Close menu

SURE

Sunderland Repository records the research produced by the University of Sunderland including practice-based research and theses.

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

Alden, Kieran, Timmis, Jonathan, Andrews, Paul. S, Veiga-Fernandes, Henrique and Coles, Mark C. (2016) Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 (2). pp. 431-442. ISSN 1545-5963

Item Type: Article

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.

[img]
Preview
PDF
Extending and Applying Spartan to Perform.pdf - Published Version
Available under License Creative Commons Attribution.

Download (4MB) | Preview

More Information

Depositing User: Klaire Purvis-Shepherd

Identifiers

Item ID: 10844
Identification Number: https://doi.org/10.1109/TCBB.2016.2527654
ISSN: 1545-5963
URI: http://sure.sunderland.ac.uk/id/eprint/10844
Official URL: https://ieeexplore.ieee.org/document/7403919

Users with ORCIDS

ORCID for Jonathan Timmis: ORCID iD orcid.org/0000-0003-1055-0471

Catalogue record

Date Deposited: 07 Jun 2019 13:56
Last Modified: 30 Sep 2020 11:15

Contributors

Author: Jonathan Timmis ORCID iD
Author: Kieran Alden
Author: Paul. S Andrews
Author: Henrique Veiga-Fernandes
Author: Mark C. Coles

University Divisions

Faculty of Technology > School of Computer Science

Subjects

Sciences > Biomedical Sciences
Computing > Software Engineering
Computing

Actions (login required)

View Item (Repository Staff Only) View Item (Repository Staff Only)