Response Surface Modelling for Performance Analysis of Scientific Workflow Application in Cloud

Scientific workflow applications are used by scientists to carry out research in various domains such as Physics, Chemistry, Astronomy etc. These applications require huge computational resources and currently cloud platform is used for efficiently running these applications. To improve the makespan and cost in workflow execution in cloud platform it requires to identify proper number of Virtual Machines (VM) and choose proper VM type. As cloud platform is dynamic, the available resources and the type of the resources are the two important factors on the cost and makespan of workflow execution. The primary objective of this work is to analyze the relationship among the cloud configuration parameters (Number of VM, Type of VM, VM configurations) for executing scientific workflow applications in cloud platform. In this work, to accurately analyze the influence of cloud platform resource configuration and scheduling polices a new predictive modelling using Box–Behnken design which is one of the modelling technique of Response Surface Methodology (RSM). It is used to build quadratic mathematical models that can be used to analyze relationships among input and output variables. Workflow cost and makespan models were built for real world scientific workflows using ANOVA and it was observed that the models fit well and can be useful in analyzing the performance of scientific workflow applications in cloud

     

A Heuristic Placement Selection of Live Virtual Machine Migration for Energy-Saving in Cloud Computing Environment

The field of live VM (virtual machine) migration has been a hotspot problem in green cloud computing. Live VM migration problem is divided into two research aspects: live VM migration mechanism and live VM migration policy. In the meanwhile, with the development of energy-aware computing, we have focused on the VM placement selection of live migration, namely live VM migration policy for energy saving. In this paper, a novel heuristic approach PS-ES is presented. Its main idea includes two parts. One is that it combines the PSO (particle swarm optimization) idea with the SA (simulated annealing) idea to achieve an improved PSO-based approach with the better global search''s ability. The other one is that it uses the Probability Theory and Mathematical Statistics and once again utilizes the SA idea to deal with the data obtained from the improved PSO-based process to get the final solution. And thus the whole approach achieves a long-term optimization for energy saving as it has considered not only the optimization of the current problem scenario but also that of the future problem. The experimental results demonstrate that PS-ES evidently reduces the total incremental energy consumption and better protects the performance of VM running and migrating compared with randomly migrating and optimally migrating. As a result, the proposed PS-ES approach has capabilities to make the result of live VM migration events more high-effective and valuable.     

Operational cost-aware resource provisioning for continuous write applications in cloud-of-clouds

The emergence of cloud computing has made it become an attractive solution for large-scale data processing and storage applications. Cloud infrastructures provide users a remote access to powerful computing capacity, large storage space and high network bandwidth to deploy various applications. With the support of cloud computing, many large-scale applications have been migrated to cloud infrastructures instead of running on in-house local servers. Among these applications, continuous write applications (CWAs) such as online surveillance systems, can significantly benefit due to the flexibility and advantages of cloud computing. However, with specific characteristics such as continuous data writing and processing, and high level demand of data availability, cloud service providers prefer to use sophisticated models for provisioning resources to meet CWAs’ demands while minimizing the operational cost of the infrastructure. In this paper, we present a novel architecture of multiple cloud service providers (CSPs) or commonly referred to as Cloud-of-Clouds. Based on this architecture, we propose two operational cost-aware algorithms for provisioning cloud resources for CWAs, namely neighboring optimal resource provisioning algorithm and global optimal resource provisioning algorithm, in order to minimize the operational cost and thereby maximizing the revenue of CSPs. We validate the proposed algorithms through comprehensive simulations. The two proposed algorithms are compared against each other to assess their effectiveness, and with a commonly used and practically viable round-robin approach. The results demonstrate that NORPA and GORPA outperform the conventional round-robin algorithm by reducing the operational cost by up to 28 and 57 %, respectively. The low complexity of the proposed cost-aware algorithms allows us to apply it to a realistic Cloud-of-Clouds environment in industry as well as academia.     

Genetic variation in comC, the gene encoding competence-stimulating peptide (CSP) in Streptococcus mutans

The genetic variability in comC , the gene encoding the quorum-sensing molecule, competence-stimulating peptide (CSP) in Streptococcus mutans is reported. Seven comC alleles encoding three distinct mature CSPs were identified among 36 geographically diverse strains, although, compared with Streptococcus pneumoniae , the amount of predicted amino acid sequence variation is low. In agreement with other studies, significant variation was found in the natural competence for DNA uptake in these strains. However, there was no correlation between the CSP genotype and the ability to transform these strains. Representative strains encoding each of the CSP variants became competent in response to synthetic CSPs of each type. Therefore, in contrast to S. pneumoniae , comC alleles in S. mutans are functionally equivalent and there is no evidence of pherotype specificity.     

