Management of large service centers and clouds requires adaptation to changing conditions and workload. Optimal deployments are possible on private clouds if there is full knowledge of the applications. Previous work,CloudOpt,combines large-scale linear optimization with a detailed non-linear performance model of every application to determine such deployments. However, when conditions change the new solution is independent of the previous deployment, and often requires excessive changes. Practical adaptive management needs a controlled compromise between the effort and cost of changing the current deployment, and the value lost by not making a change. This paper enhances CloudOpt by incorporating adjustablepersistencetechniques to constrain the deployment changes in each update. Three such techniques are compared, and the best ones reduce the reconfiguration effort at each adaptation step by about 90 percent, with about a 5-10 percent penalty in running costs. Persistence techniques impose no reduction in the scalability of CloudOpt.

MOTIVATION: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. RESULTS: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with 'inserted' domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. AVAILABILITY AND IMPLEMENTATION: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are still possible. RESULTS: Here we describe recent improvements to the fold and function assignment system (FFAS) method, including adding optimized structural features (experimental or predicted), 'symmetrical' Z-score calculation and re-ranking the templates with a neural network. The alignment accuracy in the new FFAS-3D is now 11% higher than the original and comparable with the most accurate template-based structure prediction algorithms. At the same time, FFAS-3D has high success rate at the Structural Classification of Proteins (SCOP) family, superfamily and fold levels. Importantly, FFAS-3D results are not highly correlated with other programs suggesting that it may significantly improve meta-predictions. FFAS-3D does not require 3D structures of the templates, as using predicted features instead of structure-derived does not lead to the decrease of accuracy. Because of that, FFAS-3D can be used for databases other than Protein Data Bank (PDB) such as Protein families database or Clusters of orthologous groups thus extending its applications to functional annotations of genomes and protein families. AVAILABILITY AND IMPLEMENTATION: FFAS-3D is available at http://ffas.godziklab.org.

BACKGROUND: Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and a large number of uncharacterized proteins associated with polysaccharide metabolism. RESULTS: BT_1012 from Bacteroides thetaiotaomicron VPI-5482 is a protein of unknown function and a member of a large protein family consisting entirely of uncharacterized proteins. Initial sequence analysis predicted that this protein has two domains, one on the N- and one on the C-terminal. A PSI-BLAST search found over 150 full length and over 90 half size homologs consisting only of the N-terminal domain. The experimentally determined three-dimensional structure of the BT_1012 protein confirms its two-domain architecture and structural analysis of both domains suggests their specific functions. The N-terminal domain is a putative catalytic domain with significant similarity to known glycoside hydrolases, the C-terminal domain has a beta-sandwich fold typically found in C-terminal domains of other glycosyl hydrolases, however these domains are typically involved in substrate binding. We describe the structure of the BT_1012 protein and discuss its sequence-structure relationship and their possible functional implications. CONCLUSIONS: Structural and sequence analyses of the BT_1012 protein identifies it as a glycosyl hydrolase, expanding an already impressive catalog of enzymes involved in polysaccharide metabolism in Bacteroides spp. Based on this we have renamed the Pfam families representing the two domains found in the BT_1012 protein, PF13204 and PF12904, as putative glycoside hydrolase and glycoside hydrolase-associated C-terminal domain respectively.

Deployment choices are critical in determining the availability of applications running in a cloud. But choosing good deployment for various software application components into virtual machines is a challenging task because of potential sharing of components among applications and potential interference from multi-tenancy. This paper presents an approach for improving the availability guarantee of software applications by optimizing the availability, performance and monetary cost trade-offs of different deployment choices. Our approach explicitly considers different classes of application requests during the decision process. The results of our experimental evaluation show that the approach can effectively improve the availability guarantees with little or negligible increase in the performance and monetary cost of the deployment choice.

Cloud consumers have a variety of deployment related techniques, such as auto-scaling policies and recovery strategies, for dealing with the uncertainties in the cloud. Uncertainties can be characterized as stochastic (such as failures, disasters, and workload spikes) and subjective (such as choice among various deployment options). Cloud consumers must consider both stochastic and subjective uncertainties. Analytic support for consumers in selecting appropriate techniques and setting the required parameters in the face of different types of uncertainty is currently limited. In this paper, we propose a set of application availability analysis models that capture subjective uncertainties in addition to stochastic uncertainties. We built and validated the models by using industry best practices on deployment, and actual commercial products for disaster recovery and live migration. Our results show that the models permit more informed and quantitative availability analysis than industry best practices under a wide range of scenarios.

Application dependability issues depend on increasingly sophisticated activities during operation time for deployment, upgrade, scaling out/in and reactions to various failures. Traditional approaches to improving application dependability focus on artifact-oriented troubleshooting and improvements. In this paper, we present an approach using process models to represent and analyze operations with considerations of exception handlings and fault-proneness. Our goal is to reduce diagnosis and repair time for application failures that occur during operation activities such as deployment and upgrade.

When deploying services in a cloud, a balance must be found between performance and capacity of the service, and the memory available on nodes. This is further complicated if the number of replicas of an application is limited, for instance by the available number of licenses. The analysis of interference between services must scale to large numbers of host nodes, applications, replicas of applications, and classes of users. This paper combines a multi-dimensional packing heuristic and network flow optimization to satisfy simultaneous constraints on throughputs, processor utilizations, memory availability and license availability, at a minimum cost and with a minimum of host processors.

MOTIVATION: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a powerful tool for protein structure comparison and classification, given the arsenal of sequence comparison tools developed by computational biology. However, in order to do so, there is a need to first understand how much information is contained in various possible 1D representations of protein structure. RESULTS: Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained from such a description. We show the new local structure language adds resolution to the traditional three-state (helix, strand and coil) secondary structure description, and provides a high degree of accuracy in recognizing structural similarities when used with a pairwise alignment benchmark. The results of this study have immediate applications towards fast structure recognition, and for fold prediction and classification.