HEC

HEC simulates and analyzes evolutionary dynamics of prokaryotic communities to investigate effects of horizontal gene transfer (HGT), population fitness, and phenotypic regulation on community stability.

Key Features:

• Integrated modeling approaches: Combines generalized and portrait modeling approaches for prokaryotic community simulation and analysis.
• Dynamic model structure modification: Allows modification of the structure of current models during simulations.
• Atrophic ring-like network simulation: Simulates communities structured as atrophic ring-like networks with HGT-mediated metabolic exchanges.
• Trophic ring-like antagonistic network analysis: Models trophic ring-like networks of antagonistic communities to assess effects of single-population fitness changes on system behavior.
• Fitness–stability relationship: Demonstrates that increasing the fitness of a single population in a trophic ring-like network can increase dependency on environmental fluctuations.
• HGT donor and recipient effects: Shows that horizontal gene transfer can confer selective advantages to both recipient and donor populations.
• Phenotypic regulation handling: Represents phenotypic traits influenced by genetic, epigenetic, and other regulatory factors within community models.
• Information transduction modeling: Models processes of information transduction among populations that resemble horizontal gene transfer.

Scientific Applications:

• Bacterial ecosystem dynamics: Simulates and analyzes evolutionary and ecological dynamics in bacterial communities.
• Metabolic exchange studies: Investigates HGT-driven metabolic exchanges in ring-like community structures.
• Stability and environmental response: Evaluates how population fitness changes influence community dependency on environmental fluctuations.
• Evolutionary maintenance of HGT: Explores how HGT advantages to donors and recipients affect the persistence of gene transfer in populations.
• Phenotypic regulation analysis: Studies effects of genetic, epigenetic, and regulatory influences on phenotypes within community interactions.
• Information transduction research: Examines processes analogous to HGT that mediate information flow among populations.

Methodology:

Implements generalized and portrait modeling approaches and supports dynamic modification of model structure to run simulations of prokaryotic community dynamics including horizontal gene transfer and phenotypic regulation.