Liquid Chromatographic Resolution of Mexiletine and Its Analogs on Crown Ether‐Based Chiral Stationary Phases

Mexiletine, an effective class IB antiarrhythmic agent, and its analogs were resolved on three different crown ether‐based chiral stationary phases (CSPs), one (CSP 1 ) of which is based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid and the other two (CSP 2 and CSP 3 ) are based on (3,3’‐diphenyl‐1,1’‐binaphthyl)‐20‐crown‐6. Mexiletine was resolved with a resolution (R_S) of greater than 1.00 on CSP 1 and CSP 3 containing residual silanol group‐protecting n‐octyl groups on the silica surface, but with a resolution (R_S) of less than 1.00 on CSP 2 . The chromatographic behaviors for the resolution of mexiletine analogs containing a substituted phenyl group at the chiral center on the three CSPs were quite dependent on the phenoxy group of analytes. Namely, mexiletine analogs containing 2,6‐dimethylphenoxy, 3,4‐dimethylphenoxy, 3‐methylphenoxy, 4‐methylphenoxy, and a simple phenoxy group were resolved very well on the three CSPs even though the chiral recognition efficiencies vary with the CSPs. However, mexiletine analogs containing 2‐methylphenoxy group were not resolved at all or only slightly resolved. Among the three CSPs, CSP 3 was found to show the highest chiral recognition efficiencies for the resolution of mexiletine and its analogs, especially in terms of resolution (R_S). Chirality 26:272–278, 2014. © 2014 Wiley Periodicals, Inc.     

Liquid chromatographic resolution of N-acyl-alpha-amino acids as their anilide derivatives on a chiral stationary phase based on (S)-leucine

A chiral stationary phase (CSP 1) derived from N-(3,5-dinitrobenzoyl)leucine N-phenyl N-alkylamide was used for the liquid chromatographic resolution of anilide derivatives of N-acyl-alpha-amino acids and the chromatographic resolution results were compared with those from four other commercial CSPs. The chromatographic resolution results showed that CSP 1 was most effective among five CSPs used in this study. The chiral recognition mechanism exerted by CSP 1 for the resolution of anilide derivatives of N-acyl-alpha-amino acids is proposed to involve a face-to-face pi-pi interaction and two hydrogen bonding interactions between the CSP and the analytes from the chromatographic resolution behaviors of slightly modified anilide derivatives of N-acyl-alpha-amino acids. The chiral recognition mechanism proposed is quite similar to that advanced previously for the resolution of N-(3,5-methoxybenzoyl)-alpha-amino acids on CSP 1, even though the interaction sites of the two types of analytes were totally different from each other. The apparent similarity of the two chiral recognition mechanisms was assumed to stem from the identical interaction modes of the two types of analytes with the CSP. In addition, the dependence of the enantioselectivity of anilide derivatives of N-acyl-alpha-amino acids on the length of the alkyl tail of the N-acyl group of analytes was rationalized to stem from the intercalation of the N-acyl group of the (R)-enantiomer of analytes between the tethers of the CSP.     

Towards effective science cloud provisioning for a large-scale high-throughput computing

The science cloud paradigm has been actively developed and investigated, but still requires a suitable model for science cloud system in order to support increasing scientific computation needs with high performance. This paper presents an effective provisioning model of science cloud, particularly for large-scale high throughput computing applications. In this model, we utilize job traces where a statistical method is applied to pick the most influential features to improve application performance. With these features, a system determines where VM is deployed (allocation) and which instance type is proper (provisioning). An adaptive evaluation step which is subsequent to the job execution enables our model to adapt to dynamical computing environments. We show performance achievements by comparing the proposed model with other policies through experiments and expect noticeable improvements on performance as well as reduction of cost from resource consumption through our model.     

