Success in Pump-Priming Funding Application

I am very pleased that my recent application for internal pump-priming research funds, from the University’s Risk, Decision-Making, and Evidencing research theme, has been successful. This award of just under £4,000 will enable me to investigate expanding my current research, to examine the engineering of person-centric decision-making tools for cost-effectiveness analyses that inform selection of…

ASPASIA Published in PLoS Computational Biology

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…

Perspective Published in Frontiers in Immunology

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…

Argumentation approach tutorial published in Pharmacometrics & Systems Pharmacology

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…

Multi-Objective Calibration Paper Published in Royal Society Interface

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…

COMBINE Meeting, Newcastle

I have spent this week (Sept 19-24th) attending the “Computational Modeling in Biology” Network (COMBINE) meeting. COMBINE is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. Over the years we have used and developed a number of simulation development methodologies and toolkits, and were…

Invited Industry Talk: Statisticians in the Pharmaceutical Industry Immunology

Today I gave an invited talk at the Statisticians in the Pharmaceutical Industry meeting at Roche Products Ltd in Welwyn Garden City. This meeting was attended by statisticians and analysts from a number of pharmaceutical companies and academic institutions who are using modelling and simulation to understand biological systems, with a view to proposing novel…

Invited Seminar, Centre for Research in Social Simulation, University of Surrey, April

It has always surprised me that researchers working on modelling and simulation tend to stay within the particular discipline that they are modelling. For example, when I moved to Birmingham to look at simulation of microbiological systems, I met an entirely different group of people than I met simulating immunological systems while at York, even…

Temporal Analysis Paper Published in IEEE TCBB

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…

Plenary Speaker & Judge at Biomaterials & Tissue Engineering Group 17th Annual White Rose Meeting.

I was recently invited to both give the plenary talk and judge the talk and poster contributions at this meeting in York, and gladly accepted. An audience of 100 attendees, mainly from Universities across the White Rose network, with particular interest in tissue engineering and regenerative medicine attended to give updates on their PhD and…

Agent-Based Modelling Tutorial Published

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…

New role at University of York

In April my most recent spell at York, to consolidate research and facilitate the development of the York Computational Immunology Lab, came to an end. I am pleased to say that I will be returning to the University in October, having been offered a new role at the Department of Electronics. This new role has…

Argumentation Paper in Royal Society Interface

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…

York Computational Immunology Lab Inaugural Meeting

My return to York has been funded by the Centre for Chronic Disease and Disorders (C2D2), with the grant funding us to establish, consolidate and equip the York Computational Immunology Lab at York. The grant also included funding for us to organise an international meeting of researchers interested in computer modelling and simulations for exploring…