scholarly journals Agent‐based models of inflammation in translational systems biology: A decade later

2019 ◽  
Vol 11 (6) ◽  
Author(s):  
Yoram Vodovotz ◽  
Gary An
Keyword(s):  
Systems Biology ◽  
Agent Based Models ◽  
Agent Based

scholarly journals Agent‐based models in translational systems biology

2009 ◽  
Vol 1 (2) ◽  
pp. 159-171 ◽  
Author(s):  
Gary An ◽  
Qi Mi ◽  
Joyeeta Dutta‐Moscato ◽  
Yoram Vodovotz
Keyword(s):  
Systems Biology ◽  
Agent Based Models ◽  
Agent Based

scholarly journals Review of the systems biology of the immune system using agent-based models

2018 ◽  
Vol 12 (3) ◽  
pp. 83-92 ◽  
Author(s):  
Snehal B. Shinde ◽  
Manish P. Kurhekar
Keyword(s):  
Immune System ◽  
Systems Biology ◽  
Agent Based Models ◽  
Agent Based

scholarly journals Multiscale Computational Modeling of Vascular Adaptation: A Systems Biology Approach Using Agent-Based Models

2021 ◽  
Vol 9 ◽  
Author(s):  
Anna Corti ◽  
Monika Colombo ◽  
Francesco Migliavacca ◽  
Jose Felix Rodriguez Matas ◽  
Stefano Casarin ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Modeling ◽  
Cellular Systems ◽  
Emergent Behavior ◽  
Future Research ◽  
Agent Based Models ◽  
Mortality And Morbidity ◽  
Agent Based ◽  
Vascular Adaptation ◽  
Spatial And Temporal Scales

The widespread incidence of cardiovascular diseases and associated mortality and morbidity, along with the advent of powerful computational resources, have fostered an extensive research in computational modeling of vascular pathophysiology field and promoted in-silico models as a support for biomedical research. Given the multiscale nature of biological systems, the integration of phenomena at different spatial and temporal scales has emerged to be essential in capturing mechanobiological mechanisms underlying vascular adaptation processes. In this regard, agent-based models have demonstrated to successfully embed the systems biology principles and capture the emergent behavior of cellular systems under different pathophysiological conditions. Furthermore, through their modular structure, agent-based models are suitable to be integrated with continuum-based models within a multiscale framework that can link the molecular pathways to the cell and tissue levels. This can allow improving existing therapies and/or developing new therapeutic strategies. The present review examines the multiscale computational frameworks of vascular adaptation with an emphasis on the integration of agent-based approaches with continuum models to describe vascular pathophysiology in a systems biology perspective. The state-of-the-art highlights the current gaps and limitations in the field, thus shedding light on new areas to be explored that may become the future research focus. The inclusion of molecular intracellular pathways (e.g., genomics or proteomics) within the multiscale agent-based modeling frameworks will certainly provide a great contribution to the promising personalized medicine. Efforts will be also needed to address the challenges encountered for the verification, uncertainty quantification, calibration and validation of these multiscale frameworks.

scholarly journals Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review

2021 ◽  
Vol 9 (2) ◽  
pp. 417
Author(s):  
Sherli Koshy-Chenthittayil ◽  
Linda Archambault ◽  
Dhananjai Senthilkumar ◽  
Reinhard Laubenbacher ◽  
Pedro Mendes ◽  
...  
Keyword(s):  
Species Interactions ◽  
Computational Models ◽  
Human Microbiome ◽  
Agent Based Modeling ◽  
Autonomous Agent ◽  
Agent Based Models ◽  
Agent Based ◽  
Complex Interactions ◽  
Mucosal Surfaces ◽  
Living Organisms

The human microbiome has been a focus of intense study in recent years. Most of the living organisms comprising the microbiome exist in the form of biofilms on mucosal surfaces lining our digestive, respiratory, and genito-urinary tracts. While health-associated microbiota contribute to digestion, provide essential nutrients, and protect us from pathogens, disturbances due to illness or medical interventions contribute to infections, some that can be fatal. Myriad biological processes influence the make-up of the microbiota, for example: growth, division, death, and production of extracellular polymers (EPS), and metabolites. Inter-species interactions include competition, inhibition, and symbiosis. Computational models are becoming widely used to better understand these interactions. Agent-based modeling is a particularly useful computational approach to implement the various complex interactions in microbial communities when appropriately combined with an experimental approach. In these models, each cell is represented as an autonomous agent with its own set of rules, with different rules for each species. In this review, we will discuss innovations in agent-based modeling of biofilms and the microbiota in the past five years from the biological and mathematical perspectives and discuss how agent-based models can be further utilized to enhance our comprehension of the complex world of polymicrobial biofilms and the microbiome.

Sign in / Sign up

Export Citation Format

Share Document