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Target audience: postgrad  or Life Science Researchers 

Machine Learning & BioStatistics Hackathon 2020

Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.

Scientific topics: Computer science, Statistics and probability, Machine learning

Keywords: machine learning, biostatistics, eLearning, EeLP

Resource type: Training materials

Machine Learning & BioStatistics Hackathon 2020 http://tess.elixir-uk.org/materials/machine-learning-biostatistics-hackathon-2020 Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020. Computer science Statistics and probability Machine learning machine learning, biostatistics, eLearning, EeLP Life Science Researchers statisticians Training Designers Training instructors Trainers
HPC Hackathon Materials

Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.

Scientific topics: Computer science

Keywords: HPC, high-performance computing, eLearning, EeLP

Resource type: Training materials

HPC Hackathon Materials http://tess.elixir-uk.org/materials/hpc-hackathon-materials Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021. Computer science HPC, high-performance computing, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
Containers and Workflows training materials hackathon

Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021.

Scientific topics: Computer science

Keywords: Containers, Workflows, eLearning, EeLP

Resource type: Training materials

Containers and Workflows training materials hackathon http://tess.elixir-uk.org/materials/containers-and-workflows-training-materials-hackathon Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021. Computer science Containers, Workflows, eLearning, EeLP Life Science Researchers Training Designers Training instructors Trainers
Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome,...

Keywords: Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material

Resource type: Training materials

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide http://tess.elixir-uk.org/materials/using-bioinformatics-to-hunt-sars-cov-2-its-variants-its-origins-a-practical-guide This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome, its proteins, its origins and its evolution are explored. Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material Trainers Training instructors Training Designers PhD students post-docs Life Science Researchers
Research Data Management and Sharing MOOC

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Keywords: Data Life Cycle, Data managment plan

Resource type: online modules

Research Data Management and Sharing MOOC http://tess.elixir-uk.org/materials/research-data-management-and-sharing-mooc This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans, and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories. Data management Data Life Cycle, Data managment plan Life Science Researchers Researchers
Introduction to research data management, data management planning and services provided by CSC – IT Center for Science

Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project.

Keywords: DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE

Resource type: Series of videos, Video, youtube video

Introduction to research data management, data management planning and services provided by CSC – IT Center for Science http://tess.elixir-uk.org/materials/introduction-to-research-data-management-data-management-planning-and-services-provided-by-csc-it-center-for-science Four short training videos that introduce research data management and data management planning and how to get started with a DMP. In the last part we introduce CSC and ELIXIR services available for an example research group at different stages of their project. Maria Lehtivaara DMP, RDM, plan, research data management, data management, data management plan, ELIXIR-CONVERGE Researchers Life Science Researchers Undergraduate students Master students PhD candidates postdoctoral researchers Senior Researchers, Lab Managers, Postdocs and PhD Students with basic knowledge of DMPs. Participants in the "Introduction to Data Management Plans" workshop.
Biological network data tutorial

In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to...

Keywords: Biological networks, Network Visualization

Resource type: Tutorial

Biological network data tutorial http://tess.elixir-uk.org/materials/biological-network-data-tutorial In this skills session, you will learn: how to upload a biological network from STRING how to extend a network using CyTargetLinker how to load a pathway diagram from WikiPathways how to upload a network shared via NDEx how to visualize data in a network how to create a sub network how to extend a network via R Biological networks, Network Visualization Life Science Researchers PhD students, computer scientists, bioinformaticians and developers who need to maintain/extend existing tools or develop new tools for Galaxy.
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
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
Eurordis Open Academy

The EURORDIS Open Academy currently encompasses the Winter School on Scientific Innovation and Translational Research, the Summer School on Medicines Research and Development, the Leadership School and the Digital School

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research, Rare Diseases

Resource type: course materials, e-learning

Eurordis Open Academy http://tess.elixir-uk.org/materials/eurordis-online-trainning-modules The EURORDIS Open Academy currently encompasses the Winter School on Scientific Innovation and Translational Research, the Summer School on Medicines Research and Development, the Leadership School and the Digital School Rare diseases Rare Diseases & Research, Rare Diseases Patient Advocates Life Science Researchers Biomedical researchers
galaxy.sciensano.be

This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the...

