PerMedCoE

PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe.

PerMedCoE https://tess.elixir-europe.org/content_providers/permedcoe PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe. /system/content_providers/images/000/000/637/original/LOGO_PerMedCoE.jpg?1636473064
Showing 10 materials.
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: Simulation experiment, Personalised medicine, Molecular interactions, pathways and networks

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: Personalised medicine, Simulation experiment

Keywords: cell-level simulations, Biomodelling, HPC

Resource type: Tutorial

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: Bioinformatics, Workflows, Personalised medicine

Keywords: HPC, building blocks

Resource type: Tutorial

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

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

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, Transcription factors and regulatory sites

Keywords: HPC, Biomodelling, Signalling

Resource type: Tutorial

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

Keywords: HPC, Signaling, RNAseq, transcriptomics

Resource type: Tutorial

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

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

Keywords: HPC, Biomodelling, cell simulations, Boolean

Resource type: Webinar

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

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