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8 materials found

Scientific topics: Toxicology  or Personalised medicine 


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

Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

At the lowest scale, PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion, uptake and secretion of substrates and signalling molecules. At the cell scale, PhysiCell uses mechanical equations to model individual cell...

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

Operations: Modelling and simulation

Keywords: HPC, Biomodelling, cell simulations

Resource type: Webinar

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

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

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 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

OpenRiskNet: Ontology Walkthrough and Workshop

Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.

Scientific topics: Ontology and terminology, Toxicology

Resource type: Tutorial

Adding nanomaterial data

This tutorial describes how nanomaterial data can be added to an eNanoMapper server using a RDF format.

Scientific topics: Database management, Toxicology

Keywords: nanotoxicology, enanomapper, resource description framework, ontology

Resource type: Tutorial