Scientific topics: Microbiology, Sequencing, Genomics, Public health and epidemiology, Bioinformatics

Resource type: Video, Tutorial

galaxy.sciensano.be http://tess.elixir-uk.org/materials/galaxy-sciensano-training This training is meant specifically for the “Galaxy @Sciensano” that is available at https://galaxy.sciensano.be/ and serves two purposes. First, it serves as an introduction in how to handle and employ the Galaxy instance hosted by Sciensano. Secondly, is also serves as a tutorial into both the basics of next-generation sequencing data analysis, but also more specialized topics of interest in public health (e.g. AMR detection, cgMLST analysis etc., SNP-based outbreak analysis etc.). The training consists specifically out of a series of training videos that are publicly available on YouTube. Microbiology Sequencing Genomics Public health and epidemiology Bioinformatics Microbiologists Public Health Professionals Life Science Researchers
Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing

This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Genomic Technologies in Clinical Diagnostics: Next Generation Sequencing http://tess.elixir-uk.org/materials/genomic-technologies-in-clinical-diagnostics-next-generation-sequencing This course is available on FutureLearn and developed by St George's University of London. This postgraduate-level course will help you understand these new and established genetic technologies, and their application to clinical practice. Rare diseases Rare Diseases & Research postgrad Scientists Healthcare
BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Simulation experiment, Systems biology, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

BioSimulations tutorial and help http://tess.elixir-uk.org/materials/biosimulations-help BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface. Simulation experiment Systems biology Computational biology SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE Life Science Researchers Computational biologists modelers
Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis http://tess.elixir-uk.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
Helis Academy - FAIRify your data

FAIRify your data: FAIRification & Data modelling using linked data

Keywords: linked data, Wikidata, data management

Resource type: Slides

Helis Academy - FAIRify your data http://tess.elixir-uk.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
Online course 'Learn to write your Data Management Plan'

Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for...

Keywords: Data management plan, data management

Resource type: e-learning

Online course 'Learn to write your Data Management Plan' http://tess.elixir-uk.org/materials/online-course-learn-to-write-your-data-management-plan Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data. During the course you are writing your DMP step by step. As a result you have written a DMP for you research project. While you are training, you can write your DMP in DMPonline. You can do the whole course or just parts of it. That is all up to you. Data management plan, data management Life Science Researchers
Ready For BioData Management?

"Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences.

Scientific topics: Data management

Keywords: Data managment plan

Resource type: course materials

Ready For BioData Management? http://tess.elixir-uk.org/materials/ready-for-biodata-management "Ready For BioData Management?" is BioData.pt/ELIXIR-Portugal's capacity building program in data management for the life sciences. Marta Silva Data management Data managment plan Life Science Researchers PhD students Master students Technicians
Research Data Management and Sharing

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Resource type: e-learning

Research Data Management and Sharing http://tess.elixir-uk.org/materials/research-data-management-and-sharing This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans, and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories. Today, an increasing number of funding agencies, journals, and other stakeholders are requiring data producers to share, archive, and plan for the management of their data. In order to respond to these requirements, researchers and information professionals will need the data management and curation knowledge and skills that support the long-term preservation, access, and reuse of data. Effectively managing data can also help optimize research outputs, increase the impact of research, and support open scientific inquiry. After completing this course, learners will be better equipped to manage data throughout the entire research data lifecycle from project planning to the end of the project when data ideally are shared and made available within a trustworthy repository. This course was developed by the Curating Research Assets and Data Using Lifecycle Education (CRADLE) Project in collaboration with EDINA at the University of Edinburgh. This course was made possible in part by the Institute of Museum and Library Services under award #RE-06-13-0052-13. The views, findings, conclusions or recommendations expressed in this Research Data Management and Sharing MOOC do not necessarily represent those of the Institute of Museum and Library Services. Data management Life Science Researchers
Research Data Management

Welcome to Research Data Management Training for Information Professionals! This course will provide you with training on the research data management (RDM) topics listed below in a biomedical context. The material presented began as an NIH-funded research study to assess material for teaching...

Scientific topics: Data management

Resource type: e-learning

Research Data Management http://tess.elixir-uk.org/materials/research-data-management Welcome to Research Data Management Training for Information Professionals! This course will provide you with training on the research data management (RDM) topics listed below in a biomedical context. The material presented began as an NIH-funded research study to assess material for teaching RDM to librarians. It is designed to prepare you to understand and subsequently teach RDM at your own institution, and offers strategies for identifying opportunities to teach RDM in your own environment. At the end of each module there is a link to a Teaching Toolkit that provides librarians with a script, slides, and evaluation materials to teach RDM at your institution. Data management Life Science Researchers
Tools for data management planning

Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you...

