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Authors: Patricia Palagi  or slugger70 


BLAST and multiple sequence alignment (MSA) programs

Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: Blast, E learning, Multiple sequence alignment

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/materials/blast-and-multiple-sequence-alignment-msa-programs-0b2b34d0-a157-49d4-a065-3dcad67ff99d Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   Blast, E learning, Multiple sequence alignment Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
Phylogenetics of animal viral pathogens

Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions https://tess.elixir-europe.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
ELIXIR EXCELERATE Train the Trainer

This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation *...

Keywords: Train the trainer, Pedagogy, Course development, Course design

Resource type: Training materials

ELIXIR EXCELERATE Train the Trainer https://tess.elixir-europe.org/materials/elixir-excelerate-train-the-trainer This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation * Lesson, course, and materials design * Assessment and feedback in training and teaching Train the trainer, Pedagogy, Course development, Course design Trainers Training instructors Training Designers teachers
Genome Annotation - Genome annotation with Prokka

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile...

Resource type: Tutorial

Genome Annotation - Genome annotation with Prokka https://tess.elixir-europe.org/materials/genome-annotation-genome-annotation-with-prokka Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements. Questions of the tutorial: - How to annotate a bacterial genome? - How to visualize annoted genomic features? Objectives of the tutorial: - Load genome into Galaxy - Annotate genome with Prokka - View annotations in JBrowse
Galaxy Server administration - Server Monitoring and Maintenance

Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring strategies. - Setup and start the...

Resource type: Tutorial

Galaxy Server administration - Server Monitoring and Maintenance https://tess.elixir-europe.org/materials/galaxy-server-administration-server-monitoring-and-maintenance Resources related to configuration and maintenance of Galaxy servers Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring strategies. - Setup and start the Galaxy reports app.
Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Unicycler Assembly https://tess.elixir-europe.org/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I have short reads and long reads. How do I assemble a genome? Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka
Assembly - De Bruijn Graph Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - De Bruijn Graph Assembly https://tess.elixir-europe.org/materials/assembly-de-bruijn-graph-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - What are the factors that affect genome assembly? - How does Genome assembly work? Objectives of the tutorial: - Perform an optimised Velvet assembly with the Velvet Optimiser - Compare this assembly with those we did in the basic tutorial - Perform an assembly using the SPAdes assembler.
Assembly - Introduction to Genome Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Introduction to Genome Assembly https://tess.elixir-europe.org/materials/assembly-introduction-to-genome-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How do we perform a very basic genome assembly from short read data? Objectives of the tutorial: - assemble some paired end reads using Velvet - examine the output of the assembly.
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://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
Bioinformatics for Mass spectrometry analysis

This tutorial on Bioinformatics for Mass spectrometry analysis was part of a full series of tutorials that I have organised in 2009 while sitting in the Educational Committee of the European Proteomics Association (EuPA). Some information on bioinformatics tools would need to be verified, but the...

Keywords: Bioinformatics, Mass spectrometry, Protein identification

Bioinformatics for Mass spectrometry analysis https://tess.elixir-europe.org/materials/bioinformatics-for-mass-spectrometry-analysis This tutorial on Bioinformatics for Mass spectrometry analysis was part of a full series of tutorials that I have organised in 2009 while sitting in the Educational Committee of the European Proteomics Association (EuPA). Some information on bioinformatics tools would need to be verified, but the core of slides is still up to date. It introduces the basic ideas behind mass spectrometry and bioinformatics for protein identification from mass spectrometry data. Bioinformatics, Mass spectrometry, Protein identification Bench biologists PhD students Post-Doctoral Fellows Technicians bioinformaticians master 2013-10-30 2017-10-09
Bioinformatics for MS analysis

The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry.

Keywords: Bioinformatics, Identification, Mass spectrometry

Bioinformatics for MS analysis https://tess.elixir-europe.org/materials/bioinformatics-for-ms-analysis The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry. Bioinformatics, Identification, Mass spectrometry 2013-07-05 2017-10-09