Novel chiral stationary phases based on 3,5-dimethyl phenylcarbamoylated β-cyclodextrin combining cinchona alkaloid moiety

Novel chiral selectors based on 3,5-dimethyl phenylcarbamoylated β-cyclodextrin connecting quinine (QN) or quinidine (QD) moiety were synthesized and immobilized on silica gel. Their chromatographic performances were investigated by comparing to the 3,5-dimethyl phenylcarbamoylated β-cyclodextrin (β-CD) chiral stationary phase (CSP) and 9-O-(tert-butylcarbamoyl)-QN-based CSP (QN-AX). Fmoc-protected amino acids, chiral drug cloprostenol (which has been successfully employed in veterinary medicine), and neutral chiral analytes were evaluated on CSPs, and the results showed that the novel CSPs characterized as both enantioseparation capabilities of CD-based CSP and QN/QD-based CSPs have broader application range than β-CD-based CSP or QN/QD-based CSPs. It was found that QN/QD moieties play a dominant role in the overall enantioseparation process of Fmoc-amino acids accompanied by the synergistic effect of β-CD moiety, which lead to the different enantioseparation of β-CD-QN-based CSP and β-CD-QD-based CSP. Furthermore, new CSPs retain extraordinary enantioseparation of cyclodextrin-based CSP for some neutral analytes on normal phase and even exhibit better enantioseparation than the corresponding β-CD-based CSP for certain samples.     

Identification and expression pattern of the chemosensory protein gene family in the silkworm, Bombyx mori

Insect chemosensory proteins (CSPs) as well as odorant-binding proteins (OBPs) have been supposed to transport hydrophobic chemicals to receptors on sensory neurons. Compared with OBPs, CSPs are expressed more broadly in various insect tissues. We performed a genome-wide analysis of the candidate CSP gene family in the silkworm. A total of 20 candidate CSPs, including 3 gene fragments and 2 pseudogenes, were characterized based on their conserved cysteine residues and their similarity to CSPs in other insects. Some of these genes were clustered in the silkworm genome. The gene expression pattern of these candidates was investigated using RT-PCR and microarray, and the results showed that these genes were expressed primarily in mature larvae and the adult moth, suggesting silkworm CSPs may be involved in development. The majority of silkworm CSP genes are expressed broadly in tissues including the antennae, head, thorax, legs, wings, epithelium, testes, ovaries, pheromone glands, wing disks, and compound eyes.     

HPLC with cellulose Tris (3,5‐DimethylPhenylcarbamate) chiral stationary phase: Influence of coating times and coating amount on chiral discrimination

Coating cellulose tris (3,5‐dimethylphenylcarbamate) (CDMPC) on silica gels with large pores have been demonstrated as an efficient way for the preparation of chiral stationary phase (CSP) for high‐performance liquid chromatography (HPLC). During the process, a number of parameters, including the type of coating solvent, amount of coating, and the method for subsequent solvent removing, have been proved to affect the performance of the resultant CSPs. Coating times and the concentration of coating solution, however, also makes a difference to CSPs' performance by changing the arrangement of cellulose derivatives while remaining the coating amount constant, have much less been studied before, and thereby, were systematically investigated in this work. Results showed that CSPs with more coating times exhibited higher chiral recognition and column efficiency, suggesting that resolution was determined by column efficiency herein. Afterwards, we also investigated the effect of coating amount on the performance of CSPs, and it was shown that the ability of enantio‐recognition did not increase all the time as the coating amount; and four of seven racemates achieved best resolution when the coating amount reached to 18.37%. At the end, the reproducibility of CDMPC‐coated CSPs were further confirmed by two methods, ie, reprepared the CSP‐0.15‐3 and reevaluated the effect of coating times.     

Binding preferential of chickpea cold shock protein during nucleic acid interactions

Cold shock proteins (CSPs) have a widespread occurrence from prokaryotes to eukaryotes including plants. These proteins are known to possess nucleic acid binding properties. CSPs have a single cold shock domain in prokaryotes while N-terminal and C-terminal flanking regions are present in eukaryotic CSPs. The objective of this study was to investigate nucleic acid binding preferential for the chickpea CSP. Full cDNA of chickpea CSP was cloned and sequenced. The sequence was submitted to GenBank (accession no. KM036036) at NCBI. Multiple sequence alignment and phylogenetic analysis further revealed that the inferred amino acid sequence belongs to CSP family. Molecular docking was performed between the CSP and variety of nucleic acids entities. These results suggest that CSPs of chickpea possess preferential binding affinity for single stranded nucleic acids. Docking results suggest that homo-polymer entities of RNA polyU RNA (20mer) form most stable complex.     

