Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Investigating the impact of networking capability on firm innovation performance:using the resource-action-performance framework

The author's final peer reviewed version can be found by following the URI link. The Publisher's final version can be found by following the DOI link.Purpose The experience of successful firms has proven that one of the most important ways to promote co-learning and create successful networked innovations is the proper application of inter-organizational knowledge mechanisms. This study aims to use a resource-action-performance framework to open the black box on the relationship between networking capability and innovation performance. The research population embraces companies in the Iranian automotive industry. Design/methodology/approach Due to the latent nature of the variables studied, the required data are collected through a web-based cross-sectional survey. First, the content validity of the measurement tool is evaluated by experts. Then, a pre-test is conducted to assess the reliability of the measurement tool. All data are gathered by the Iranian Vehicle Manufacturers Association (IVMA) and Iranian Auto Parts Manufacturers Association (IAPMA) samples. The power analysis method and G*Power software are used to determine the sample size. Moreover, SmartPLS 3 and IBM SPSS 25 software are used for data analysis of the conceptual model and relating hypotheses. Findings The results of this study indicated that the relationships between networking capability, inter-organizational knowledge mechanisms and inter-organizational learning result in a self-reinforcing loop, with a marked impact on firm innovation performance. Originality/value Since there is little understanding of the interdependencies of networking capability, inter-organizational knowledge mechanisms, co-learning and their effect on firm innovation performance, most previous research studies have focused on only one or two of the above-mentioned variables. Thus, their cumulative effect has not examined yet. Looking at inter-organizational relationships from a network perspective and knowledge-based view (KBV), and to consider the simultaneous effect of knowledge mechanisms and learning as intermediary actions alongside, to consider the performance effect of the capability-building process, are the main advantages of this research

Modeling the Internet of Things: a simulation perspective

This paper deals with the problem of properly simulating the Internet of Things (IoT). Simulating an IoT allows evaluating strategies that can be employed to deploy smart services over different kinds of territories. However, the heterogeneity of scenarios seriously complicates this task. This imposes the use of sophisticated modeling and simulation techniques. We discuss novel approaches for the provision of scalable simulation scenarios, that enable the real-time execution of massively populated IoT environments. Attention is given to novel hybrid and multi-level simulation techniques that, when combined with agent-based, adaptive Parallel and Distributed Simulation (PADS) approaches, can provide means to perform highly detailed simulations on demand. To support this claim, we detail a use case concerned with the simulation of vehicular transportation systems.Comment: Proceedings of the IEEE 2017 International Conference on High Performance Computing and Simulation (HPCS 2017

Transfer Learning for Improving Model Predictions in Highly Configurable Software

Modern software systems are built to be used in dynamic environments using configuration capabilities to adapt to changes and external uncertainties. In a self-adaptation context, we are often interested in reasoning about the performance of the systems under different configurations. Usually, we learn a black-box model based on real measurements to predict the performance of the system given a specific configuration. However, as modern systems become more complex, there are many configuration parameters that may interact and we end up learning an exponentially large configuration space. Naturally, this does not scale when relying on real measurements in the actual changing environment. We propose a different solution: Instead of taking the measurements from the real system, we learn the model using samples from other sources, such as simulators that approximate performance of the real system at low cost. We define a cost model that transform the traditional view of model learning into a multi-objective problem that not only takes into account model accuracy but also measurements effort as well. We evaluate our cost-aware transfer learning solution using real-world configurable software including (i) a robotic system, (ii) 3 different stream processing applications, and (iii) a NoSQL database system. The experimental results demonstrate that our approach can achieve (a) a high prediction accuracy, as well as (b) a high model reliability.Comment: To be published in the proceedings of the 12th International Symposium on Software Engineering for Adaptive and Self-Managing Systems (SEAMS'17

Modeling good research practices - overview: a report of the ISPOR-SMDM modeling good research practices task force - 1.

Models—mathematical frameworks that facilitate estimation of the consequences of health care decisions—have become essential tools for health technology assessment. Evolution of the methods since the first ISPOR modeling task force reported in 2003 has led to a new task force, jointly convened with the Society for Medical Decision Making, and this series of seven papers presents the updated recommendations for best practices in conceptualizing models; implementing state–transition approaches, discrete event simulations, or dynamic transmission models; dealing with uncertainty; and validating and reporting models transparently. This overview introduces the work of the task force, provides all the recommendations, and discusses some quandaries that require further elucidation. The audience for these papers includes those who build models, stakeholders who utilize their results, and, indeed, anyone concerned with the use of models to support decision making