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 7 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...

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
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.
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

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
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

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 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

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
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
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