Determination of the domain of the Lactobacillus delbrueckii subsp. bulgaricus cell surface proteinase PrtB involved in attachment to the cell wall after heterologous expression of the prtB gene in Lactococcus lactis

Belonging to the subtilase family, the cell surface proteinase (CSP) PrtB of Lactobacillus delbrueckii subsp. bulgaricus differs from other CSPs synthesized by lactic acid bacteria. Expression of the prtB gene under its own promoter was shown to complement the proteinase-deficient strain MG1363 (PrtP(-) PrtM(-)) of Lactococcus lactis subsp. cremoris. Surprisingly, the maturation process of PrtB, unlike that of lactococcal CSP PrtPs, does not require a specific PrtM-like chaperone. The carboxy end of PrtB was previously shown to be different from the consensus anchoring region of other CSPs and exhibits an imperfect duplication of 59 amino acids with a high lysine content. By using a deletion strategy, the removal of the last 99 amino acids, including the degenerated anchoring signal (LPKKT), was found to be sufficient to release a part of the truncated PrtB into the culture medium and led to an increase in PrtB activity. This truncated PrtB is still active and enables L. lactis MG1363 to grow in milk supplemented with glucose. By contrast, deletion of the last 806 amino acids of PrtB led to the secretion of an inactive proteinase. Thus, the utmost carboxy end of PrtB is involved in attachment to the bacterial cell wall. Proteinase PrtB constitutes a powerful tool for cell surface display of heterologous proteins like antigens.     

Odorant-binding proteins and chemosensory proteins in pheromone detection and release in the silkmoth Bombyx mori

The genome of the silkmoth Bombyx mori contains 44 genes encoding odorant-binding proteins (OBPs) and 20 encoding chemosensory proteins (CSPs). In this work, we used a proteomic approach to investigate the expression of proteins of both classes in the antennae of adults and in the female pheromone glands. The most abundant proteins found in the antennae were the 4 OBPs (PBP, GOBP1, GOBP2, and ABP) and the 2 CSPs (CSP1 and CSP2) previously identified and characterized. In addition, we could detect only 3 additional OBPs and 2 CSPs, with clearly different patterns of expression between the sexes. Particularly interesting, on the other hand, is the relatively large number of binding proteins (1 OBP and 7 CSPs) expressed in the female pheromone glands, some of them not present in the antennae. In the glands, these proteins could be likely involved in the solubilization of pheromonal components and their delivery in the environment.     

Mvmotion: a metadata based virtual machine migration in cloud

As one of the most important features of virtualization, virtual machine (VM) migration provides great benefits for load balancing, resources-saving, fault tolerance in modern cloud data centers. Considering the network traffic caused by transferring data during VM migration imposes a huge pressure on network bandwidth of cloud data centers, and by analyzing the characteristic of the transferred data, we found that the redundant data, which is produced between two physical hosts by hosting virtual machines cloned from same VM template, can be reduced to relieve the network traffic pressure. This paper presents a Metadata based VM migration approach (Mvmotion) to reduce the amount of transferred data during migration by utilizing memory de-redundant technique between two physical hosts. Mvmotion utilizes the hash based fingerprints to generate Metadata of memory, which is used to identify redundant memory of VMs between two hosts. Based on the Metadata, the transfer of redundant memory data during migration can be eliminated. Experiment demonstrates that, compare to Xen’s default migration approach, Mvmotion can reduce the total transferred data by 29–97 %, and decreases the migration time by 16–53 %.     

Ensuring performance and provider profit through data replication in cloud systems

Cloud computing is a relatively recent computing paradigm that is often the answer for dealing with large amounts of data. Tenants expect the cloud providers to keep supplying an agreed upon quality of service, while cloud providers aim to increase profits as it is a key ingredient of any economic enterprise. In this paper, we propose a data replication strategy for cloud systems that satisfies the response time objective for executing queries while simultaneously enables the provider to return a profit from each execution. The proposed strategy estimates the response time of the queries and performs data replication in a way that the execution of any particular query is still estimated to be profitable for the provider. We show with simulations that how the proposed strategy fulfills these two criteria.