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11 materials found

Authors: Aidan Budd  or Alexander Botzki 


Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

Containers & Workflow pipelines workshop http://tess.elixir-uk.org/materials/containers-workflow-pipelines-workshop The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well. On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Containers, Nextflow bioinformaticians
Introduction to Protein Structure Analysis

This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure....

Operations: Visualisation

Keywords: Protein structure visualisation

Resource type: e-learning

Introduction to Protein Structure Analysis http://tess.elixir-uk.org/materials/introduction-to-protein-structure-analysis This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins (without any structure information) and to find homologous structures. We will use online tools to quantify various interactions in the structures. ## Objectives * Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it. * Display protein structure data and compare structures, through the use of Yasara. * Create high-quality graphical representations of the structures. * Calculate the effect of mutations on the stability of your protein. Janick Mathys Protein structure visualisation Life Science Researchers
Preserve, publish and share your data

- why preserve data - what data should be preserved - how share data - where to deposit your data - Fairsharing, re3data - ELIXIR Core Resources - Data Formats - Generic archives

Scientific topics: Data management, Data submission, annotation, and curation

Keywords: data formats, ELIXIR Core resources, FAIR data submission

Resource type: Presentation

Preserve, publish and share your data http://tess.elixir-uk.org/materials/preserve-publish-and-share-your-data - why preserve data - what data should be preserved - how share data - where to deposit your data - Fairsharing, re3data - ELIXIR Core Resources - Data Formats - Generic archives Data management Data submission, annotation, and curation data formats, ELIXIR Core resources, FAIR data submission life scientists
Reusing existing data

- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations

Scientific topics: Data management

Keywords: data licenses, software licenses, data journal

Resource type: Presentation

Reusing existing data http://tess.elixir-uk.org/materials/reusing-existing-data - how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations Data management data licenses, software licenses, data journal life scientists
Research Data Management in Life Sciences

The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.

Scientific topics: Data management

Resource type: Presentation, Vignette, Video

Research Data Management in Life Sciences http://tess.elixir-uk.org/materials/research-data-management-in-life-sciences The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences. Data management Life Science Researchers
Data Management and Writing a Data Management Plan

Writing a Data Management Plan A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data.

Scientific topics: Data management

Resource type: e-learning

Data Management and Writing a Data Management Plan http://tess.elixir-uk.org/materials/data-management-and-writing-a-data-management-plan Writing a Data Management Plan A good data management plan is crucial for any scientist and researcher. In this course, you will learn how to write one. You will find out how you can prepare, handle and share your research data. Geert Bonamie Data management
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 http://tess.elixir-uk.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
Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Summarising sets of phylogenies http://tess.elixir-uk.org/materials/summarising-sets-of-phylogenies A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Multiple Sequence Alignment http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignment An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of alignmetns (structural and evolutionary), and ways of building manual and automatic alignments, and an introduction to JalView Multiple sequence analysis, Protein structure, Sequence analysis Bench biologists 2013-10-23 2017-10-09
Introduction to Bioinformatics

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: Introduction bioinformatics

Introduction to Bioinformatics http://tess.elixir-uk.org/materials/introduction-to-bioinformatics An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could be wrong, and what we can do to spot it. Introduction bioinformatics Bench biologists 2013-10-23 2017-10-09
Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics

Interpreting Phylogenies http://tess.elixir-uk.org/materials/interpreting-phylogenies Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09