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Target audience: beginner bioinformaticians 

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 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 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 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. 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...

Scientific topics: Image

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   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 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. 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 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 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 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. 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 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. 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 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 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. 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 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. 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 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. 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 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. 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 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. 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 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. 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 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. 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 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. 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 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. 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 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. 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 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... 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...

Scientific topics: DNA

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

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

Keywords: Programming, Python, Python biologists

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

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: Pattern matching, Programming, Python, Python biologists

Pattern Matching http://tess.elixir-uk.org/materials/pattern-matching This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file. Pattern matching, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Writing functions in Python programming

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

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

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

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

Keywords: Programming, Python, Python biologists

Python Programs http://tess.elixir-uk.org/materials/python-programs This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
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 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. 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 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.  Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09