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Target audience: PhD 

Using the Norwegian e-infrastructure for Life Science and usegalaxy.no

Online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the national supported Galaxy (usegalaxy.no). The course will consist of lessons covering the necessary topics alternating with hands-on sessions to gain practical experience.

Keywords: NeLS, Data storage, data sharing, Data analysis

Using the Norwegian e-infrastructure for Life Science and usegalaxy.no http://tess.elixir-uk.org/materials/using-the-norwegian-e-infrastructure-for-life-science-and-usegalaxy-no Online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the national supported Galaxy (usegalaxy.no). The course will consist of lessons covering the necessary topics alternating with hands-on sessions to gain practical experience. NeLS, Data storage, data sharing, Data analysis PhD postdocs Researchers
Practicalities of data handling

Slides for the "Practicalities of data handling" session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg.

Scientific topics: Data management, Data acquisition, Data security

Operations: Data handling

Keywords: data encryption, data protection, setup, checksums, Data transfer, Data storage, data organisation

Resource type: Presentation

Practicalities of data handling http://tess.elixir-uk.org/materials/practicalities-of-data-handling Slides for the "Practicalities of data handling" session of the "Research Data Management and Stewardship Training" held regularly by ELIXIR-Luxembourg. Pinar Alper Roland Krause Nene Barry Data management Data acquisition Data security data encryption, data protection, setup, checksums, Data transfer, Data storage, data organisation Researchers PhD Master students
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics http://tess.elixir-uk.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
Metagenomics 2015

Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015

Scientific topics: Metagenomics

Keywords: Metagenomics

Metagenomics 2015 http://tess.elixir-uk.org/materials/metagenomics-2015 Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015 Metagenomics Metagenomics PhD post-docs 2015-11-23 2017-10-09
De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly

De Novo http://tess.elixir-uk.org/materials/de-novo Training Materials from the 2015 De Novo course run by TGAC De novo, De novo genome assembly PhD PhD students post-docs postdoctoral researchers 2015-09-17 2017-10-09
Python @ TGAC - Python for Life Scientists: Managing biological data with Python

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input,...

Keywords: Biopython, Python, Python biologists

Python @ TGAC - Python for Life Scientists: Managing biological data with Python http://tess.elixir-uk.org/materials/python-tgac-python-for-life-scientists-managing-biological-data-with-python Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover: Working with DNA and protein sequences Data retrieval from files and their manipulation Running applications, such as BLAST, locally and from a script Finding motifs in sequences Parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc. Biopython will be also introduced and applied to some of the mentioned examples. The course is meant to be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts. Unix/Linux basic skills will be provided at the beginning of the course. Biopython, Python, Python biologists PhD post-docs 2015-07-14 2017-10-09
De Novo Assembly @ TGAC 2015

This course took place between 12-15 May 2015 Overview: The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing...

Keywords: De novo

De Novo Assembly @ TGAC 2015 http://tess.elixir-uk.org/materials/de-novo-assembly-tgac-2015 This course took place between 12-15 May 2015 Overview: The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing project, quality control and preprocessing of datasets, generation and evaluation of first pass assemblies, assembly improvement and finishing. Practical exercises will be performed on small-scale real datasets, including Illumina and Pacbio sequences, including best practices and tips based on TGAC’s faculty experience. The course will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities and discussions. The participants will gain first-hand experience and understanding on NGS assembly, working with the assistance of the faculty, troubleshooting small problems, and reviewing the results. De novo PhD post-docs 2015-07-14 2017-10-09
TGAC Metagenomics: From bench to data analysis

This course took place at TGAC on 8-12 September 2014 What is the workshop about? A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem...

Scientific topics: Metagenomics

Keywords: Metagenomics

TGAC Metagenomics: From bench to data analysis http://tess.elixir-uk.org/materials/tgac-metagenomics-from-bench-to-data-analysis This course took place at TGAC on 8-12 September 2014 What is the workshop about? A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem solving activity utilizing the bioinformatics training they will be receiving during the course. What will it cover? To provide an overview of the main aspects involved in metagenomics from the bench to data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research Target Audience: This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics. Metagenomics Metagenomics PhD postdocs 2015-06-25 2017-10-09