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WikiPathways Academy

Organized training examples for new WikiPathways authors

Scientific topics: Systems biology, Biology

Keywords: Pathway

WikiPathways Academy http://tess.elixir-uk.org/materials/wikipathways-academy Organized training examples for new WikiPathways authors Systems biology Biology Pathway
Compartición, análisis y almacenamiento de datos genómicos con RD-Connect GPAP y EGA

El Centro Nacional de Análisis Genómico (CNAG-CRG) y la European Genome-Phenome Archive (EGA) organizan un curso práctico sobre el uso de herramientas para compartir y analizar datos genómicos en el marco del proyecto VEIS - Valorización de EGA para la Industria y la Sociedad. En el primer...

Scientific topics: Data integration and warehousing, Database management, Genomics

Resource type: Video

Compartición, análisis y almacenamiento de datos genómicos con RD-Connect GPAP y EGA http://tess.elixir-uk.org/materials/comparticion-analisis-y-almacenamiento-de-datos-genomicos-con-rd-connect-gpap-y-ega El Centro Nacional de Análisis Genómico (CNAG-CRG) y la European Genome-Phenome Archive (EGA) organizan un curso práctico sobre el uso de herramientas para compartir y analizar datos genómicos en el marco del proyecto VEIS - Valorización de EGA para la Industria y la Sociedad. En el primer módulo del curso se presentará la plataforma RD-Connect GPAP que permite integrar, compartir y analizar datos genómicos y fenotípicos de manera segura entre los equipos clínicos y de investigación autorizados, facilitando el diagnóstico de Enfermedades Raras y la identificación de nuevas asociaciones gen-enfermedad. La interfaz gráfica de la plataforma y sus numerosos recursos conectados permiten analizar e interpretar datos de manera eficaz e intuitiva sin necesidad de tener formación en Bioinformática. La RD-Connect GPAP, coordinada y desarrollada por el CNAG-CRG y reconocida por el International Rare Disease Consortium (IRDiRC), hospeda actualmente datos pseudonimizados de más de 20.000 pacientes y familiares y ha contribuido al diagnóstico de cientos de casos. En el segundo módulo se seguirá la demostración de la plataforma RD-Connect GPAP para el análisis y reanálisis de datos de pacientes con enfermedades raras y se explicará cómo las herramientas ofrecidas por EGA hacen más fácil y segura la compartición y el almacenamiento de los datos. El curso lo impartirán Gemma Bullich y Leslie Matalonga de la Unidad de Bionformática del CNAG-CRG y Teresa d'Altri y Babita Singh de EGA el 17 de diciembre de 10 a 14 h. La agenda del curso es la siguiente: Parte 1. Módulo clínico (RD-Connect GPAP) 1.1 Introducción a la plataforma RD-Connect e importancia del uso de ontologías y estándares (HPO, ORDO, etc) para la integración de datos fenotípicos en el análisis (gen)ómico 1.2 Hands-on: Phenostore: entrada de datos fenotípicos de pacientes con enfermedades raras para el posterior análisis de datos genómicos Parte 2. Módulo genético (EGA y RD-Connect GPAP) 2.1 Secuenciación y análisis de datos genómicos 2.2 European Genome-Phenome Archive y compartición de datos (en inglés) 2.3 Hands-on: Resolución de casos de pacientes con enfermedades raras entrados en parte 1 con RD-Connect GPAP Parte 3. Discusión y preguntas Data integration and warehousing Database management Genomics Clinical Scientists
Making sense of genomic data: COVID-19 web-based bioinformatics

On this COG-Train course, you will learn the basics of bioinformatics concepts and explore the web-based tools used for viral data and sequencing analyses and learn to prepare data and share outputs and visualisations.

Keywords: bioinformatics, NGS bioinformatics, Next generation sequencing data analysis, covid-19, sars-cov-2, coronavirus, data-analysis, data visualization, genomics, Genomic data, pipelines, Galaxy, nexstrain

Resource type: FREE online course

Making sense of genomic data: COVID-19 web-based bioinformatics http://tess.elixir-uk.org/materials/making-sense-of-genomic-data-covid-19-web-based-bioinformatics On this COG-Train course, you will learn the basics of bioinformatics concepts and explore the web-based tools used for viral data and sequencing analyses and learn to prepare data and share outputs and visualisations. Our list of contributors can be found on our course page. bioinformatics, NGS bioinformatics, Next generation sequencing data analysis, covid-19, sars-cov-2, coronavirus, data-analysis, data visualization, genomics, Genomic data, pipelines, Galaxy, nexstrain scientific researchers, public health professionals and clinicians
From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic

Sampling and testing are key to understanding where a disease is spreading. In the COVID-19 pandemic, the number of samples taken, analysed, tracked, and shared have far surpassed any previous pandemic. On this course from COG-Train, you will learn about the process that samples undergo to...

