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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.
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
SARS-CoV-2 : Studying a new virus

In December 2019, a new type of virus of the family Coronaviridae called SARS-CoV-2 (formerly 2019-nCoV) was identified as the cause of an outbreak. In this e-learning course, you will learn to find, use or interpret information about a new virus. Knowledge of the basic molecular biology of...

SARS-CoV-2 : Studying a new virus http://tess.elixir-uk.org/materials/sars-cov-2-studying-a-new-virus In December 2019, a new type of virus of the family Coronaviridae called SARS-CoV-2 (formerly 2019-nCoV) was identified as the cause of an outbreak. In this e-learning course, you will learn to find, use or interpret information about a new virus. Knowledge of the basic molecular biology of viruses is presumed.
Explore and visualize your data with Python

In this e-learning course, you will reproduce a typical analysis pipeline using Python, an open-source and general-purpose scripting language which runs on all major operating systems. Basic knowledge of Python programming is required.

Explore and visualize your data with Python http://tess.elixir-uk.org/materials/explore-and-visualize-your-data-with-python In this e-learning course, you will reproduce a typical analysis pipeline using Python, an open-source and general-purpose scripting language which runs on all major operating systems. Basic knowledge of Python programming is required.
Cybersecurity Quiz for SIB employees only (internal use)

No description provided.

Cybersecurity Quiz for SIB employees only (internal use) http://tess.elixir-uk.org/materials/cybersecurity-quiz-for-sib-employees-only-internal-use No description provided.
neXtProt : Exploring human proteins

In this 1-hour e-learning course, you will learn what type of information on human proteins is found in neXtProt, where it comes from and how it is organized in topic-specific entry views. Basic knowledge of biology and proteins is required.

neXtProt : Exploring human proteins http://tess.elixir-uk.org/materials/nextprot In this 1-hour e-learning course, you will learn what type of information on human proteins is found in neXtProt, where it comes from and how it is organized in topic-specific entry views. Basic knowledge of biology and proteins is required.
Information Security Awareness (BioMedIT)

No description provided.

Information Security Awareness (BioMedIT) http://tess.elixir-uk.org/materials/demo-cyber-security-awareness-biomedit No description provided.
DS Wizard and its Use

This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind [Data Stewardship Wizard](https://ds-wizard.org), and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make...

Scientific topics: Data management

Keywords: DMP, DMP tools, data stewardship, FAIR, FAIR data

Resource type: Presentation

DS Wizard and its Use http://tess.elixir-uk.org/materials/ds-wizard-and-its-use This training gives an overview and explains what is the purpose of smart data management plans as living documents, core ideas behind [Data Stewardship Wizard](https://ds-wizard.org), and how to use it in practice. Furthermore, it shows the versability of DSW, its top-notch features that make data management planning easier and more efficient, as well as possibilities of customization and integrations with other systems in institutions. Data management DMP, DMP tools, data stewardship, FAIR, FAIR data Researchers data stewards
ELIXIR AAI Engagement Meetings Materials

ELIXIR AAI is an ELIXIR Compute Platform service that other services can use to authenticate their users and manage their access rights. In the **ELIXIR AAI Tas**, we are preparing regular **Community engagement meetings** where we would like to share and discuss together new AAI needs,...

Scientific topics: Computer science

Keywords: AAI, IAM, Authentication, authorisation

Resource type: Documentation, Presentation

ELIXIR AAI Engagement Meetings Materials http://tess.elixir-uk.org/materials/elixir-aai-engagement-meetings-materials ELIXIR AAI is an ELIXIR Compute Platform service that other services can use to authenticate their users and manage their access rights. In the **ELIXIR AAI Tas**, we are preparing regular **Community engagement meetings** where we would like to share and discuss together new AAI needs, requirements and ideas collected from the community, as well as share success stories with other infrastructures. Topics will be selected based on needs and interest and also in regard to future migration to LS AAI. Computer science AAI, IAM, Authentication, authorisation software developers, bioinformaticians
Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

Computational simulations of cellular processes (e.g. metabolism, gene expression, signal transduction) are critical tools to formulate mechanistic explanations that facilitate the interpretation of experimental results. However, complex biological processes such as tumour evolution span across...

Scientific topics: Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations

Resource type: Webinar

Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research http://tess.elixir-uk.org/materials/biomedicine-supercomputers-and-simulations-in-silico-experiments-and-its-applications-in-cancer-research Computational simulations of cellular processes (e.g. metabolism, gene expression, signal transduction) are critical tools to formulate mechanistic explanations that facilitate the interpretation of experimental results. However, complex biological processes such as tumour evolution span across different time-space scales. For instance, a population-level description is needed to account for genetic heterogeneity and phenotypic variability due to environmental noise, whereas intracellular models, such as cell signalling networks need to address the effect of mutated genes. In this context, multi-scale models are ideal tools to address systems biology questions as they can consider several time-space scales by combining different approaches into a hybrid simulation. PhysiCell is an open-source, agent-based extensible multi-scale modelling framework that allows simulating complex multicellular systems such as healthy tissues and tumours. Molecular interactions, pathways and networks Personalised medicine Simulation experiment HPC, Biomodelling, cell simulations Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Introduction to qualitative modelling with MaBoSS

Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the...

