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Network and equation-based (EB) models are two prominent methods used in the study of epidemics. While EB models use a global approach to model aggregate population, network models focus on the behavior of individuals in the population. The two approaches have been used in several areas of research, including finance, computer science, social science and epidemiology. In this study, epidemiology is used to contrast EB models with network models. The methods are based on the assumptions and properties of compartmental models. In EB models we solve a system of ordinary differential equations and in network models we simulate the spread of epidemics on contact networks using bond percolation. We examine the impact of network structures on the spread of infection by considering various networks, including Poisson, Erdős Rényi, Scale-free, and Watts–Strogatz small-world networks, and discuss how control measures can make use of the network structures. In addition, we simulate EB assumptions on Watts–Strogatz networks to determine when the results are similar to that of EB models. As a case study, we use data from the 1918 Spanish flu pandemic and that from measles outbreak to validate our results.

Motivation Accurate and efficient predictions of protein structures play an important role in understanding their functions. I-TASSER (Iterative Threading Assembly Refinement) is one of the most successful and widely used protein structure prediction methods in the recent community-wide CASP experiments. Yet, the computational efficiency of I-TASSER is one of the limiting factors that prevent its application for large-scale structure modelling. Results We present GPU-I-TASSER, a GPU accelerated I-TASSER protein structure prediction tool for fast and accurate protein structure prediction. Our implementation is based on OpenACC parallelization of the replica-exchange Monte Carlo simulations to enhance the speed of I-TASSER by extending its capabilities to the GPU architecture. On a benchmark dataset of 71 protein structures, GPU-I-TASSER achieves on average a 10x speedup with comparable structure prediction accuracy compared to the CPU version of the I-TASSER. Availability The complete source code for GPU-I-TASSER can be downloaded and used without restriction from https://zhanggroup.org/GPU-I-TASSER/ Supplementary information Supplementary data are available at Bioinformatics online.

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