Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models

Kieran Alden, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles

Research output: Contribution to journalArticlepeer-review

7 Citations (SciVal)

Abstract

Through integrating real time imaging, computational modelling, and statistical analysis approaches, previous work has suggested that the induction of and response to cell adhesion factors is the key initiating pathway in early lymphoid tissue development, in contrast to the previously accepted view that the process is triggered by chemokine mediated cell recruitment. These model derived hypotheses were developed using spartan, an open-source sensitivity analysis toolkit designed to establish and understand the relationship between a computational model and the biological system that model captures. Here, we extend the functionality available in spartan to permit the production of statistical analyses that contrast the behavior exhibited by a computational model at various simulated time-points, enabling a temporal analysis that could suggest whether the influence of biological mechanisms changes over time. We exemplify this extended functionality by using the computational model of lymphoid tissue development as a time-lapse tool. By generating results at twelve-hour intervals, we show how the extensions to spartan have been used to suggest that lymphoid tissue development could be biphasic, and predict the time-point when a switch in the influence of biological mechanisms might occur.

Original languageEnglish
Article number7403919
Pages (from-to)431-442
Number of pages12
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume14
Issue number2
DOIs
Publication statusPublished - 01 Mar 2017
Externally publishedYes

Keywords

  • computational model
  • lymphoid organs
  • peyer's patches (PP)
  • Sensitivity analysis
  • spartan
  • Models, Biological
  • Computer Simulation
  • Peyer's Patches/cytology
  • Chemokines/metabolism
  • Software
  • Computational Biology/methods

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