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78 materials found

Difficulty level: Intermediate 


Tutorial on using MPI with containers

In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers.

Keywords: MPI, Containers

Resource type: Tutorial

Tutorial on using MPI with containers https://tess.elixir-europe.org/materials/tutorial-on-using-mpi-with-containers In this material we will briefly touch upon why MPI is such a tricky component, explain the main approaches to combine MPI with containers and discuss when it is actually worthwhile to use MPI containers. MPI, Containers
Tutorial on CARNIVAL

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

Scientific topics: RNA-Seq, Omics, Gene expression, Molecular interactions, pathways and networks

Operations: RNA-Seq analysis, Network analysis

Keywords: HPC, Signaling, RNAseq, transcriptomics

Resource type: Tutorial

Tutorial on CARNIVAL https://tess.elixir-europe.org/materials/tutorial-on-carnival This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL RNA-Seq Omics Gene expression Molecular interactions, pathways and networks HPC, Signaling, RNAseq, transcriptomics
Tutorials on COBREXA

COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them. The documentation contains basic tutorials (explaining the core package concepts and basic design...

Scientific topics: Personalised medicine, Simulation experiment

Operations: Modelling and simulation

Keywords: cell-level simulations, Biomodelling, HPC

Resource type: Tutorial

Tutorials on COBREXA https://tess.elixir-europe.org/materials/tutorials-on-cobrexa COBREXA.jl provides tutorials and notebooks with the purpose of explaining the most important concepts and functions for metabolic modelling and model handling to users, and then practicing them. The documentation contains basic tutorials (explaining the core package concepts and basic design ideas), advanced tutorials (describing complicated functionality required for optimised execution of large analyses) and Jupyter notebooks that demonstrate the concepts from tutorials in a more practical setting, with realistic data. Personalised medicine Simulation experiment cell-level simulations, Biomodelling, HPC
Tutorial on CellNOpt

This tutorial aims to be an introduction to i) the preparation of the Prior knowledge network (PKN) of signaling pathways and ii) the training of the PKN against biochemical data to create cell-specific models.

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

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, Signalling

Resource type: Tutorial

Tutorial on CellNOpt https://tess.elixir-europe.org/materials/tutorial-on-cellnopt This tutorial aims to be an introduction to i) the preparation of the Prior knowledge network (PKN) of signaling pathways and ii) the training of the PKN against biochemical data to create cell-specific models. Personalised medicine Simulation experiment Molecular interactions, pathways and networks HPC, Biomodelling, Signalling
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...

Introduction to qualitative modelling with MaBoSS https://tess.elixir-europe.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.
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 https://tess.elixir-europe.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 https://tess.elixir-europe.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
DSW Template Development Kit: The Tutorial

[Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines...

Scientific topics: Data management

Keywords: data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development

Resource type: Video, Slides, Webinar

DSW Template Development Kit: The Tutorial https://tess.elixir-europe.org/materials/dsw-template-development-kit-the-tutorial [Data Stewardship Wizard](ds-wizard.org) is a flexible questionnaire-based tool that uses Jinja2 templates to produce documents. It allows creating documents in practically any textual format. Such documents can be intended for both humans (HTML, Markdown, reStructuredText, etc.) and machines (e.g. RDF, YAML, or JSON). Our Template Development Kit (DSW TDK) is a command-line tool to make the work on templates efficient. Data management data stewardship, data management plan, FAIR, data management, software tools, DMP templates, template development data stewards data managers
Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

Containers & Workflow pipelines workshop https://tess.elixir-europe.org/materials/containers-workflow-pipelines-workshop The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well. On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Containers, Nextflow bioinformaticians
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, data management plan, research data management, FAIR principles, DMP tools, DMP templates, tools, template, competency, DMP evaluation, evaluation, on-line, e-learning, Spanish

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

Elaboración de un Plan de Gestión de Datos (DMP): teoria y práctica https://tess.elixir-europe.org/materials/elaboracion-de-un-plan-de-gestion-de-datos-dmp-teoria-y-practica-1cb1388d-cb82-458f-8f72-62bb55e66180 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 Data management FAIR data 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, Spanish project manager Researchers
GA4GH Passports and ELIXIR AAI

The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.