Scientific topics: Statistics and probability, Molecular interactions, pathways and networks, Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations, Boolean

Resource type: Webinar

Introduction to qualitative modelling with MaBoSS http://tess.elixir-uk.org/materials/introduction-to-qualitative-modelling-with-maboss Boolean modelling uses a simple representation of biological entities as either active or inactive, and describes their relations with logical formulas. MaBoSS extends Boolean modelling by adding a notion of continuous time, with the introduction of rates of (in)activation. This enable the representation of physical time, and of processes with different time scales. MaBoSS simulate multiple stochastic trajectories, and produces trajectories of the probabilities of the system state. This webinar will introduce the concepts of boolean modelling, and MaBoSS’ continuous time boolean modelling, and will then demonstrate the use of WebMaBoSS, a web interface designed for easily simulating MaBoSS models. Statistics and probability Molecular interactions, pathways and networks Personalised medicine Simulation experiment HPC, Biomodelling, cell simulations, Boolean Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Analysis of huge metabolic models with COBREXA.jl

COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base...

Scientific topics: Simulation experiment

Keywords: cell-level simulations, HPC, Biomodelling

Resource type: Webinar

Analysis of huge metabolic models with COBREXA.jl http://tess.elixir-uk.org/materials/analysis-of-huge-metabolic-models-with-cobrexa-jl COBREXA.jl is a new software package to enable the analysis and simulation of large metabolic models by taking advantages of modern HPC infrastructure. Mainly, it advanced the scalability of constraint-based method, using the Julia programing language and its mathematic ecosystem as a base building block. We will talk about the problems that motivated the development of COBREXA.jl and show several of its main applications. Simulation experiment cell-level simulations, HPC, Biomodelling Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Introduction to PerMedCoE: Exascale-ready cell-level simulations for European Personalised Medicine

PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance.

Scientific topics: Personalised medicine

Keywords: HPC, Biomodelling, cell-level simulations

Resource type: Webinar

Introduction to PerMedCoE: Exascale-ready cell-level simulations for European Personalised Medicine http://tess.elixir-uk.org/materials/introduction-to-permedcoe-exascale-ready-cell-level-simulations-for-european-personalised-medicine PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe. The goal of PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance. Personalised medicine HPC, Biomodelling, cell-level simulations Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
ELIXIR CZ Friday Coffee #5: Data Management with Data Stewardship Wizard

This short presentation was presented as part of the Friday Coffee presentation series organized by the ELIXIR CZ infrastructure and offered students a basic insight into data management and data management plans, which are important (not only) for the success of scientific projects, but...

Scientific topics: Data management

Keywords: data management plan, data stewardship, FAIR, data management, software tools

Resource type: Video, Webinar

ELIXIR CZ Friday Coffee #5: Data Management with Data Stewardship Wizard http://tess.elixir-uk.org/materials/elixir-cz-friday-coffee-5-data-management-with-data-stewardship-wizard This short presentation was presented as part of the Friday Coffee presentation series organized by the ELIXIR CZ infrastructure and offered students a basic insight into data management and data management plans, which are important (not only) for the success of scientific projects, but increasingly for grant applications as well. The presentation also introduced students to the possibility of creating these plans using the [Data Stewardship Wizard](https://ds-wizard.org), a tool that creates the data management plan by filling out a simple, synoptic questionnaire. It offers a simple and very effective solution without the need for deep knowledge of data stewardship or data management. Video available [here](https://www.youtube.com/watch?v=2YGrVGa9JYY). Data management data management plan, data stewardship, FAIR, data management, software tools Researchers data managers data stewards
Using the Norwegian e-infrastructure for Life Science and usegalaxy.no

Online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the national supported Galaxy (usegalaxy.no). The course will consist of lessons covering the necessary topics alternating with hands-on sessions to gain practical experience.

Keywords: NeLS, Data storage, data sharing, Data analysis

Using the Norwegian e-infrastructure for Life Science and usegalaxy.no http://tess.elixir-uk.org/materials/using-the-norwegian-e-infrastructure-for-life-science-and-usegalaxy-no Online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the national supported Galaxy (usegalaxy.no). The course will consist of lessons covering the necessary topics alternating with hands-on sessions to gain practical experience. NeLS, Data storage, data sharing, Data analysis PhD postdocs Researchers
Identifier mapping with Cytoscape

This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a...

Keywords: ELIXIR RIR, BridgeDb

Identifier mapping with Cytoscape http://tess.elixir-uk.org/materials/identifier-mapping-with-cytoscape This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a network but you don’t have matching keys. ELIXIR RIR, BridgeDb
BridgeDb-Matlab Usage Instructions

Instructions on how to install and use the BridgeDb functionality in Matlab.

Keywords: ELIXIR RIR, BridgeDb

BridgeDb-Matlab Usage Instructions http://tess.elixir-uk.org/materials/bridgedb-matlab-usage-instructions Instructions on how to install and use the BridgeDb functionality in Matlab. ELIXIR RIR, BridgeDb
Ten simple rules for making training materials FAIR

Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to...

Scientific topics: FAIR data

Operations: Data handling

Keywords: FAIR data, FAIR, ELIXIR-CONVERGE

Resource type: Video

Ten simple rules for making training materials FAIR http://tess.elixir-uk.org/materials/ten-simple-rules-for-making-training-materials-fair Sharing, reusing and reproducing data, software and other digital objects are the basis for open science practices, and to ease this the scientific community has developed the Findable, Accessible, Interoperable and Reusable (FAIR) principles. FAIR principles are however not so simple to understand and adopt, and may be quite convoluted for some. The ELIXIR Training Platform in cooperation with other associated partner ZB MED has put together a Ten Simple Rules for Making Training Materials FAIR which simplify the FAIR principles by breaking them down into very practical steps. This webinar introduced these ten rules and discussed the challenges and ideas to put them into practice. FAIR data FAIR data, FAIR, ELIXIR-CONVERGE PhD students Post Docs Undergraduate students
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