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Authors: Alexander Botzki 


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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
Custom training: OpenRefine

The aim of this training is to help you use OpenRefine on your own data. This can contain subjects like: load data files, import and parse data files from a URL clean data files: rename columns, transform and edit cells, split multivalue cells... transform data from one format to another:...

Scientific topics: Data quality management

Custom training: OpenRefine https://tess.elixir-europe.org/materials/custom-training-openrefine The aim of this training is to help you use OpenRefine on your own data. This can contain subjects like: load data files, import and parse data files from a URL clean data files: rename columns, transform and edit cells, split multivalue cells... transform data from one format to another: e.g. merge data from two files using  a column that is common to both data files, create new rows based on columns and vice versa... export cleaned, transformed data data manipulation pipelines data dashboards Data quality management Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
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....

Scientific topics: Protein structure analysis

Protein Structure Analysis https://tess.elixir-europe.org/materials/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 homologuous structures. We will use the FoldX program to quantify various interactions in the structures. Protein structure analysis Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
Data manipulation in OpenRefine

Most statistical and data mining tools assume that the data files are in a specific format, often completely different from the format that is created by the instrument that generates the data. Moreover, most of these tools only provide limited functionality for getting the raw data files in the...

Data manipulation in OpenRefine https://tess.elixir-europe.org/materials/data-manipulation-in-openrefine Most statistical and data mining tools assume that the data files are in a specific format, often completely different from the format that is created by the instrument that generates the data. Moreover, most of these tools only provide limited functionality for getting the raw data files in the correct format. OpenRefine is a powerful tool for cleaning up messy data and transforming it in the required format.  Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15