A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment

Molecular docking is a computational technique which predicts the binding energy and the preferred binding mode of a ligand to a protein target. Virtual screening is a tool which uses docking to investigate large chemical libraries to identify ligands that bind favorably to a protein target. We have developed a novel scoring based distributed protein docking application to improve enrichment in virtual screening. The application addresses the issue of time and cost of screening in contrast to conventional systematic parallel virtual screening methods in two ways. Firstly, it automates the process of creating and launching multiple independent dockings on a high performance computing cluster. Secondly, it uses a N˙ aive Bayes scoring function to calculate binding energy of un-docked ligands to identify and preferentially dock (Autodock predicted) better binders. The application was tested on four proteins using a library of 10,573 ligands. In all the experiments, (i). 200 of the 1000 best binders are identified after docking only 14% of the chemical library, (ii). 9 or 10 best-binders are identified after docking only 19% of the chemical library, and (iii). no significant enrichment is observed after docking 70% of the chemical library. The results show significant increase in enrichment of potential drug leads in early rounds of virtual screening

Research on Batch Scheduling in Cloud Computing

In the existing cloud computing environment, batch scheduling strategies mainly focus on the management of resources allocation. This paper provides the task scheduling algorithm based on service quality which fully considers priority and scheduling deadline. The improved algorithm combines the advantages of Min-min algorithm with higher throughput and linear programming with global optimization, considers not only all the tasks but also the high priority tasks. The experiment result shows that compared with the Min-min and DBCT the completed tasks of the improved algorithm increase about 10.6% and 22.0%, on the other hand the completed high priority tasks also increases approximately 20% and 40%

Live Prefetching for Mobile Computation Offloading

The conventional designs of mobile computation offloading fetch user-specific data to the cloud prior to computing, called offline prefetching. However, this approach can potentially result in excessive fetching of large volumes of data and cause heavy loads on radio-access networks. To solve this problem, the novel technique of live prefetching is proposed in this paper that seamlessly integrates the task-level computation prediction and prefetching within the cloud-computing process of a large program with numerous tasks. The technique avoids excessive fetching but retains the feature of leveraging prediction to reduce the program runtime and mobile transmission energy. By modeling the tasks in an offloaded program as a stochastic sequence, stochastic optimization is applied to design fetching policies to minimize mobile energy consumption under a deadline constraint. The policies enable real-time control of the prefetched-data sizes of candidates for future tasks. For slow fading, the optimal policy is derived and shown to have a threshold-based structure, selecting candidate tasks for prefetching and controlling their prefetched data based on their likelihoods. The result is extended to design close-to-optimal prefetching policies to fast fading channels. Compared with fetching without prediction, live prefetching is shown theoretically to always achieve reduction on mobile energy consumption.Comment: To appear in IEEE Trans. on Wireless Communicatio

Integrating Technology With Student-Centered Learning

Reviews research on technology's role in personalizing learning, its integration into curriculum-based and school- or district-wide initiatives, and the potential of emerging digital technologies to expand student-centered learning. Outlines implications