Colorectal tumour simulation using agent based modelling and high performance computing

450,000 European citizens are diagnosed every year with colorectal cancer (CRC) and more than 230,000 succumb to the disease annually. For this reason, significant resources are dedicated to the identification of more effective therapies for this disease. However, classical assessment techniques for these treatments are slow and costly. Consequently, systems biology researchers at the Royal College of Surgeons in Ireland (RCSI) are developing computational agent-based models simulating tumour growth and treatment responses with the objective of speeding up the therapeutic development process while, at the same time, producing a tool for adapting treatments to patient-specific characteristics. However, the model complexity and the high number of agents to be simulated require a thorough optimisation of the process in order to execute realistic simulations of tumour growth on currently available platforms. We propose to apply the most advanced HPC techniques to achieve the efficient and realistic simulation of a virtual tissue model that mimics tumour growth or regression in space and time. These techniques combine extensions of the previously developed agent-based simulation software platform (FLAME) with autotuning capabilities and optimisation strategies for the current tumour model. Development of such a platform could advance the development of novel therapeutic approaches for the treatment of CRC which can also be applied other solid tumours.This work has been partially supported by MICINN-Spain under contract TIN2011- 28689-C02-01 and TIN2014-53234-C2-1-R and GenCat-DIUiE(GRR) 2014-SGR-576. This research was also funded by the European Community’s Framework Programme Seven (FP7) Programme under contract No. 278981 680 AngioPredict and supported by the DJEI/DES/SFI/HEA Irish Centre for High- End Computing (ICHEC).Peer ReviewedPostprint (author's final draft

Effects of antidromic and orthodromic activation of STN afferent axons during DBS in Parkinson\u27s disease: a simulation study

Recent studies suggest that subthalamic nucleus (STN)-Deep Brain Stimulation (DBS) may exert at least part of its therapeutic effect through the antidromic suppression of pathological oscillations in the cortex in 6-OHDA treated rats and in parkinsonian patients. STN-DBS may also activate STN neurons by initiating action potential propagation in the orthodromic direction, similarly resulting in suppression of pathological oscillations in the STN. While experimental studies have provided strong evidence in support of antidromic stimulation of cortical neurons, it is difficult to separate relative contributions of antidromic and orthodromic effects of STN-DBS. The aim of this computational study was to examine the effects of antidromic and orthodromic activation on neural firing patterns and beta-band (13-30 Hz) oscillations in the STN and cortex during DBS of STN afferent axons projecting from the cortex. High frequency antidromic stimulation alone effectively suppressed simulated beta activity in both the cortex and STN-globus pallidus externa (GPe) network. High frequency orthodromic stimulation similarly suppressed beta activity within the STN and GPe through the direct stimulation of STN neurons driven by DBS at the same frequency as the stimulus. The combined effect of both antidromic and orthodromic stimulation modulated cortical activity antidromically while simultaneously orthodromically driving STN neurons. While high frequency DBS reduced STN beta-band power, low frequency stimulation resulted in resonant effects, increasing beta-band activity, consistent with previous experimental observations. The simulation results indicate effective suppression of simulated oscillatory activity through both antidromic stimulation of cortical neurons and direct orthodromic stimulation of STN neurons. The results of the study agree with experimental recordings of STN and cortical neurons in rats and support the therapeutic potential of stimulation of cortical neurons

Effects of antidromic and orthodromic activation of STN afferent axons during DBS in Parkinson's disease: a simulation study

Recent studies suggest that subthalamic nucleus (STN)-Deep Brain Stimulation (DBS) may exert at least part of its therapeutic effect through the antidromic suppression of pathological oscillations in the cortex in 6-OHDA treated rats and in parkinsonian patients. STN-DBS may also activate STN neurons by initiating action potential propagation in the orthodromic direction, similarly resulting in suppression of pathological oscillations in the STN. While experimental studies have provided strong evidence in support of antidromic stimulation of cortical neurons, it is difficult to separate relative contributions of antidromic and orthodromic effects of STN-DBS. The aim of this computational study was to examine the effects of antidromic and orthodromic activation on neural firing patterns and beta-band (13-30 Hz) oscillations in the STN and cortex during DBS of STN afferent axons projecting from the cortex. High frequency antidromic stimulation alone effectively suppressed simulated beta activity in both the cortex and STN-globus pallidus externa (GPe) network. High frequency orthodromic stimulation similarly suppressed beta activity within the STN and GPe through the direct stimulation of STN neurons driven by DBS at the same frequency as the stimulus. The combined effect of both antidromic and orthodromic stimulation modulated cortical activity antidromically while simultaneously orthodromically driving STN neurons. While high frequency DBS reduced STN beta-band power, low frequency stimulation resulted in resonant effects, increasing beta-band activity, consistent with previous experimental observations. The simulation results indicate effective suppression of simulated oscillatory activity through both antidromic stimulation of cortical neurons and direct orthodromic stimulation of STN neurons. The results of the study agree with experimental recordings of STN and cortical neurons in rats and support the therapeutic potential of stimulation of cortical neurons

Colorectal tumour simulation using agent based modelling and high performance computing

450,000 European citizens are diagnosed every year with colorectal cancer (CRC) and more than 230,000 succumb to the disease annually. For this reason, significant resources are dedicated to the identification of more effective therapies for this disease. However, classical assessment techniques for these treatments are slow and costly. Consequently, systems biology researchers at the Royal College of Surgeons in Ireland (RCSI) are developing computational agent-based models simulating tumour growth and treatment responses with the objective of speeding up the therapeutic development process while, at the same time, producing a tool for adapting treatments to patient-specific characteristics. However, the model complexity and the high number of agents to be simulated require a thorough optimisation of the process in order to execute realistic simulations of tumour growth on currently available platforms. We propose to apply the most advanced HPC techniques to achieve the efficient and realistic simulation of a virtual tissue model that mimics tumour growth or regression in space and time. These techniques combine extensions of the previously developed agent-based simulation software platform (FLAME) with autotuning capabilities and optimisation strategies for the current tumour model. Development of such a platform could advance the development of novel therapeutic approaches for the treatment of CRC which can also be applied other solid tumours.This work has been partially supported by MICINN-Spain under contract TIN2011- 28689-C02-01 and TIN2014-53234-C2-1-R and GenCat-DIUiE(GRR) 2014-SGR-576. This research was also funded by the European Community’s Framework Programme Seven (FP7) Programme under contract No. 278981 680 AngioPredict and supported by the DJEI/DES/SFI/HEA Irish Centre for High- End Computing (ICHEC).Peer Reviewe