Archive For The “publications” Category

ASPASIA Published in PLoS Computational Biology

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After two years of working on this project and manuscript revisions alongside Dr Stephanie Evans, I am pleased to say that our paper describing our new software tool, ASPASIA, has now been published in PLoS Computational Biology. ASPASIA was developed during Steph’s PhD rotation at GSK, where she identified a deficiency in tools available for…

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Perspective Published in Frontiers in Immunology

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Our new perspective on the potential of model-driven experimentation in understanding lymphoid tissue has been published in Frontiers in Immunology. In this perspective, we make the case for applying model-driven experimentation using two case studies which combined simulations with experiments to identify mechanisms driving lymphoid tissue formation and function, and then discuss potential applications of…

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Argumentation approach tutorial published in Pharmacometrics & Systems Pharmacology

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Following our previous Royal Society Interface publication on the potential use of argumentation in designing, implementing, and analysing models of biological systems, we were invited to write a tutorial for CPT: Pharmacometrics and Systems Pharmacology that would detail the process of developing these arguments. The paper is co-written with SimOmics Ltd, who are developing the…

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Multi-Objective Calibration Paper Published in Royal Society Interface

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For a while now we have been working with Mark Read (now at the University of Sydney) on the potential to calibrate complex models of biological systems using multi-objective optimisation approaches, such as genetic algorithms. I am pleased to say that a paper describing this work has now been published in the Journal of the…

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Temporal Analysis Paper Published in IEEE TCBB

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A new paper, detailing a study I led into the use of simulation as a tool for exploring the temporal development of secondary lymphoid tissue, has been published in IEEE Transactions on Computational Biology and Bioinformatics. The intention of the study was to determine the key timepoints where the influence of biological factors on cell…

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Agent-Based Modelling Tutorial Published

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Agent-Based models (ABM) are becoming of interest in a wide variety of applications given their advantages in capturing time, space, and individual heterogeneity. We were recently asked to write a tutorial for CPT: Systems Pharmacology and Pharmacometrics that described when an ABM would be appropriate and how these should be developed. This tutorial is now…

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Argumentation Paper in Royal Society Interface

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During my PhD, we examined the adoption of structured argumentation approaches in the engineering of models of biological systems. These approaches are commonly used in the field of safety critical systems, where evidence must accompany all software to show it has been designed appropriately and rigorously tested, with accompanying evidence. We wondered if this approach…

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