Levine Lab research has generated a range of numerical models from cellular-scale proteome allocation models to water column biogeochemical models.  We are committed to keeping our work accessible and open source to promote knowledge sharing within and beyond the scientific community. Below, you will find numerous resources on our different models and their intended purposes.

  • Phytoplankton Proteome Model
  • Bacterial Proteome Model
  • Particle Degradation Model
  • AB Guild Model
  • TRACE Model
  • EpiGen Model
  • EcoTRACE – coming soon!
  • Plastic Model – coming soon!

Phytoplankton Proteome Model

We developed a proteome allocation model for phytoplankton that optimizes for cell size, the relative investment into different protein pools, and the concentration of different macromolecules in order to maximize growth rate according to temperature, light, and external inorganic nutrient availability.

Read the paper where we used this model here

Find the model code here

Bacterial Proteome Model

The model represents molecular-level transport and cellular proteome allocation specifically designed to compare the performance of ABC transport and PTS.

Read the paper where we used this model here

Find the model code here



Particle Degradation Model

This model captures key micro-scale dynamics occurring on particulate organic carbon (POC) in a manner scalable to the water column. We represent 18 groups of particle-associated heterotrophic microbes, encounter rates, enzymatic production and degradation of POC, and dynamic sinking rates.

Read the paper where we used this model here

Find the model code here



AB Guild Model

This model extracts a low-dimensional representation of binary data into groups of features that are tightly linked and co-occur with high specificity. The model pipeline is designed for use with binary presence/absence data of genomic features (e.g., presence/absence of genes, KO pathways, metabolic reaction components, etc.) to identify marine microbial functional guilds as an alternative to taxonomic community structure.

Read the paper where we used this model here

Find the model code here



TRACE Model

The TRAit Correlation Evolution (TRACE) model framework simulates the adaptive walk of a microbial population across a trait landscape (trait-scape) towards a high-fitness area.

Read the paper where we used this model here

Find the model code here



EpiGen Model

An individual-based model of adaptation modified from Fisher’s model in which the simulated population moved between the “new” and “ancestral” environments. Adaptation is driven by both fast variation, low transmission and slow variation, high transmission modifications.

Read the paper where we used this model here

Find the model code here



EcoTRACE – coming soon!

This model combines a quota-based phytoplankton model with a stochastic evolution step for certain traits (similar to the TRACE model). The goal of this model is to explore the possible evolutionary trajectories within phytoplankton and their effect on intra- and interspecific population dynamics.

Plastic Model – coming soon!

This model competes multiple populations of phytoplankton grown on a single nutrient and allows for specific nutrient response strategies to be toggled on or off for each population.