Welcome to scarcc’s documentation!

For installation instructions, please see INSTALL.rst.

Example notebooks can be download at docs.

Basic Setup

• 1. Harcombe Lab Mutualism Model Setup
  • 1.1. Making E0
  • 1.2. compare E_WT vs. E0 growth in lactose env +- methionine
  • 1.3. Making S0
  • 1.4. Examine secretion of S_WT vs. S0 on acetate medium:
  • 1.5. Making M0.
  • 1.6. Now lets run a mutualism simulation:
• 2. Modifying E.coli Carbon Byproduct Secretion Profile
  • 2.1. Flux weighting
  • 2.2. Secretion profiles after flux weighting
• 3. Preparing Single Gene Target and Double Gene Combinations
  • 3.1. Read double gene from first column of GeneCombos file
  • 3.2. Get all single genes from double gene list
• 4. Stoichiometry Scaling

Simulation Procedures

• 1. Deriving Alpha Table from FBA
  • 1.1. Search for \(\alpha\) that corresponds to IC50
  • 1.2. Production of alpha_table
  • 1.3. Passing detailed dataframe as argument to retrieve alpha_table
  • 1.4. Essentiality difference between models
  • 1.5. Heterogeneity of \(\alpha\) across medium property
• 2. Simulation Workflow
  • 2.1. Multiprocessing to derive results
  • 2.2. Detailed break down of steps
    • 2.2.1. Step 1: Stiochiometric Scaling
    • 2.2.2. Step 2: Construction layout object for cultures with perturbed metabolic models
    • 2.2.3. Step 3: Run simulation with layout
  • 2.3. Integration of all steps
    • 2.3.1. Streamlined Process for Simulation Workflow
  • 2.4. Display of data frames inside df_container
• 3. Checkerboard simulation
  • 3.1. Data Input
  • 3.2. Generate and save alpha_table_checkerboard
  • 3.3. Intrinsic resistance of each species
  • 3.4. Simulation

Data Analysis

• 1. Preprocessing Flux Data for Plots
• 2. Checkerboard plots
  • 2.1. Heatmaps
• 3. Analyzing carbon allocation profile
  • 3.1. Read dataframe with carbon allocation data
  • 3.2. Heatmap

Indices and tables

• Index

• Module Index

• Search Page