GeneGrid: Architecture, Implementation and Application

The emergence of Grid computing technology has opened up an unprecedented opportunity for biologists to share and access data, resources and tools in an integrated environment leading to a greater chance of knowledge discovery. GeneGrid is a Grid computing framework that seamlessly integrates a myriad of heterogeneous resources spanning multiple administrative domains and locations. It provides scientists an integrated environment for the streamlined access of a number of bioinformatics programs and databases through a simple and intuitive interface. It acts as a virtual bioinformatics laboratory by allowing scientists to create, execute and manage workflows that represent bioinformatics experiments. A number of cooperating Grid services interact in an orchestrated manner to provide this functionality. This paper gives insight into the details of the architecture, components and implementation of GeneGrid.

rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi.

In Europe, the last 20 years have seen a spectacular increase in accidental introductions of marine species, but it has recently been suggested that both the actual number of invaders and their impacts have been seriously underestimated because of the prevalence of sibling species in marine habitats. The red alga Polysiphoniaharveyi is regarded as an alien in the British Isles and Atlantic Europe, having appeared in various locations there during the past 170 years. Similar or conspecific populations are known from Atlantic North America and Japan. To choose between three competing hypotheses concerning the origin of P. harveyi in Europe, we employed rbcL sequence analysis in conjunction with karyological and interbreeding data for samples and isolates of P. harveyi and various congeners from the Pacific and North Atlantic Oceans. All cultured isolates of P. harveyi were completely interfertile, and there was no evidence of polyploidy or aneuploidy. Thus, this biological species is both morphologically and genetically variable: intraspecific rbcL divergences of up to 2.1% are high even for red algae. Seven rbcL haplotypes were identified. The four most divergent haplotypes were observed in Japanese samples from Hokkaido and south-central Honshu, which are linked by hypothetical 'missing' haplotypes that may be located in northern Honshu. These data are consistent with Japan being the centre of diversity and origin for P. harveyi. Two non-Japanese lineages were linked to Hokkaido and Honshu, respectively. A single haplotype was found in all North Atlantic and Mediterranean accessions, except for North Carolina, where the haplotype found was the same as that invading in New Zealand and California. The introduction of P. harveyi into New Zealand has gone unnoticed because P. strictissima is a morphologically indistinguishable native sibling species. The sequence divergence between them is 4–5%, greater than between some morphologically distinct red algal species. Two different types of cryptic invasions of P. harveyi have therefore occurred. In addition to its introduction as a cryptic sibling species in New Zealand, P. harveyi has been introduced at least twice into the North Atlantic from presumed different source populations. These two introductions are genetically and probably also physiologically divergent but completely interfertile.

Technology and the architecture of markets: re-configuring the Canadian equity market

This paper examines the relation between technical possibilities, liberal logics, and the concrete reconfiguration of markets. It focuses on the enrolling of innovations in communication and information technologies into the markets traditionally dominated by stock exchanges. With the development of capacities to trade on-screen, the power of incumbent market makers has been challenged as a less stable array of competing quasi-public and private marketplaces emerges. Developing a case study of the Toronto Stock Exchange, I argue that narrative emphasis on the performative power of sociotechnical innovations, the deterritorialisation of financial relations, and the erosion of state capacities needs qualification. A case is made for the importance of developing an understanding of: the spaces of encounter between emerging social technologies and property rights, rules of exchange, and structures of governance; and the interplay of orderings of different institutional composition and spatial reach in the reconfiguration of market architectures. Only then can a better grasp be gained of the evolving dynamics between making markets, the regulatory powers of the state, and their delimitations.

A VLSI Architecture for Variable Block Size Video Motion Estimation

With the advent of new video standards such as MPEG-4 part-10 and H.264/H.26L, demands for advanced video coding, particularly in the area of variable block size video motion estimation (VBSME), are increasing. In this paper, we propose a new one-dimensional (1-D) very large-scale integration architecture for full-search VBSME (FSVBSME). The VBS sum of absolute differences (SAD) computation is performed by re-using the results of smaller sub-block computations. These are distributed and combined by incorporating a shuffling mechanism within each processing element. Whereas a conventional 1-D architecture can process only one motion vector (MV), this new architecture can process up to 41 MV sub-blocks (within a macroblock) in the same number of clock cycles.

Generic Architecture and Semiconductor Intellectual Property Cores for Avanced Encryption Standard Cryptography

A generic architecture for implementing the advanced encryption standard (AES) encryption algorithm in silicon is proposed. This allows the instantiation of a wide range of chip specifications, with these taking the form of semiconductor intellectual property (IP) cores. Cores implemented from this architecture can perform both encryption and decryption and support four modes of operation: (i) electronic codebook mode; (ii) output feedback mode; (iii) cipher block chaining mode; and (iv) ciphertext feedback mode. Chip designs can also be generated to cover all three AES key lengths, namely 128 bits, 192 bits and 256 bits. On-the-fly generation of the round keys required during decryption is also possible. The general, flexible and multi-functional nature of the approach described contrasts with previous designs which, to date, have been focused on specific implementations. The presented ideas are demonstrated by implementation in FPGA technology. However, the architecture and IP cores derived from this are easily migratable to other silicon technologies including ASIC and PLD and are capable of covering a wide range of modem communication systems cryptographic requirements. Moreover, the designs produced have a gate count and throughput comparable with or better than the previous one-off solutions.