DiBELLA: Distributed long read to long read alignment

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies

Efficient and Privacy-Preserving Ride Sharing Organization for Transferable and Non-Transferable Services

Ride-sharing allows multiple persons to share their trips together in one vehicle instead of using multiple vehicles. This can reduce the number of vehicles in the street, which consequently can reduce air pollution, traffic congestion and transportation cost. However, a ride-sharing organization requires passengers to report sensitive location information about their trips to a trip organizing server (TOS) which creates a serious privacy issue. In addition, existing ride-sharing schemes are non-flexible, i.e., they require a driver and a rider to have exactly the same trip to share a ride. Moreover, they are non-scalable, i.e., inefficient if applied to large geographic areas. In this paper, we propose two efficient privacy-preserving ride-sharing organization schemes for Non-transferable Ride-sharing Services (NRS) and Transferable Ride-sharing Services (TRS). In the NRS scheme, a rider can share a ride from its source to destination with only one driver whereas, in TRS scheme, a rider can transfer between multiple drivers while en route until he reaches his destination. In both schemes, the ride-sharing area is divided into a number of small geographic areas, called cells, and each cell has a unique identifier. Each driver/rider should encrypt his trip's data and send an encrypted ride-sharing offer/request to the TOS. In NRS scheme, Bloom filters are used to compactly represent the trip information before encryption. Then, the TOS can measure the similarity between the encrypted trips data to organize shared rides without revealing either the users' identities or the location information. In TRS scheme, drivers report their encrypted routes, an then the TOS builds an encrypted directed graph that is passed to a modified version of Dijkstra's shortest path algorithm to search for an optimal path of rides that can achieve a set of preferences defined by the riders