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Helis Academy course FAIR data stewardship 2021, Day 1, (Reviewing) Data Management Plans

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: FAIR data, Data management

Operations: Data handling

Keywords: Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 1, (Reviewing) Data Management Plans http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-1-reviewing-data-management-plans This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 FAIR data Data management Data management planning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 6, Metadata FAIR Data Point

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: FAIR data, Metadata

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 6, Metadata FAIR Data Point http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-6-metadata-fair-data-point This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 Data management FAIR data FAIR data, Metadata PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 3, Electronic Lab Notebooks (ELN)

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Electronic Lab Notebooks (ELN), Data processing, Data analysis

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 3, Electronic Lab Notebooks (ELN) http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-3-electronic-lab-notebooks-eln This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021 Data management FAIR data Electronic Lab Notebooks (ELN), Data processing, Data analysis PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 3, Software carpentry/Versioning

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Software Carpentry, Versioning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 3, Software carpentry/Versioning http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-3-software-carpentry-versioning This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021 Data management FAIR data Software Carpentry, Versioning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 2, Informed consent procedures

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Informed consent procedures, Data management planning, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Informed consent procedures http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-informed-consent-procedures This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 Data management FAIR data Informed consent procedures, Data management planning, FAIR data PhD candidate
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
Helis Academy course FAIR data stewardship 2021, Day 2, Introduction Wrap up

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: FAIR, Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Introduction Wrap up http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-introduction-wrap-up This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 Data management FAIR data FAIR, Data management planning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 2, Data security and privacy

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data security, Data privacy, Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Data security and privacy http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-data-security-and-privacy This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 Data management FAIR data Data security, Data privacy, Data management planning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 4, Data carpentry

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data carpentry, Data analysis

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 4, Data carpentry http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-4-data-carpentry This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021 Data management FAIR data Data carpentry, Data analysis PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 5, Introduction Wrap up

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: FAIR data, Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 5, Introduction Wrap up http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-5-introduction-wrap-up This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021 Data management FAIR data FAIR data, Data management planning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 4, Introduction Wrap up

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: FAIR data, Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 4, Introduction Wrap up http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-4-introduction-wrap-up This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021 Data management FAIR data FAIR data, Data management planning PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 5, Preregistration

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data management planning, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 5, Preregistration http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-5-preregistration This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021 Data management FAIR data Data management planning, FAIR data PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 6, Introduction Wrap up

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data management planning, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 6, Introduction Wrap up http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-6-introduction-wrap-up This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 Data management FAIR data Data management planning, FAIR data PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 3, Introduction Wrap up

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data management planning, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 3, Introduction Wrap up http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-3-introduction-wrap-up This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 3, March 22, 2021 Data management FAIR data Data management planning, FAIR data PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 4, Software carpentry

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data analysis, Software Carpentry

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 4, Software carpentry http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-4-software-carpentry This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 4, March 24, 2021 Data management FAIR data Data analysis, Software Carpentry PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 5, Archiving data

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021

Scientific topics: Data management, FAIR data

Operations: Data handling

Keywords: Data preserving, Data sharing

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 5, Archiving data http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-5-archiving-data This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 5, March 29, 2021 Data management FAIR data Data preserving, Data sharing PhD candidate
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
BioExcel Building Blocks (BioBB) Training Material

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Keywords: molecular dynamics, Docking, Modeling, life sciences

Resource type: Jupyter notebook

BioExcel Building Blocks (BioBB) Training Material http://tess.elixir-uk.org/materials/bioexcel-building-blocks-biobb-training-material BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR. Josep Lluís Gelpí Stian Soiland-Reyes molecular dynamics, Docking, Modeling, life sciences PhD students computational scientists Computational biologists
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, Computer Programming, Documentation and help

Resource type: Tutorial

Tutorial on using MPI with containers http://tess.elixir-uk.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, Computer Programming, Documentation and help Users wanting to construct MPI containers Developers wanting to distribute their MPI dependent software HPC system maintainers wanting to enable 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 http://tess.elixir-uk.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
Helis Academy course FAIR data stewardship 2021, Day 2, Infrastructure for storing and sharing data

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: FAIR data, Data management

Operations: Data handling, Analysis

Keywords: Data analysis, Data processing, Data sharing

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Infrastructure for storing and sharing data http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-infrastructure-for-storing-and-sharing-data This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 FAIR data Data management Data analysis, Data processing, Data sharing PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 2, Tools for processing and analysing data

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: Data management, FAIR data

Operations: Analysis, Data handling

Keywords: Data analysis, Data processing

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Tools for processing and analysing data http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-tools-for-processing-and-analysing-data This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 Data management FAIR data Data analysis, Data processing PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 1, Institute requirements

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021

Scientific topics: Data management, FAIR data

Operations: Analysis, Data handling

Keywords: Data preserving, Data reuse, Data management planning, Data sharing, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 1, Institute requirements http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-1-institute-requirements This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021 Data management FAIR data Data preserving, Data reuse, Data management planning, Data sharing, FAIR data PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 1, Publisher requirements

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021

Scientific topics: Data management, FAIR data

Operations: Analysis, Data handling

Keywords: Data management planning, FAIR data, Data preserving, Data sharing

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 1, Publisher requirements http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-1-publisher-requirements This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021 Data management FAIR data Data management planning, FAIR data, Data preserving, Data sharing PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 1, Funder requirements

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021

Scientific topics: Data management, FAIR data

Operations: Analysis, Data handling

Keywords: Data management planning, FAIR data

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 1, Funder requirements http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-1-funder-requirements This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 1, March 17, 2021 Data management FAIR data Data management planning, FAIR data PhD candidate
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: Simulation experiment, Personalised medicine

Operations: Modelling and simulation

Keywords: cell-level simulations, Biomodelling, HPC

Resource type: Tutorial

Tutorials on COBREXA http://tess.elixir-uk.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. Simulation experiment Personalised medicine 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: Molecular interactions, pathways and networks, Simulation experiment, Personalised medicine

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, Signalling

Resource type: Tutorial

Tutorial on CellNOpt http://tess.elixir-uk.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. Molecular interactions, pathways and networks Simulation experiment Personalised medicine 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...

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
Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 2

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: FAIR data, Data management

Operations: Data handling

Keywords: Data collection

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 2 http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-finding-and-capturing-data-f94ad623-4ae5-4e48-925e-2afdc8567c6d This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 FAIR data Data management Data collection PhD candidate
Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 1

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021

Scientific topics: FAIR data, Data quality management

Operations: Analysis

Keywords: Data collection

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 1 http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-2-finding-and-capturing-data This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 2, March 18, 2021 FAIR data Data quality management Data collection PhD candidate