Large-scale biological sequence assembly and alignment by using computing grid

Large-scale sequence assembly and alignment are fundamental parts of biological computing. However, most of the large-scale sequence assembly and alignment require intensive computing power and normally take very long time to complete. To speedup the assembly and alignment process, this paper parallelizes the Euler sequence assembly and pair-wise/multiple sequence assembly, two important sequence assembly methods, and takes advantage of Computing Grid which has a colossal computing capacity to meet the large-scale biological computing demand.

Eulerian superpath approach to correct sequencing error in shotgun assembly

This work describes an error correction method based on the Euler Superpath problem. Sequence data is mapped to an Euler Superpath dynamically by Merging Transformation. With restriction and guiding rules, data consistency is maintained and error paths are separated from correct data: Error edges are mapped to the correct ones and after substitution (of error edges with right paths), corresponding errors in the sequencing data are eliminated.

Benchmark generation algorithm for stochastic mixed model assembly shop simulation and optimization

The Operations Research (OR) community have defined many deterministic manufacturing control problems mainly focused on scheduling. Well-defined benchmark problems provide a mechanism for communication of the effectiveness of different optimization algorithms. Manufacturing problems within industry are stochastic and complex. Common features of these problems include: variable demand, machine part specific breakdown patterns, part machine specific process durations, continuous production, Finished Goods Inventory (FGI) buffers, bottleneck machines and limited production capacity. Discrete Event Simulation (DES) is a commonly used tool for studying manufacturing systems of realistic complexity. There are few reports of detail-rich benchmark problems for use within the simulation optimization community that are as complex as those faced by production managers. This work details an algorithm that can be used to create single and multistage production control problems. The reported software implementation of the algorithm generates text files in eXtensible Markup Language (XML) format that are easily edited and understood as well as being cross-platform compatible. The distribution and acceptance of benchmark problems generated with the algorithm would enable researchers working on simulation and optimization of manufacturing problems to effectively communicate results to benefit the field in general.

Multi-agent model for robotic assembly system

In this paper, a multi-agent based model for a robotic assembly system is presented. Firstly, an organization model is used to construct the multi-agent model. Secondly, a dynamic self-organizing method is then put forward for the multi-agent robotic system to bid and contract the operations. Thirdly, a real multi-agent robotic system is built and assembly experiments are carried out. Finally, the experimental results confirm that the present multi-agent robotic system has flexibility, adaptation and stability.

A parallel Euler approach for large-scale biological sequence assembly

Biological sequence assembly is an essential step for sequencing the genomes of organisms. Sequence assembly is very computing intensive especially for the large-scale sequence assembly. Parallel computing is an effective way to reduce the computing time and support the assembly for large amount of biological fragments. Euler sequence assembly algorithm is an innovative algorithm proposed recently. The advantage of this algorithm is that its computing complexity is polynomial and it provides a better solution to the notorious “repeat” problem. This paper introduces the parallelization of the Euler sequence assembly algorithm. All the Genome fragments generated by whole genome shotgun (WGS) will be assembled as a whole rather than dividing them into groups which may incurs errors due to the inaccurate group partition. The implemented system can be run on supercomputers, network of workstations or even network of PC computers. The experimental results have demonstrated the performance of our system.

Anion recognition and anion-mediated self-assembly with thiourea-functionalised fused [3]polynorbornyl frameworks

Three conformationally preorganised host molecules based on the [3]polynorbornyl framework and incorporating di-urea receptors were synthesised and their interaction with a series of anions investigated by 1H NMR spectroscopy. A high affinity of each host molecule for dihydrogenphosphate (H2PO4–) and dihydrogenpyrophosphate (H2P2O72–) was identified. In addition to binding to the urea receptors of the host molecules, evidence for an interaction involving the non-polar C–H groups within the binding cavity of the framework and guest anions was also discovered. Furthermore, an unusual 2 : 1 host-to-anion stoichiometry was indicated when binding H2P2O72–, and a model for the anion-mediated self-assembly of this complex species is proposed.

