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Content provider: GOBLET 

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Keywords: Exploratory-analysis  or metagenomics  or Chip-seq  or Systems  or Sequence alignment  or Ngs bioinformatics 


Using Bioinformatics to Understand Genetic Diseases: A Practical Guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases. A rare variation in the insulin gene is discussed, and the impact of the variation on the gene...

Keywords: Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material

Using Bioinformatics to Understand Genetic Diseases: A Practical Guide https://tess.elixir-europe.org/materials/using-bioinformatics-to-understand-genetic-diseases-a-practical-guide This Practical Guide in the Bringing Bioinformatics into the Classroom series outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases. A rare variation in the insulin gene is discussed, and the impact of the variation on the gene product, and how this results in disease, is explored. Specifically, this Guide introduces a range of commonly used bioinformatics tools and databases with which to analyse both DNA and protein sequences, and protein structures. On reading the Guide and completing the exercises, users will be able to: i) investigate the locations of genes on the human genome using a genome browser; ii) compare DNA sequences using an alignment tool; iii) translate a DNA sequence into its protein product; iv) search a protein structure database, and visualise the 3D structure of insulin; and v) infer whether insulin is specific to humans by using protein sequence database search tools. Basic bioinformatics, Bioinformatics schools, Gene finding, Genetic mutation, Insulin structure, Sequence alignment, Sequence database searching, Training material 2019-03-18
EMBL-EBI Train Online

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently.

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems

EMBL-EBI Train Online https://tess.elixir-europe.org/materials/embl-ebi-train-online If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently. Bioinformatics Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems Beginner informatics Life sciences 2018-05-11
TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/tgac_seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data analysis for plant species data Data quality checks Estimation of reproducibility Batch effects Statistical concepts Importance of standards Data formats Data integration What will I learn? To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions Identify key challenges, opportunities and bottlenecks Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics Sequence analysis Plant biology Database management Bioinformatics Ngs, Ngs bioinformatics, Plants bioinformatics PhD students plant researchers post-docs 2015-06-22 2017-10-09
SV-Autopilot: the new face of Structural Variant Detection

Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager...

Keywords: Ngs bioinformatics, Structural variations

SV-Autopilot: the new face of Structural Variant Detection https://tess.elixir-europe.org/materials/sv-autopilot-the-new-face-of-structural-variant-detection Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager to identify large structural variants in multiple accessions of Arabidopsis. What is needed is a tool which can identify the type and quality of the sequencing reads, assemble them with regards to a reference genome, and predict large structural variants (>30nt). Lastly, it is desirable that the tool should have a user-friendly interface with which bench scientists can easily examine structural variants in their accession(s) of interest that need to be validated. Here we have not only created the benchmark data, but have also created a Virtual Machine framework that can automate this process using multiple SV prediction algorithms in parallel and refine the output to reduce false positive calls. We call this SV-AUTOPILOT, a Structural Variation AUTOmated PIpeLine Optimization Tool. This tool was tested by participants during the workshop. Link to SV-Autopilot: https://github.com/ALLBio/allbiotc2 Ngs bioinformatics, Structural variations Biologists bioinformaticians software developers, bioinformaticians 2014-09-10 2017-10-09
Quality Control of Illumina Sequencing data in the cloud

This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data...

Keywords: Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data

Quality Control of Illumina Sequencing data in the cloud https://tess.elixir-europe.org/materials/quality-control-of-illumina-sequencing-data-in-the-cloud This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data and learn to trim both bad quality bases and adapter sequences Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data Beginners 2014-01-13 2017-10-09
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies https://tess.elixir-europe.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Sequence comparison - undergraduate lab https://tess.elixir-europe.org/materials/sequence-comparison-undergraduate-lab This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of the lab should be easy to adapt to other environments. This lab makes use of EMBOSS programs, prss in the FASTA package, as well as the NCBI BLAST website. I usually deliver this lab after a series of lectures discussing dotmatrix plots and sequence alignment. Students enter their answers to the questions into a quiz set up within moodle which allows for easier marking. Dotmatrix plots, Scoring matrices, Sequence alignment Undergraduate students 2013-11-12 2017-10-09