Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft

Data as a Service (DaaS) for sharing and processing of large data collections in the cloud

Data as a Service (DaaS) is among the latest kind of services being investigated in the Cloud computing community. The main aim of DaaS is to overcome limitations of state-of-the-art approaches in data technologies, according to which data is stored and accessed from repositories whose location is known and is relevant for sharing and processing. Besides limitations for the data sharing, current approaches also do not achieve to fully separate/decouple software services from data and thus impose limitations in inter-operability. In this paper we propose a DaaS approach for intelligent sharing and processing of large data collections with the aim of abstracting the data location (by making it relevant to the needs of sharing and accessing) and to fully decouple the data and its processing. The aim of our approach is to build a Cloud computing platform, offering DaaS to support large communities of users that need to share, access, and process the data for collectively building knowledge from data. We exemplify the approach from large data collections from health and biology domains.Peer ReviewedPostprint (author's final draft

On distributed mobile edge computing

Mobile Cloud Computing (MCC) has been proposed to offload the workloads of mobile applications from mobile devices to the cloud in order to not only reduce energy consumption of mobile devices but also accelerate the execution of mobile applications. Owing to the long End-to-End (E2E) delay between mobile devices and the cloud, offloading the workloads of many interactive mobile applications to the cloud may not be suitable. That is, these mobile applications require a huge amount of computing resources to process their workloads as well as a low E2E delay between mobile devices and computing resources, which cannot be satisfied by the current MCC technology. In order to reduce the E2E delay, a novel cloudlet network architecture is proposed to bring the computing and storage resources from the remote cloud to the mobile edge. In the cloudlet network, each mobile user is associated with a specific Avatar (i.e., a dedicated Virtual Machine (VM) providing computing and storage resources to its mobile user) in the nearby cloudlet via its associated Base Station (BS). Thus, mobile users can offload their workloads to their Avatars with low E2E delay (i.e., one wireless hop). However, mobile users may roam among BSs in the mobile network, and so the E2E delay between mobile users and their Avatars may become worse if the Avatars remain in their original cloudlets. Thus, Avatar handoff is proposed to migrate an Avatar from one cloudlet into another to reduce the E2E delay between the Avatar and its mobile user. The LatEncy aware Avatar handDoff (LEAD) algorithm is designed to determine the location of each mobile user\u27s Avatar in each time slot in order to minimize the average E2E delay among all the mobile users and their Avatars. The performance of LEAD is demonstrated via extensive simulations. The cloudlet network architecture not only facilitates mobile users in offloading their computational tasks but also empowers Internet of Things (IoT). Popular IoT resources are proposed to be cached in nearby brokers, which are considered as application layer middleware nodes hosted by cloudlets in the cloudlet network, to reduce the energy consumption of servers. In addition, an Energy Aware and latency guaranteed dynamic reSourcE caching (EASE) strategy is proposed to enable each broker to cache suitable popular resources such that the energy consumption from the servers is minimized and the average delay of delivering the contents of the resources to the corresponding clients is guaranteed. The performance of EASE is demonstrated via extensive simulations. The future work comprises two parts. First, caching popular IoT resources in nearby brokers may incur unbalanced traffic loads among brokers, thus increasing the average delay of delivering the contents of the resources. Thus, how to balance the traffic loads among brokers to speed up IoT content delivery process requires further investigation. Second, drone assisted mobile access network architecture will be briefly investigated to accelerate communications between mobile users and their Avatars

Two levels autonomic resource management in virtualized IaaS

International audienceVirtualized cloud infrastructures are very popular as they allow resource mutualization and therefore cost reduction. For cloud providers, minimizing the number of used resources is one of the main services that such environments must ensure. Cloud customers are also concerned with the minimization of used resources in the cloud since they want to reduce their invoice. Thus, resource management in the cloud should be considered by the cloud provider at the virtualization level and by the cloud customers at the application level. Many research works investigate resource management strategies in these two levels. Most of them study virtual machine consolidation (according to the virtualized infrastructure utilization rate) at the virtualized level and dynamic application sizing (according to its workload) at the application level. However, these strategies are studied separately. In this article, we show that virtual machine consolidation and dynamic application sizing are complementary. We show the efficiency of the combination of these two strategies, in reducing resource usage and keeping an application’s Quality of Service. Our demonstration is done by comparing the evaluation of three resource management strategies (implemented at the virtualization level only, at the application level only, or complementary at both levels) in a private cloud infrastructure, hosting typical JEE web applications (evaluated with the RUBiS benchmark)

Effective and Economical Content Delivery and Storage Strategies for Cloud Systems

Cloud computing has proved to be an effective infrastructure to host various applications and provide reliable and stable services. Content delivery and storage are two main services provided by the cloud. A high-performance cloud can reduce the cost of both cloud providers and customers, while providing high application performance to cloud clients. Thus, the performance of such cloud-based services is closely related to three issues. First, when delivering contents from the cloud to users or transferring contents between cloud datacenters, it is important to reduce the payment costs and transmission time. Second, when transferring contents between cloud datacenters, it is important to reduce the payment costs to the internet service providers (ISPs). Third, when storing contents in the datacenters, it is crucial to reduce the file read latency and power consumption of the datacenters. In this dissertation, we study how to effectively deliver and store contents on the cloud, with a focus on cloud gaming and video streaming services. In particular, we aim to address three problems. i) Cost-efficient cloud computing system to support thin-client Massively Multiplayer Online Game (MMOG): how to achieve high Quality of Service (QoS) in cloud gaming and reduce the cloud bandwidth consumption; ii) Cost-efficient inter-datacenter video scheduling: how to reduce the bandwidth payment cost by fully utilizing link bandwidth when cloud providers transfer videos between datacenters; iii) Energy-efficient adaptive file replication: how to adapt to time-varying file popularities to achieve a good tradeoff between data availability and efficiency, as well as reduce the power consumption of the datacenters. In this dissertation, we propose methods to solve each of aforementioned challenges on the cloud. As a result, we build a cloud system that has a cost-efficient system to support cloud clients, an inter-datacenter video scheduling algorithm for video transmission on the cloud and an adaptive file replication algorithm for cloud storage system. As a result, the cloud system not only benefits the cloud providers in reducing the cloud cost, but also benefits the cloud customers in reducing their payment cost and improving high cloud application performance (i.e., user experience). Finally, we conducted extensive experiments on many testbeds, including PeerSim, PlanetLab, EC2 and a real-world cluster, which demonstrate the efficiency and effectiveness of our proposed methods. In our future work, we will further study how to further improve user experience in receiving contents and reduce the cost due to content transfer