The effect of clamping sequence on dimensional variability in sheet metal assembly

Finite element (FE) modelling techniques have become a popular tool for exploring welding and clamping sequence dependence in sheet metal assemblies. In the current paper, the dimensional variability associated with different assembly clamping sequences is investigated with a FE contact modelling approach implemented in the commercial code Abaqus. A simplified channel section assembly consisting of a top hat and bottom plate is the case study investigated. Expected variation modes of bow and twist were used to simulate key variability sources in the main structural component under investigation; the top hat of the channel section. It was found that final assembly variability can change considerably depending on clamp sequence selection. It was also found that different clamp sequences can control particular modes of variation better than others, and that there is not one particular clamping sequence that is the best for containing all variation modes. An adaptable assembly process is therefore suggested, where given the shape of input components the best available clamping sequence is selected. Comparison of the performance of the proposed adaptable clamping sequence to traditional fixed clamping sequences shows improvements for the dimensional control of variability in non-rigid components. While introducing such a method in production would require inspection of each component being assembled and investigation of the alternative clamping sequences, given access to fast and detailed dimensional inspection technology such as optical coordinate measuring machines (OCMM's), the approach shows promise for future application.

A parallel DNA fragment assembly algorithm based on eulerian superpath approach

Fragments assembly is among the core problems in the research of Genome. Although many assembly tools based on the "overlap-layout-consensus" paradigm are widely used such as in the Human Genome Project currently, they still can not resolve the "repeats problem" in the DNA sequencing. For the purpose of resolving such problem, Pevzner et al. put forward a new Euler Superpath assembly algorithm. But it needs a big and complex de Bruijin graph which consumes large amounts of memories i.e. becomes the bottleneck of the performance. We present a parallel DNA fragment assembly algorithm based on the Eularian Superpath theory and solve the bottleneck in the current assembly program. The experimental results demonstrate that our approach has a good scalability, and can be used in DNA assembly of middle and large size of eukaryote genome.

Chinese consumers' perceptions of country design, assembly and parts capabilities : does country considered or consumer acculturation matter?

Chinese consumers are facing a diverse range of choices in regards to products produced wholly or in part overseas or by overseas corporations based in China. This study examines how consumers from China, both residing at home and abroad, perceived capability of Germany, Japan, US and China in regard to three dimensions of country capabilities- design, assembly and parts/components. The findings show that consumers have different perceptions concerning country capabilities and that Chinese consumers residing overseas appear to have more positive perceptions of foreign countries’ capabilities.

Haptically enabled interactive virtual reality prototype for general assembly

Desktop computers based virtual training systems are attracting paramount attention from manufacturing industries due to their potential advantages over the conventional training practices. Significant cost savings can be realized due to the shorter training-scenarios development times and reuse of existing engineering models. In addition, by using computer based virtual reality (VR) training systems, the time span from the product design to commercial production can be shortened due to non-reliance on hardware parts. Within the aforementioned conceptual framework, a haptically enabled interactive and immersive virtual reality (HIIVR) system is presented. Unlike existing VR systems, the presented idea tries to imitate real physical training scenarios by providing comprehensive user interaction, constrained within the physical limitations of the real world imposed by the haptics devices within the virtual environment. As a result, in contrast to the existing VR systems, capable of providing knowledge generally about assembly sequences only, the proposed system helps in procedural learning and procedural skill development as well, due to its high physically interactive nature.

Flux-assisted self-assembly of monodisperse colloids

We have developed a novel method to grow ordered layers of monodisperse colloids on a flat substrate. The evaporation of the colloidal suspension in the presence of the inclined substrate is strengthened by an external gas flux directed on the meniscus. The meniscus oscillations caused by the gas flux have an evident effect on the ordering of the spheres on the substrate. Thick films (more than 150 layers in a single-step deposition) of large area single crystals (1 cm2) can be obtained in a very short time (~1 cm/h maximum growth rate) and from very diluted suspensions (up to 0.022% volume fraction).

Tunable wettability of polyimide films based on electrostatic self-assembly of ionic liquids

We have demonstrated that the surface wettability of negatively charged polyimide films could be turned by electrostatic self-assembly of ionic liquids. The water contact angles of the polyimide films varied in the range 27-80 degrees for 13 different ionic liquids based on imidazolium and ammonium salts. The surface morphology of the resulting surfaces was characterized using atomic force microscopy. The results revealed that the assembly of longer-substituent cations was characterized by the formation of spherical nanoparticles that were formed due to sequent aggregation of cations on those electrostatically assembled ones via hydrophobic interaction. In this case, the counteranions are present in the assembled layers and the wettability is accordingly affected. Whereas for shorter-substituent cations, no aggregates were formed due to the less hydrophobic interaction than the electrostatic repulsive interaction between the cations, and the counteranions were absent from the assembled layers. This method can also be utilized to quantify the hydrophobicity of various ionic liquids.