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32 materials found

Difficulty level: Beginner 

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Resource type: e-learning  or Computer Software  or Training materials 


An introduction to MobiDB

In this course you will learn what type of information is stored in the MobiDB database (URL: https://mobidb.org/) that provides predictions and annotations for intrinsically disordered proteins. You will explore the main features of the database, its entries along with the related documentation....

Keywords: intrinsically disordered proteins, Databases, intrinsic disorder prediction, protein sequence

Resource type: Webinar, Training materials

Cloud-SPAN Prenomics

Prenomics prepares learners for the Cloud-SPAN Genomics course. It teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file...

Scientific topics: Bioinformatics, Software engineering, Genomics

Operations: Query and retrieval, Data handling

Keywords: Cloud computing, Shell, Command line, Amazon Web Services, genomics, HPC, Data analysis, bioinformatics

Resource type: course materials, online course, Training materials

An introduction to DisProt

In this course you will learn what type of information is stored in DisProt, gold standard resource of manually curated Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) from the literature. You will explore the main features of the database, its entries and...

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

Expanding the SPHN RDF Schema

Expanding the SPHN RDF Schema is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

Operations: Editing, Ontology visualisation, Visualisation, Data handling

Keywords: Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL

Resource type: Video, Training materials, E-learning

Training Primer (RDF and SPARQL)

The RDF and SPARQL training primer was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology

Operations: Query and retrieval, Database search, Data handling, Data retrieval

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology

Resource type: Video, Training materials, E-learning

Semantic Standards

This video was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and serves as an introduction to the main standards used within the [SPHN Interoperability...

Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology

Operations: Data handling, Standardisation and normalisation

Keywords: Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD, Interoperability

Resource type: Video, Training materials, E-learning

RDF Schema and Data Visualization

RDF Schema and Data Visualization is a training that was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

Scientific topics: Data visualisation, Medical informatics, FAIR data, Data management, Computer science

Operations: Ontology visualisation, Visualisation, Data retrieval, Data handling, Query and retrieval

Keywords: Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data

Resource type: Video, Training materials, Mock data, E-learning

BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course

BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations....

Scientific topics: FAIR data, Open science, Data management

Keywords: Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle

Resource type: Training 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.

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

Keywords: machine learning, biostatistics, eLearning, EeLP

Resource type: Training materials

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

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

Research Data Management Introduction for researchers

Short summary of the previous session
1.Scope of the DM
2.DMP Content and structure
Practical activities
3.Planning the DM of a simple project
4.DMP evaluation

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

Data Management Plans and Policies

PDF with slides of the course:
- Data management definitions
- RDM and DM policy
- DMPs: content and competencies
- DMPs for European and National funded projects

Scientific topics: FAIR data, Data management

Keywords: ELIXIR-CONVERGE, DMP, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, on-line, e-learning

Resource type: PDF, e-learning, slideck/ presentation

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

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica

PDF with slides of the course in Spanish
- Data management definitions
- DMP Objectives
- DMP Content and structure
- Competencies needed
- Practical session: DMP content analysis and evaluation

Scientific topics: Data management, FAIR data

Keywords: ELIXIR-CONVERGE, DMP, DMP tools, DMP templates, DMP evaluation, Data managment plan, research data management, FAIR principles, tools, template, competency, evaluation, online, e-learning, Spanish

Resource type: PDF, e-learning, slideck/ presentation

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

Plant Phenotyping Data managment (MIAPPE)

This training material has been used in a two-day training workshop on data management organized by Elixir and the Wheat Initiative.

It provides an overview of current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity...

Scientific topics: Phenomics, Plant biology, Data management

Operations: Annotation, Formatting

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Eurordis Open Academy

Through the Open Academy, EURORDIS empowers patient advocates to have the confidence and knowledge needed to bring their expertise to discussions on health care, research and medicines development. EURORDIS alumni engage in these discussions as equal partners, side by side with policy makers,...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research, Rare Diseases

Resource type: course materials, e-learning

Patient-Centered Outcomes Research Institute (PCORI) Training : A Program for Rare Disease Patient Advocates

In response to rare-disease patients’ desire to make research more meaningful to their community, PCORI created an online Program for Rare Disease Patient Advocates.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: educational materials, e-learning

Findacure's e-learning resources on rare diseases

The portal is aimed at rare disease advocates, patient groups and charities, though anyone with an interest in rare diseases or advocacy is welcome to sign-up. It is completely free to use, and users are encouraged to contact Findacure with suggestions for new content.
The portal shares ‘how to’...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, Video, Presentation, Training materials, e-learning

How to use V-pipe (SARS-CoV-2 data)

This tutorial demonstrate how to use V-pipe - Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.

For the purpose of this toturial, we use the sars-cov2 branch of V-pipe and analyse SARS-CoV-2 runs downloaded from NCBI SRA.

Scientific topics: Virology, Genetic variation, Workflows

Operations: Variant calling, Alignment, Read pre-processing

Keywords: coronavirus, NGS bioinformatics, Variant-calling

Resource type: Computer Software, workflow

Integrated DEsign and AnaLysis of small population group trials (IDeAl)

There is a pressing need to integrate a broad range of innovative methodologies improving clinical trials in the setting of small sample population groups (SPG). The objective of IDeAl is to produce methods of general applicability irrespective of indication by Integrated DEsign and AnaLysis of...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research, Training material

Resource type: Webinar, e-learning

Introduction to GitHub

The aim for today is to learn the basics of GitHub so that you can use it for your own projects.

  • Background
  • What is version control? What is Git? What is GitHub?
  • How can you use GitHub? How can it be useful for your work?
  • Practical session: working with GitHub

Keywords: GitHub, Reproducibility

Resource type: Training materials

Beginners introduction to Git and GitHub

Morning session (Sergio and Mark) https://tinyurl.com/git-intro-zoology:

  • Background and motivation
  • What is version control? What is Git? What is GitHub?
  • How can you use Git and GitHub? How can they be useful for you?
  • Practical session: working with Git and GitHub

__Afternoon...

Keywords: Git, GitHub, control version, Reproducibility

Resource type: Training 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...

Keywords: Data management plan, data management

Resource type: e-learning

Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Mascot training course

The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.

Scientific topics: Proteomics

Keywords: Protein identification, Protein Mass Spectrometry

Resource type: Slides, Video, Training materials

ELIXIR Beacons (at ISMB / ECCB)

Large cohorts, with potentially millions of participants, are needed to understand the genetic and molecular signatures of diseases, and they provide a cornerstone for the creation of personalised treatments. The ELIXIR::GA4GH Strategic Partnership will facilitate the responsible sharing of these...

Keywords: beacon

Resource type: Slides, Computer Software

FAIR Data Stewardship - Data sharing, archiving and publishing

In this workshop we focus on three aspects of FAIR data stewardship: Data sharing, publishing and archiving. Many scientists have an insufficient overview over data services, roles and their responsibilities towards safe data sharing, archiving and publishing. Shedding light on these roles helps...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training materials

Adding schema.org to a GitHub Pages site

​GitHub Pages are an excellent platform for creating informative websites. The hosting is (currently) free which is a huge plus; the collaborative tools allow teams (that may be widely distributed, fluctuating, and/or voluntary) to contribute in a well-structured, verifiable, and open manner; and...

Scientific topics: Computer science

Keywords: Mark-up, Bioschemas, Interoperability

Resource type: Training materials