Scientific topics: Data management

Keywords: Data managment plan

Resource type: Video

Tools for data management planning http://tess.elixir-uk.org/materials/tools-for-data-management-planning Having a data management plan is essential if we're to make the most of our own data and share it with others. Just like planning an experiment, we should plan what we are going to do with our data and how we are going to do it to ensure that we (and others) can use and re-use the data. If you have never made a data management plan before the process may initially seem daunting, but fortunately there are many tools out there to help you think through the what, where, how, why and when of data management. In this webinar Sarah Jones from the Digital Curation Centre and Rob Hooft from ELIXIR Netherlands show us two tools - DMP online and the ELIXIR Data Stewardship Wizard - and explain how they can help you apply data management and FAIR data practices in your own research. Data management Data managment plan Life Science Researchers
What happens to your data?

This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data...

Scientific topics: Data management

Keywords: metadata, ArrayExpress

Resource type: Video

What happens to your data? http://tess.elixir-uk.org/materials/what-happens-to-your-data This webinar focuses on what happens to your data after you submit it to a public repository and addresses the question of data ownership. Keeva and Nancy introduce the concepts of FAIR data, metadata and standards. They then show you where you can find an appropriate place to share your data and give examples of how metadata and standards are used when you submit data to Metabolights and ArrayExpress. They also answer a few frequently asked data submission-related questions. Data management metadata, ArrayExpress Life Science Researchers
Why share your data?

Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we...

Scientific topics: Data management

Keywords: data sharing

Resource type: Video

Why share your data? http://tess.elixir-uk.org/materials/why-share-your-data Presented in two parts, this webinar will explore the value of sharing your data from an institutional and researcher perspective. Our first speaker, Ewan Birney, is one of the directors of EMBL-EBI. He speaks about how the growth in data over the past decade has changed the way that we approach biology and how EMBL-EBI provides some of the infrastructure to allow data sharing. He finishes up by highlighting the benefits of data sharing to the EMBL-EBI and shares his top four reasons for sharing data. Our second speaker, Elisabeth Busch, is the head of the Vertebrate Genetics and Genomics Group at the Wellcome Sanger Institute and the University of Cambridge. She tells us about her experiences in sharing her own research data, and the reasons that she felt compelled to share her data including the advantages for her own research. Elisabeth Busch Data management data sharing Life Science Researchers
eLearning course about the importance of good research data management (RDM)

Within the framework of the Danish National Forum for Data Management, the Danish Universities have developed the eLearning course “Research Data Management”. This eLearning course in Research Data Management is brought to you by the Danish National Forum for Data Management, and is funded by...

Scientific topics: Data management

Resource type: Video

eLearning course about the importance of good research data management (RDM) http://tess.elixir-uk.org/materials/elearning-course-about-the-importance-of-good-research-data-management-rdm Within the framework of the Danish National Forum for Data Management, the Danish Universities have developed the eLearning course “Research Data Management”. This eLearning course in Research Data Management is brought to you by the Danish National Forum for Data Management, and is funded by Denmark’s Electronic Research Library (DEFF) and the Danish eInfrastructure Cooperation (DeiC). Data management Life Science Researchers
FAIRification & Data modelling

Wikidata fairification

Keywords: FAIR, linked data, ontologies, metadata

Resource type: Slides

FAIRification & Data modelling http://tess.elixir-uk.org/materials/fairification-data-modelling Wikidata fairification FAIR, linked data, ontologies, metadata Life Science Researchers bioinformaticians
Helis Academy - Persistent identifiers and their use cases

Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source

Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

Resource type: Slides

Helis Academy - Persistent identifiers and their use cases http://tess.elixir-uk.org/materials/persistent-identifiers-and-their-use-cases Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source Referencing data and code, Findability of data and code, Identifying data and code, data management data stewards Life Science Researchers bioinformaticians
Introduction to FAIR data stewardship

FAIR data Stewardship: How to improve the reuse of nanosafety data

Scientific topics: Data management

Keywords: FAIR

Introduction to FAIR data stewardship http://tess.elixir-uk.org/materials/introduction-to-fair-data-stewardship FAIR data Stewardship: How to improve the reuse of nanosafety data Data management FAIR Life Science Researchers
Helis Academy - Data Management Plans, why and how?

Research Data Management The organisation of data throughout the research project everyday management of research data (storage, file naming, preservation) how will data be preserved and shared after the project is completed?

Scientific topics: Data management

Keywords: Data managment plan, Data Life Cycle

Resource type: Slides, PDF

Helis Academy - Data Management Plans, why and how? http://tess.elixir-uk.org/materials/data-management-plans-why-and-how Research Data Management The organisation of data throughout the research project everyday management of research data (storage, file naming, preservation) how will data be preserved and shared after the project is completed? Data management Data managment plan, Data Life Cycle Life Science Researchers
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences http://tess.elixir-uk.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
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
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R http://tess.elixir-uk.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers