Watanabe2018_State transition model dependent on changing parameters

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Short description
Model dependent on changing parameters. There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal. The yearly transition probabilities are: Healthy to Dead: Age/1000; Healthy to Sick: according to function F1 depending on Age and Male parameters; Sick to Healthy: 0.1; Sick to Dead: according to function F2 depending on Age and Male parameters. Pre-Transition Rules: Age increased by 1 each cycle. Initial conditions: Healthy = (50 Male, 50 Female with Age =1,2,…,50 for each individual), Sick = (0,0) and Dead = (0,0). Output: Number of men and women in each disease state for years 1-10 and their ages in each state.
Original code
Related Publication
  • Toward reproducible disease models using the Systems Biology Markup Language
  • Leandro Watanabe, Jacob Barhak, Chris Myers
  • SAGE journals , 9/ 2018
  • Department of Electrical and Computer Engineering, University of Utah, USA 2Jacob Barhak, Austin, TX, USA
  • Disease modelers have been modeling progression of diseases for several decades using such tools as Markov models or microsimulation. However, they need to address a serious challenge; many models they create are not reproducible. Moreover, there is no proper practice that ensures reproducible models, since modelers rely on loose guidelines that change periodically, rather than well-defined machine-readable standards. The Systems Biology Markup Language (SBML) is one such standard that allows exchange of models between different software tools. Recently, the SBML Arrays package has been developed, which extends the standard to allow handling simulation of populations. This paper demonstrates through several abstract examples how microsimulation disease models can be encoded using the SBML Arrays package, enabling reproducible disease modeling.
Leandro Watanabe, Rahuman Sheriff

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Example4.xml SBML level 3 version 2, representation of Example4: State Transition Model Dependent on Changing Parameters 70.52 KB Preview | Download

  • Model originally submitted by : Leandro Watanabe
  • Submitted: Jan 30, 2019 5:02:36 PM
  • Last Modified: Jan 30, 2019 5:02:36 PM
  • Version: 4 public model Download this version
    • Submitted on: Jan 30, 2019 5:02:36 PM
    • Submitted by: Rahuman Sheriff
    • With comment: Edited model metadata online.