Keywords: AAI , GA4GH, Passports, Auhtorisation

Resource type: Training materials, Video

GA4GH Passports and ELIXIR AAI https://tess.elixir-europe.org/materials/ga4gh-passports-and-elixir-aai The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API. Stefan Negru Teemu Kataja AAI , GA4GH, Passports, Auhtorisation software developers, bioinformaticians
EJP RD MOOC "Diagnosing Rare Diseases: from the Clinic to Research and back"

Discover the role of research, clinical investigation and data sharing in diagnosing rare diseases. This course offers an exploration of key questions around rare disease diagnostic research and issues today, as well as insights into patient experiences.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

EJP RD MOOC "Diagnosing Rare Diseases: from the Clinic to Research and back" https://tess.elixir-europe.org/materials/ejp-rd-mooc-diagnosing-rare-diseases-from-the-clinic-to-research-and-back Discover the role of research, clinical investigation and data sharing in diagnosing rare diseases. This course offers an exploration of key questions around rare disease diagnostic research and issues today, as well as insights into patient experiences. Rare diseases Rare Diseases & Research PhD students postdoctoral researchers Researchers healthcare professionals Patient Advocates rare disease patients representatives
CINECA discovery service catalog

Description and demonstration of the CINECA service catalog

Keywords: Cohort data, Standards, federated data analysis, Beacon queries

Resource type: Series of videos

CINECA discovery service catalog https://tess.elixir-europe.org/materials/cineca-discovery-service-catalog Description and demonstration of the CINECA service catalog Cohort data, Standards, federated data analysis, Beacon queries
A common framework for designing portable federated pipelines

This video describes a common framework for designing portable federated pipelines

Scientific topics: Data architecture, analysis and design

Keywords: data access, federated data analysis

Resource type: Video

A common framework for designing portable federated pipelines https://tess.elixir-europe.org/materials/a-common-framework-for-designing-portable-federated-pipelines This video describes a common framework for designing portable federated pipelines Alvaro Gonzalez Data architecture, analysis and design data access, federated data analysis
Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects

CINECA webinar discussing when to bring compute to the data

Scientific topics: Data architecture, analysis and design

Keywords: Cloud computing, Data analysis, Standards, Translational research

Resource type: Video

Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects https://tess.elixir-europe.org/materials/data-gravity-in-the-life-sciences-lessons-learned-from-the-hca-and-other-federated-data-projects CINECA webinar discussing when to bring compute to the data Data architecture, analysis and design Cloud computing, Data analysis, Standards, Translational research
IFB Shiny training

Shiny package training (in french)

Keywords: R-programming, Reproducible Science

IFB Shiny training https://tess.elixir-europe.org/materials/ifb-shiny-training Shiny package training (in french) Hélène Chiapello Jacques van Helden R-programming, Reproducible Science bioinformaticians statisticians
Status Update Code of Conduct: Teaming up & Talking about it

CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR

Keywords: GDPR, Healthcare research, data harmonization

Resource type: Video

Status Update Code of Conduct: Teaming up & Talking about it https://tess.elixir-europe.org/materials/status-update-code-of-conduct-teaming-up-talking-about-it CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR GDPR, Healthcare research, data harmonization
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics https://tess.elixir-europe.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help https://tess.elixir-europe.org/materials/biosimulators-help BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. The BioSimulators help describes how to use this registry: - How to find a containerized simulation tools that are capable of executing a modeling study. - How to use containerized simulation tools to execute modeling studies. - How to containerize a simulation tool and submit it to the BioSimulators registry. Ion Moraru Bilal Shaikh Simulation experiment Computational biology Systems biology Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL modelers Computational biologists software developers, bioinformaticians
Webinars from the European Reference Network in Rare Hematological Diseases (EuroBloodNet)

The aim of these educational activities is to promote the interest on very innovative topics in order to stress among health professionals the cutting-edge advances in the field of Rare Hematological Diseases. One or 2 webinars per month, each of them lasting 45 minutes.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Webinars from the European Reference Network in Rare Hematological Diseases (EuroBloodNet) https://tess.elixir-europe.org/materials/ern-eurobloodnet-thursdays-webinars The aim of these educational activities is to promote the interest on very innovative topics in order to stress among health professionals the cutting-edge advances in the field of Rare Hematological Diseases. One or 2 webinars per month, each of them lasting 45 minutes. Rare diseases Rare Diseases & Research Health Care Professionals health professionals Patient Advocates rare disease patients representatives
Webinars on Hereditary metabolic diseases (MetabERN)

To share information and documentation with stakeholders involved in the field of hereditary metabolic disorders.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Webinars on Hereditary metabolic diseases (MetabERN) https://tess.elixir-europe.org/materials/metabern-library-teaching-and-training-programmes To share information and documentation with stakeholders involved in the field of hereditary metabolic disorders. Rare diseases Rare Diseases & Research Health Care Professionals health professionals
Webinars and Pills of knowledge Videos on rare vascular diseases (VASCERN)

Short single video lessons (of approximately 3-5 minutes long) and webinars.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning, Video