Keywords: metadata, Sequencing, genomics, Genomic data, data quality, scientific quality assurance, data sharing, ethics, data ethics, public health, coronavirus, sars-cov-2, covid-19, data linkage

Resource type: FREE online course

From Swab to Server: Testing, Sequencing, and Sharing During a Pandemic http://tess.elixir-uk.org/materials/from-swab-to-server-testing-sequencing-and-sharing-during-a-pandemic Sampling and testing are key to understanding where a disease is spreading. In the COVID-19 pandemic, the number of samples taken, analysed, tracked, and shared have far surpassed any previous pandemic. On this course from COG-Train, you will learn about the process that samples undergo to become datasets. You’ll also gain the knowledge of how this data is handled in order to satisfy public health concerns during a pandemic. Our list of contributors can be found on our course page. metadata, Sequencing, genomics, Genomic data, data quality, scientific quality assurance, data sharing, ethics, data ethics, public health, coronavirus, sars-cov-2, covid-19, data linkage scientific researchers, public health professionals and clinicians
The Power of Genomics to Understand the COVID-19 Pandemic

On this course, you’ll learn key concepts in viral genomics, how they can be applied to the COVID-19 pandemic, and how they can help us prepare for future pandemics.

Keywords: coronavirus, covid-19, sars-cov-2, mutations, Variant calling, Sequencing, pandemic, surveillance, genomics, public health, Genomic data

Resource type: FREE online course

The Power of Genomics to Understand the COVID-19 Pandemic http://tess.elixir-uk.org/materials/the-power-of-genomics-to-understand-the-covid-19-pandemic On this course, you’ll learn key concepts in viral genomics, how they can be applied to the COVID-19 pandemic, and how they can help us prepare for future pandemics. Our list of contributors can be found on our course page. coronavirus, covid-19, sars-cov-2, mutations, Variant calling, Sequencing, pandemic, surveillance, genomics, public health, Genomic data Policy makers journalists Graduate students undergraduate students researchers
Introduction to using containers - OpenShift, Kubernetes and Docker oriented view

This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez

Keywords: Containers, Kubernetes, Cloud computing

Introduction to using containers - OpenShift, Kubernetes and Docker oriented view http://tess.elixir-uk.org/materials/introduction-to-using-containers-openshift-kubernetes-and-docker-oriented-view This material is CSC's Rahti basic cloud course which consists of lectures and hands-on exercises on creating and managing virtual resources in OpenShift OKD (Kubernetes). The original material was produced by Shubham Kapoor and Juhani Kataja, and updated by Tewodros Deneke and Alvaro Gonzalez Containers, Kubernetes, Cloud computing Cloud users
Expanding the SPHN RDF Schema

This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor.

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

Expanding the SPHN RDF Schema http://tess.elixir-uk.org/materials/expanding-the-sphn-rdf-schema This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor. Kristin Gnodke Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Training Primer (RDF and SPARQL)

This training provides a first introduction to RDF and SPARQL.

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

Training Primer (RDF and SPARQL) http://tess.elixir-uk.org/materials/training-primer-rdf-and-sparql This training provides a first introduction to RDF and SPARQL. Sabine Österle Computer science Data management FAIR data Medical informatics Ontology and terminology Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Semantic Standards

This training module provides an introduction on the key semantic standards used within SPHN.

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

Operations: Standardisation and normalisation, Data handling

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

Resource type: Video, Training materials, E-learning

Semantic Standards http://tess.elixir-uk.org/materials/semantic-standards This training module provides an introduction on the key semantic standards used within SPHN. Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
RDF Schema and Data Visualization

This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data.

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

RDF Schema and Data Visualization http://tess.elixir-uk.org/materials/rdf-schema-and-data-visualization This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data. Vasundra Touré Sabine Österle Data visualisation Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Validate Graph Data with SHACL

This training module will provide researchers with an introduction on SHACL for RDF graphs validation.

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

Operations: Data handling, Validation

Keywords: Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation

Resource type: Video, Training materials, E-learning

Validate Graph Data with SHACL http://tess.elixir-uk.org/materials/validate-graph-data-with-shacl This training module will provide researchers with an introduction on SHACL for RDF graphs validation. Sabine Österle Vasundra Touré Computer science Data management FAIR data Medical informatics Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
How to use Python and R with RDF Data

This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data.

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

Operations: Data retrieval, Data handling, Query and retrieval

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB

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

How to use Python and R with RDF Data http://tess.elixir-uk.org/materials/how-to-use-python-and-r-with-rdf-data This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data. Sabine Österle Vasundra Touré Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
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: Data management, Open science, FAIR data

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

BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course http://tess.elixir-uk.org/materials/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. Data management Open science FAIR data Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle Researchers
SPHN/BioMedIT Data Privacy and IT Security Training

No description provided.

SPHN/BioMedIT Data Privacy and IT Security Training http://tess.elixir-uk.org/materials/sphn-biomedit-data-privacy-and-it-security-training No description provided.
Cellosaurus : A resource on cell lines

No description provided.

