16 citations · 47 across the 8 of their papers we have counts for
8 papers
A novel scalable high performance diffusion solver for multiscale cell simulations
Jose-Luis Estragues-Muñoz, Carlos Alvarez, Arnau Montagud +2
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surroundi…
PhysiBoSS-Models: A database for multiscale models
Vincent Noel, Marco Ruscone, Randy Heiland +5
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of com…
Lessons learned from a performance analysis and optimization of a multiscale cellular simulation
Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud +2
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performan…
Parallel Model Exploration for Tumor Treatment Simulations
Charilaos Akasiadis, Miguel Ponce-de-Leon, Arnau Montagud +6
Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth…
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction
Daniel Gamermann, Arnau Montagud, J. Alberto Conejero +2
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into a…
Phylogenetic tree reconstruction from genome-scale metabolic models
D. Gamermann, A. Montagud, J. A. Conejero +2
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from…
Automation on the generation of genome scale metabolic models
R. Reyes, D. Gamermann, A. Montagud +4
Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requir…
A modular synthetic device to calibrate promoters
D. Gamermann, A. Montagud, P. Aparicio +5
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications an…