SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: [email protected]: 3 pages, 2 figure

FMCW rail-mounted SAR: Porting spotlight SAR imaging from MATLAB to FPGA

In this work, a low-cost laptop-based radar platform derived from the MIT open courseware has been implemented. It can perform ranging, Doppler measurement and SAR imaging using MATLAB as the processor. In this work, porting the signal processing algorithms onto a FPGA platform will be addressed as well as differences between results obtained using MATLAB and those obtained using the FPGA platform. The target FPGA platforms were a Virtex6 DSP kit and Spartan3A starter kit, the latter was also low-cost to further reduce the cost for students to access radar technology

Event-Driven Network Programming

Software-defined networking (SDN) programs must simultaneously describe static forwarding behavior and dynamic updates in response to events. Event-driven updates are critical to get right, but difficult to implement correctly due to the high degree of concurrency in networks. Existing SDN platforms offer weak guarantees that can break application invariants, leading to problems such as dropped packets, degraded performance, security violations, etc. This paper introduces EVENT-DRIVEN CONSISTENT UPDATES that are guaranteed to preserve well-defined behaviors when transitioning between configurations in response to events. We propose NETWORK EVENT STRUCTURES (NESs) to model constraints on updates, such as which events can be enabled simultaneously and causal dependencies between events. We define an extension of the NetKAT language with mutable state, give semantics to stateful programs using NESs, and discuss provably-correct strategies for implementing NESs in SDNs. Finally, we evaluate our approach empirically, demonstrating that it gives well-defined consistency guarantees while avoiding expensive synchronization and packet buffering

Probabilistic Programming Concepts

A multitude of different probabilistic programming languages exists today, all extending a traditional programming language with primitives to support modeling of complex, structured probability distributions. Each of these languages employs its own probabilistic primitives, and comes with a particular syntax, semantics and inference procedure. This makes it hard to understand the underlying programming concepts and appreciate the differences between the different languages. To obtain a better understanding of probabilistic programming, we identify a number of core programming concepts underlying the primitives used by various probabilistic languages, discuss the execution mechanisms that they require and use these to position state-of-the-art probabilistic languages and their implementation. While doing so, we focus on probabilistic extensions of logic programming languages such as Prolog, which have been developed since more than 20 years