Cellosaurus : A resource on cell lines http://tess.elixir-uk.org/materials/cellosaurus-a-resource-on-cell-lines No description provided.
Introduction to Workflows with Common Workflow Language

Introduction to workflow thinking for novices, using the Common Workflow Language

Scientific topics: Workflows

Operations: RNA-Seq analysis

Keywords: cwl, commonwl, sciworkflows, workflows

Resource type: Carpentries style curriculum

Introduction to Workflows with Common Workflow Language http://tess.elixir-uk.org/materials/introduction-to-workflows-with-common-workflow-language Introduction to workflow thinking for novices, using the Common Workflow Language Stian Soiland-Reyes Toby Hodges Sehrish Kanwal Pedro L Fernandes Workflows cwl, commonwl, sciworkflows, workflows esearchers and research software engineers who would like to begin automating their analyses in workflows.
Querying Data with SPARQL

This training module will provide researcher with an introduction to SPARQL queries for health-related data.

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

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

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC

Resource type: Video, Training materials with mock data, E-learning

Querying Data with SPARQL http://tess.elixir-uk.org/materials/querying-data-with-sparql This training module will provide researcher with an introduction to SPARQL queries for health-related data. Philip Krauss Sabine Österle Computer science Data management FAIR data Medical informatics Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
PSLS22 Practical Statistics for the Life Sciences

This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data...

PSLS22 Practical Statistics for the Life Sciences http://tess.elixir-uk.org/materials/psls22-practical-statistics-for-the-life-sciences This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression. Lieven Clement Milan Malfait Jeroen Gilis Graduate students All postgraduates
Schema.org, what and why?

In this tutorial you will get an idea on what Schema.org is and how it is useful

Keywords: schemaorg, markup, structured data, schemaorg, markup, structured data

Schema.org, what and why? http://tess.elixir-uk.org/materials/schema-org-what-and-why In this tutorial you will get an idea on what Schema.org is and how it is useful schemaorg, markup, structured data, schemaorg, markup, structured data
Bioschemas, what and why?

In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

Bioschemas, what and why? http://tess.elixir-uk.org/materials/bioschemas-what-and-why In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Schema.org markup examples

With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup

Keywords: schemaorg, markup, structured data, example, schemaorg, markup, structured data, example

Schema.org markup examples http://tess.elixir-uk.org/materials/schema-org-markup-examples With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup schemaorg, markup, structured data, example, schemaorg, markup, structured data, example
How to select the right profile for your resource

In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources

Keywords: schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile

How to select the right profile for your resource http://tess.elixir-uk.org/materials/how-to-select-the-right-profile-for-your-resource In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile
How to update a profile

In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to update a profile http://tess.elixir-uk.org/materials/how-to-update-a-profile In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll. schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to create a new Bioschemas profile

In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile.

Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile

How to create a new Bioschemas profile http://tess.elixir-uk.org/materials/how-to-create-a-new-bioschemas-profile In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile. schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to check your Bioschemas deployment

This guide will show you how to check your deployed markup, both locally and what is retrieved by external services.

Keywords: schemaorg, JSON-LD, bioschemas

How to check your Bioschemas deployment http://tess.elixir-uk.org/materials/how-to-check-your-bioschemas-deployment This guide will show you how to check your deployed markup, both locally and what is retrieved by external services. schemaorg, JSON-LD, bioschemas
How to mark up your own resource with Bioschemas

In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile

Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas

How to mark up your own resource with Bioschemas http://tess.elixir-uk.org/materials/how-to-mark-up-your-own-resource-with-bioschemas In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Adding Schema.org to a GitHub Pages site

This guide will show you how to do add Schema.org markup to a GitHub Pages site.

Keywords: schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages

Adding Schema.org to a GitHub Pages site http://tess.elixir-uk.org/materials/adding-schema-org-to-a-github-pages-site-deb50140-9274-4c87-9eda-5361cb287e71 This guide will show you how to do add Schema.org markup to a GitHub Pages site. schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages
Tutorial on developing Building Blocks

This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.

Scientific topics: Personalised medicine, Workflows, Bioinformatics

Keywords: HPC, building blocks

Resource type: Tutorial

Tutorial on developing Building Blocks http://tess.elixir-uk.org/materials/tutorial-on-developing-building-blocks This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them. Personalised medicine Workflows Bioinformatics HPC, building blocks Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Tutorial on working with computing clusters

This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system.

Keywords: HPC

Resource type: Tutorial

Tutorial on working with computing clusters http://tess.elixir-uk.org/materials/tutorial-on-working-with-computing-clusters This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system. HPC Novice users of HPC and anyone who expects to need to use HPC systems at some stage in their research
SARS-CoV-2 : Studying a new virus

No description provided.

SARS-CoV-2 : Studying a new virus http://tess.elixir-uk.org/materials/sars-cov-2-studying-a-new-virus No description provided.