute GATK workflows.
Geraldine Van der Auwera
RNA-Seq
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
Building bioinformatics workflows
This course presents a comprehensive overview of the principles and applications of scientific workflow systems. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real biomedical datasets. The course will be based on freely available...
Building bioinformatics workflows
https://www.bits.vib.be/training-overview/building-bioinformatics-worksflows
http://tess.elixir-uk.org/materials/building-bioinformatics-workflows
This course presents a comprehensive overview of the principles and applications of scientific workflow systems. The course combines lectures with hands-on exercises in which the participants learn to apply these principles to real biomedical datasets. The course will be based on freely available open source software and more specifically on Galaxy and KNIME.
Tim Van den Bulcke
Life Science Researchers
PhD students
post-docs
beginner bioinformaticians
2016-04-22
2016-06-15
Basics of databases and MySQL
This hands-on training provides a comprehensive introduction to relational databases and the use of the MySQL relational database management system. MySQL is the leading free management system for relational databases. The training shows you how to use MySQL to efficiently store your data in...
Basics of databases and MySQL
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/127-basics-of-databases-and-mysql
http://tess.elixir-uk.org/materials/basics-of-databases-and-mysql
This hands-on training provides a comprehensive introduction to relational databases and the use of the MySQL relational database management system. MySQL is the leading free management system for relational databases. The training shows you how to use MySQL to efficiently store your data in databases and manage both data and access to the data. The training gives an overview of the SQL syntax that allows you to access and manipulate the data. Additionally, the use of Python to automatically access MySQL databases is explained.
Gerben Menschaert
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
Basic statistics in R, part II
This training builds further on the Basic statistics in R training, showing you how to do statistical analyses in R. Where the Basic statistics in R training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents), this training...
Basic statistics in R, part II
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/290-r-2
http://tess.elixir-uk.org/materials/basic-statistics-in-r-part-ii
This training builds further on the Basic statistics in R training, showing you how to do statistical analyses in R. Where the Basic statistics in R training is an introduction to the use of R and RStudio and stops at very basic analyses (t-tests and non-parametric equivalents), this training gives you a full overview of statistical analyses in R including regression, ANOVA... Emphasis will be placed on practical applications. To this end, theory will be complemented with hands-on exercises in R, a free software environment for statistical computing and graphics. Topics include distributions, plots, confidence intervals, hypothesis testing...
Veronique Storme
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
Hands-on introduction to NGS variant analysis
This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.
This training does not cover all methods available today. It does...
Hands-on introduction to NGS variant analysis
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/201-ngs-variant-analysis
http://tess.elixir-uk.org/materials/hands-on-introduction-to-ngs-variant-analysis
This training gives an introduction to the use of popular NGS analysis software packages at the command line. It reviews several exchangeable tools and provide hints to evaluate quality and content of DNA-Seq data by a biologist.
This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs.
St├®phane Plaisance
DNA
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
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
http://tess.elixir-uk.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
Plant and Pathogen Bioinformatics
This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an...
Keywords: Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants
Plant and Pathogen Bioinformatics
https://www.mygoblet.org/training-portal/materials/plant-and-pathogen-bioinformatics
http://tess.elixir-uk.org/materials/plant-and-pathogen-bioinformatics
This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an introduction to researchers wishing to work in the plant-pathogen interactions area, covering major database resources and basis data analysis techniques. The aims of the course were to teach participants how to browse and access a range of data types from leading public repositories; use bioinformatic tools to explore plant and pathogen-related biological data; discuss the benefits and limitations of various bioinformatic techniques; and assess the purpose of specific analyses in a wider context. We would like to thank all presenters for their contributions and their willingness to further distribute their material via Goblet.
Paul Kersey
Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants
beginner bioinformaticians
early stage phytopathogen researchers
2014-09-11
2017-10-09
Training Bioinformatics in the Cloud
I present the points of view, the challenges and advantages of developing training materials through the cloud.
Keywords: Advanced bioinformatics training, Cloud computing, Training
Training Bioinformatics in the Cloud
https://www.mygoblet.org/training-portal/materials/training-bioinformatics-cloud
http://tess.elixir-uk.org/materials/training-bioinformatics-in-the-cloud
I present the points of view, the challenges and advantages of developing training materials through the cloud.
Manuel Corpas
Advanced bioinformatics training, Cloud computing, Training
Bench biologists
beginner bioinformaticians
2014-05-20
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://www.mygoblet.org/training-portal/materials/using-r-python
http://tess.elixir-uk.org/materials/using-r-with-python
This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented are also provided.
allegra.via Via
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://www.mygoblet.org/training-portal/materials/searching-data-using-python
http://tess.elixir-uk.org/materials/searching-data-using-python
This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and how to use sets to find unique records in two datasets and remove redundancy.
allegra.via Via
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://www.mygoblet.org/training-portal/materials/pattern-matching
http://tess.elixir-uk.org/materials/pattern-matching
This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file.
allegra.via Via
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://www.mygoblet.org/training-portal/materials/writing-functions-python-programming
http://tess.elixir-uk.org/materials/writing-functions-in-python-programming
This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.
allegra.via Via
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://www.mygoblet.org/training-portal/materials/python-programs
http://tess.elixir-uk.org/materials/python-programs
This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.
allegra.via Via
Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
2013-11-04
2017-10-09
Bioinformatics: Gene-protein-structure-function
This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...
Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast
Bioinformatics: Gene-protein-structure-function
https://www.mygoblet.org/training-portal/materials/bioinformatics-gene-protein-structure-function
http://tess.elixir-uk.org/materials/bioinformatics-gene-protein-structure-function
This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The presentation concludes with an analysis of 'expert' systems and integrated approaches (GeneQuiz, MAGPIE, InterPro, etc.), and dispels the commonly held notion that one database and/or one analysis tool is best.
Terri Attwood
Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast
beginner bioinformaticians
biocurators
postdoc
postgrad
2013-07-12
2017-10-09
InterPro: An introduction
This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.
Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis
InterPro: An introduction
https://www.mygoblet.org/training-portal/materials/interpro-introduction
http://tess.elixir-uk.org/materials/interpro-an-introduction
This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.
Terri Attwood
Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis
beginner bioinformaticians
biocurators
postdoc
postgrad
2013-07-12
2017-10-09