There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

International Technology Roadmap for Semiconductors 2003の要求清浄度について － シリコンウエハ表面と雰囲気環境に要求される清浄度, 分析方法の現状について －

To alleviate the complex communication problems that arise as the number of on-chip components increases, network-on-chip (NoC) architectures have been recently proposed to replace global interconnects. In this paper, we first provide a general description of NoC architectures and applications. Then, we enumerate several related research problems organized under five main categories: Application characterization, communication paradigm, communication infrastructure, analysis, and solution evaluation. Motivation, problem description, proposed approaches, and open issues are discussed for each problem from system, microarchitecture, and circuit perspectives. Finally, we address the interactions among these research problems and put the NoC design process into perspective.

Outstanding Research Problems in NoC Design: System, Microarchitecture, and Circuit Perspectives

IEEE transactions on computer-aided design of integrated circuits and systems : a publication of the IEEE Circuits and Systems Society

In this paper, we present a novel HitME (Hit-MEmory) buffer to reduce the energy consumption of memory hierarchy in embedded processors. The HitME buffer is a small direct-mapped cache memory that is added as additional memory into existing cache memory hierarchies. The HitME buffer is loaded only when there is a hit on L1 cache. Otherwise, L1 cache is updated from the memory and the processor's memory request is served directly from the L1 cache. The strategy works due to the fact that 90% of memory accesses are only accessed once, and these often pollute the cache. Energy reduction is achieved by reducing the number of accesses to the L1 cache memory. Experimental results show that the use of HitME buffer will reduce the L1 cache accesses resulting in a reduction in the energy consumption of the memory hierarchy. This decrease in L1 cache accesses reduces the cache system energy consumption by an average of 60.9% when compared to traditional L1 cache memory architecture and an energy reduction of 6.4% when compared to filter cache architecture for 70nm cache technology.

/pdf/hitme-low-power-hit-memory-buffer-for-embedded-systems-1g1mz0csc3.pdf

HitME: low power Hit MEmory buffer for embedded systems

The authors introduce two low-cost, modular, totally self checking (TSC), edge triggered and error propagating (code disjoint) flip-flops: one, a D flip-flop used in TSC and strongly fault secure (SFS) synchronous circuits with two-rail codes, the other a T flip-flop, used in a similar way as the D flip-flop but retaining the error as an indicator until the next presetting, to aid error propagation. Thus, the self checking T flip-flop can be used as an error indicator. The self checking D flip-flop is smaller than the duplicate D flip-flop circuitry by 30%. The self checking T flip-flop error indicator is 60% smaller than the pervious error indicator in the literature. These circuits, unlike previously reported circuits, can also detect stuck-at faults in the clock inputs. The authors have also presented TSC/error propagating applications for the above flip-flops: a counter and a shift register.

http://www.cse.unsw.edu.au/~sridevan/index_files/00674986.pdf

Designs for self checking flip-flops

In this paper, we propose to explore design space of a unified last-level cache to improve system performance and energy efficiency. The challenge is to quickly estimate the execution time and energy consumption of the system with distinct cache configurations using minimal number of slow full-system cycle-accurate simulations. To this end, we propose a novel, simple yet highly accurate execution time estimator and a simple, reasonably accurate energy estimator. Our framework, RExCache, combines a cycle-accurate simulator and a trace-driven cache simulator with our novel execution time estimator and energy estimator to avoid cycle-accurate simulations of all the last-level cache configurations. Once execution time and energy estimates are available from the estimators, RExCache chooses minimum execution time or minimum energy consumption cache configuration. Our experiments with nine different applications from mediabench, and 330 last-level cache configurations show that the execution time and energy estimators had at least average absolute accuracy of 99.74% and 80.31% respectively. RExCache took only a few hours (21 hours for H.264enc) to explore last-level cache configurations compared to several days of traditional method (36 days for H.264enc) and cycle-accurate simulations (257 days for H.264enc), enabling quick exploration of the last-level cache. When 100 different real-time constraints on execution time and energy were used, all the cache configurations found by RExCache were similar to those from cycle-accurate simulations. On the other hand, the traditional method found correct cache configurations for only 69 out of 100 constraints. Thus, RExCache has better absolute accuracy than the traditional method, yet reducing the simulation time by at least 97%.

/pdf/rexcache-rapid-exploration-of-unified-last-level-cache-2t73une074.pdf

RExCache: Rapid exploration of unified last-level cache

Automation of the hardware/software codesign methodology brings with it the need to develop sophisticated high-level synthesis tools. This paper presents a tool which is the result of such development. This tool converts standard C code into an equivalent VHDL behavioural description. This description is used to generate a chip-level hardware interconnect of identical functionality to the original C code. >

http://cse.unsw.edu.au/~sridevan/index_files/00323960.pdf

C to VHDL converter in a codesign environment

We consider a wiretap channel and use previously transmitted messages to generate a secret key which increases the secrecy capacity. This can be bootstrapped to increase the secrecy capacity to the Shannon capacity without using any feedback or extra channel while retaining the strong secrecy of the wiretap channel.

Sri Parameswaran

Papers

HitME: low power Hit MEmory buffer for embedded systems

Designs for self checking flip-flops

RExCache: Rapid exploration of unified last-level cache

C to VHDL converter in a codesign environment

Previous messages provide the key to achieve shannon capacity in a wiretap channel