1. Home
  2. Materials
Register training material
5 materials found

Target audience: Anyone interested in simula... 

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

Tutorial on developing Building Blocks http://tess.elixir-uk.org/materials/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. Personalised medicine Workflows Bioinformatics HPC, building blocks Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
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
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
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 http://tess.elixir-uk.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 http://tess.elixir-uk.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