Keywords: Populus-tremula or HPC
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
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
Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.
Scientific topics: Computer science
Keywords: HPC, high-performance computing, eLearning, EeLP
Resource type: Training materials
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
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
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
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
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
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
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