On-line Supplement for

Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach

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Item File
Supplementary Text containing:
  • Pharmacodynamic parameter estimation (Figure S1)
  • Fluoroquinolone dynamics in uninvolved rabbit lung samples (Figure S2)
  • Spatial fluoroquinolone distribution in granulomas with rabbit and human PK (Figure S3)
  • Bacterial and immune responses following treatment interruption after 70 days (Figure S4)
  • Host immune parameters varied to capture granuloma variability for tissue PK calibration (Table S1)
  • Tissue PK parameter fitting (Table S2)
  • Sensitivity analysis (Table S3, S4)
Virtual machine (Virtual Box) containing:
  • Model executable
  • Parameter files to run untreated controls or fluoroquinolone treatment
  • Model states with existing granulomas for treatment simulations
  • Instructions for running the model
If you’d like to modify values in the parameter files, please see supplement Table S1 for physiological ranges that reproduce bacterial dynamics from Mtb-infected non-human primates.
See details below ...

Virtual Box Install Instructions

To install VirtualBox and required extensions, see: 'Virtualbox and Virtualbox extensions'. Note that this requires about 10G of free disk space.

'Virtualbox and Virtualbox extensions'.

Next, download the 'Model Web Deployment Virtualbox Appliance'. This appliance contains the model executable and all libraries, parameter files and instructions needed to run it.

Start VirtualBox.

Use File | Import Appliance to import the downloaded appliance. Once imported it should appear as an available virtual machine. Start the virtual machine, login as Guest (no password is required).
Open a terminal window by clicking on the top menu bar or click Applications | Accessories | Terminal.

The terminal window will open in the directory for running the model (model-files).

To see detailed instructions for running the model type: ‘vi README.txt’ then press enter.

To exit this file from vi, type: ‘:q’ then press enter.

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