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14 materials found

Scientific topics: Personalised medicine 


Data-driven modelling of intercellular interactions in the tumour microenvironment

Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumours, recent studies have uncovered complex macrophage populations, including tumour-associated macrophages, which support tumorigenesis through cancer hallmarks such as...

Scientific topics: Computational biology, Oncology, Personalised medicine

Resource type: Recorded webinar

Introducing PerMedCoE Building Blocks and Workflows to streamline biological analysis pipelines

Analysing biological datasets is nearly always a multi-step process involving many interconnected stages. Even so, the lack of transparent approaches to managing complex data analysis pipelines remains a common challenge in the life sciences. Another limiting factor is that completing such...

Scientific topics: Computational biology, Personalised medicine, Workflows

Resource type: Recorded webinar

Croupier, an user-centric meta-orchestrator for cross-platform workflow delivery and execution

The orchestration of complex application workflows executed in the context of High Performance Computing (HPC) infrastructures requires the joint collaboration of application designers/developers, HPC engineers and application consumers (i.e. end-users). In the context of HPC, complex workflows...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

Data protection and security aspects of running simulations on personal data with HPC

When processing health and genetic data in High Performance Computing (HPC) clusters, researchers must consider the application of research ethics principles as well as the General Data Protection Regulation, including issues of identifiability, duties of confidentiality and security, and...

Scientific topics: Computer science, Data security, Personalised medicine

Resource type: Recorded webinar

HPC boosts mathematical models’ promises of personalised medicine

Mathematical models of the biological processes that are deregulated in diseases show a high complexity not only because of the number of genes and pathways involved, but also because of the numerous patients or samples to include in the simulations in order to be predictive. One way to address...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

The PerMedCoE competency framework to guide training and career development

PerMedCoE aims at providing an efficient and sustainable infrastructure to support personalised medicine, adapting cell-level simulation methods to pre-exascale systems to translate omics data into molecular disease models. One of the activities to achieve this consists of a training programme to...

Scientific topics: Computational biology, Personalised medicine

Resource type: Recorded webinar

Mathematical modelling as knowledge mapping in PhysiCell: a guided tour

Tissues are complex multiscale biological systems where cells communicate to modulate their behaviour in response to dynamical microenvironmental conditions. Small perturbations to cells—such as injuries or therapy—can have unanticipated "ripple effects" that percolate through the system. We can...

Scientific topics: Computational biology, Personalised medicine

Resource type: Recorded webinar

Computer-assisted functional precision medicine in cancer

Biological mechanisms provide a link between anti cancer compounds and therapy responses. Insight to biological mechanisms is central for tomorrow’s clinical decision support systems and personalised cancer therapy. I will present the NTNU DrugLogics software that combines cancer signalling prior...

Scientific topics: Computational biology, Personalised medicine, Simulation experiment

Resource type: Recorded webinar

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

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

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: Personalised medicine, Simulation experiment

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: Personalised medicine, Simulation experiment, Molecular interactions, pathways and networks, Transcription factors and regulatory sites

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

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