Webinars and Pills of knowledge Videos on rare vascular diseases (VASCERN) https://tess.elixir-europe.org/materials/vascern-webinars-and-pills-of-knowledge-videos Short single video lessons (of approximately 3-5 minutes long) and webinars. Rare diseases Rare Diseases & Research medical students Health Care Professionals health professionals
The Genomics Era: the Future of Genetics in Medicine

This free online course is available on FutureLearn and developed by the St George's University of London and St George's University Hospitals NHS Foundation Trust. It provides healthcare professionals with a basic grounding in genomic medicine. It will introduce you to new genomic technologies,...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

The Genomics Era: the Future of Genetics in Medicine https://tess.elixir-europe.org/materials/the-genomics-era-the-future-of-genetics-in-medicine This free online course is available on FutureLearn and developed by the St George's University of London and St George's University Hospitals NHS Foundation Trust. It provides healthcare professionals with a basic grounding in genomic medicine. It will introduce you to new genomic technologies, which are revolutionizing medicine and will, in time, provide the mainstay of patient diagnosis, treatment and disease prevention. Rare diseases Rare Diseases & Research healthcare professionals
Genetics education for primary care resources from the Gen-Equip project

Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions...

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Documentation, Video, Training materials, online modules, e-learning

Genetics education for primary care resources from the Gen-Equip project https://tess.elixir-europe.org/materials/genetics-education-for-primary-care-resources Gen-Equip project is a project combining education, primary care and genetics. Its aim is to enable health professionals who are working in primary care to update their knowledge and skills in genetics. The aims is the long-term outcome of improvement in care of patients with genetic conditions or concerns. They offer genetics education free of charge to those who want continuing medical or professional education in genetics. Rare diseases Rare Diseases & Research Primary care doctors health professionals
Rheumatic and musculoskeletal diseases online resources from EULAR (European League Against Rheumatism)

Several online courses on rheumatic and musculoskeletal diseases encompassing several rare diseases.

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: online modules, e-learning

Rheumatic and musculoskeletal diseases online resources from EULAR (European League Against Rheumatism) https://tess.elixir-europe.org/materials/rheumatic-and-musculoskeletal-diseases-resources Several online courses on rheumatic and musculoskeletal diseases encompassing several rare diseases. Rare diseases Rare Diseases & Research Health Care Professionals health professionals physisians Patient Advocates rare disease patients representatives
Alkaptonuria online course

Royal College of General Practitioners webinar on Alkaptonuria – "Black Bone Disease"

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Alkaptonuria online course https://tess.elixir-europe.org/materials/alkaptonuria-resources Royal College of General Practitioners webinar on Alkaptonuria – "Black Bone Disease" Rare diseases Rare Diseases & Research General Physicians healthcare professionals
Granulomatosis with polyangiitis screencast

Royal College of General Practitioners webinars on Granulomatosis with polyangiitis (GPA)

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Video, e-learning

Granulomatosis with polyangiitis screencast https://tess.elixir-europe.org/materials/granulomatosis-with-polyangiitis-resources Royal College of General Practitioners webinars on Granulomatosis with polyangiitis (GPA) Rare diseases Rare Diseases & Research General Physicians
Integrating to ELIXIR AAI -- instructions for developers

This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation.

Scientific topics: Computer science

Keywords: AAI, IAM, Authentication, authorisation

Resource type: Webinar, Presentation, Documentation

Integrating to ELIXIR AAI -- instructions for developers https://tess.elixir-europe.org/materials/integrating-to-elixir-aai-instruction-for-developers This is a collection of videos, presentations and on-line materials for developers and administrators for integrating a service to ELIXIR AAI, the ELIXIR Compute platform service for user authentication and authorisation. Computer science AAI, IAM, Authentication, authorisation software developers, bioinformaticians
Medics4RareDiseases (M4RD) video library

e-learning for medical students and doctors about the fundamentals of rare diseases

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: e-learning

Medics4RareDiseases (M4RD) video library https://tess.elixir-europe.org/materials/medics4rarediseases-m4rd-video-library e-learning for medical students and doctors about the fundamentals of rare diseases Rare diseases Rare Diseases & Research healthcare professionals General Physicians medical students
Transplantchild Webinars (ERN TransplantChild)

E-learning webinars on various pediatric transplantation items

Scientific topics: Rare diseases

Keywords: Rare Diseases & Research

Resource type: Webinar, e-learning

Transplantchild Webinars (ERN TransplantChild) https://tess.elixir-europe.org/materials/transplantchild-webinars-ern-transplantchild E-learning webinars on various pediatric transplantation items Rare diseases Rare Diseases & Research