A Cost-Benefit Study of Doing Astrophysics On The Cloud: Production of Image Mosaics

Utility grids such as the Amazon EC2 and Amazon S3 clouds offer computational and storage resources that can be used on-demand for a fee by compute- and data-intensive applications. The cost of running an application on such a cloud depends on the compute, storage and communication resources it will provision and consume. Different execution plans of the same application may result in significantly different costs. We studied via simulation the cost performance trade-offs of different execution and resource provisioning plans by creating, under the Amazon cloud fee structure, mosaics with the Montage image mosaic engine, a widely used data- and compute-intensive application. Specifically, we studied the cost of building mosaics of 2MASS data that have sizes of 1, 2 and 4 square degrees, and a 2MASS all-sky mosaic. These are examples of mosaics commonly generated by astronomers. We also study these trade-offs in the context of the storage and communication fees of Amazon S3 when used for long-term application data archiving. Our results show that by provisioning the right amount of storage and compute resources cost can be significantly reduced with no significant impact on application performance

Condor services for the Global Grid:interoperability between Condor and OGSA

In order for existing grid middleware to remain viable it is important to investigate their potentialfor integration with emerging grid standards and architectural schemes. The Open Grid ServicesArchitecture (OGSA), developed by the Globus Alliance and based on standard XML-based webservices technology, was the first attempt to identify the architectural components required tomigrate towards standardized global grid service delivery. This paper presents an investigation intothe integration of Condor, a widely adopted and sophisticated high-throughput computing softwarepackage, and OGSA; with the aim of bringing Condor in line with advances in Grid computing andprovide the Grid community with a mature suite of high-throughput computing job and resourcemanagement services. This report identifies mappings between elements of the OGSA and Condorinfrastructures, potential areas of conflict, and defines a set of complementary architectural optionsby which individual Condor services can be exposed as OGSA Grid services, in order to achieve aseamless integration of Condor resources in a standardized grid environment

M-grid: Using Ubiquitous Web Technologies to create a Computational Grid

There are many potential users and uses for grid computing. However, the concept of sharing computing resources excites security concerns and, whilst being powerful and flexible, at least for novices, existing systems are complex to install and use. Together these represent a significant barrier to potential users who are interested to see what grid computing can do. This paper describes m-grid, a system for building a computational grid which can accept tasks from any user with access to a web browser and distribute them to almost any machine with access to the internet and manages to do this without the installation of additional software or interfering with existing security arrangements

How Deep Is Deep enough for RNA-Seq Profiling of Bacterial Transcriptomes?

Background: High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. A central challenge in designing RNA-Seq-based experiments is estimating a priori the number of reads per sample needed to detect and quantify thousands of individual transcripts with a large dynamic range of abundance. Results: We have conducted a systematic examination of how changes in the number of RNA-Seq reads per sample influences both profiling of a single bacterial transcriptome and the comparison of gene expression among samples. Our findings suggest that the number of reads typically produced in a single lane of the Illumina HiSeq sequencer far exceeds the number needed to saturate the annotated transcriptomes of diverse bacteria growing in monoculture. Moreover, as sequencing depth increases, so too does the detection of cDNAs that likely correspond to spurious transcripts or genomic DNA contamination. Finally, even when dozens of barcoded individual cDNA libraries are sequenced in a single lane, the vast majority of transcripts in each sample can be detected and numerous genes differentially expressed between samples can be identified. Conclusions: Our analysis provides a guide for the many researchers seeking to determine the appropriate sequencing depth for RNA-Seq-based studies of diverse bacterial species

Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis

Tuberculosis (TB) is a major global health problem, infecting millions of people each year. The causative agent of TB, Mycobacterium tuberculosis, is one of the world’s most ancient and successful pathogens. However, until recently, no work on small regulatory RNAs had been performed in this organism. Regulatory RNAs are found in all three domains of life, and have already been shown to regulate virulence in well-known pathogens, such as Staphylococcus aureus and Vibrio cholera. Here we report the discovery of 34 novel small RNAs (sRNAs) in the TB-complex M. bovis BCG, using a combination of experimental and computational approaches. Putative homologues of many of these sRNAs were also identified in M. tuberculosis and/or M. smegmatis. Those sRNAs that are also expressed in the non-pathogenic M. smegmatis could be functioning to regulate conserved cellular functions. In contrast, those sRNAs identified specifically in M. tuberculosis could be functioning in mediation of virulence, thus rendering them potential targets for novel antimycobacterials. Various features and regulatory aspects of some of these sRNAs are discussed

Transactional Client-Server Cache Consistency: Alternatives and Performance

Client-server database systems based on a page server model can exploit client memory resources by caching copies of pages across transaction boundaries. Caching reduces the need to obtain data from servers or other sites on the network. In order to ensure that such caching does not result in the violation of transaction semantics, a cache consistency maintenance algorithm is required. Many such algorithms have been proposed in the literature and, as all provide the same functionality, performance is a primary concern in choosing among them. In this paper we provide a taxonomy that describes the design space for transactional cache consistency maintenance algorithms and show how proposed algorithms relate to one another. We then investigate the performance of six of these algorithms, and use these results to examine the tradeoffs inherent in the design choices identified in the taxonomy. The insight gained in this manner is then used to reflect upon the characteristics of other algorithms that have been proposed. The results show that the interactions among dimensions of the design space can impact performance in many ways, and that classifications of algorithms as simply Pessimistic" or Optimistic" do not accurately characterize the similarities and differences among the many possible cache consistency algorithms. (Also cross-referenced as UMIACS-TR-95-84

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data

Multiclass Query Scheduling in Real-Time Database Systems

In recent years, a demand for real-time systems that can manipulate large amounts of shared data has led to the emer-gence of real-time database systems (RTDBS) as a research area. This paper focuses on the problem of scheduling queries in RTDBSs. We introduce and evaluate a new algorithm called Priority Adaptation Query Resource Scheduling (PAQRS) for handling both single class and multiclass query workloads. The performance objective of the algorithm is to minimize the number of missed deadlines, while at the same time ensuring that any deadline misses are scattered across the different classes according to an administratively-defined miss distribution. This objective is achieved by dynamically adapting the system’s admission, mem-ory allocation, and priority assignment policies according to its current resource configuration and workload characteristics. A series of experiments confirms that PAQRS is very effective for real-time query scheduling

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.Peer reviewe

Flexible Session Management in a Distributed Environment

Many secure communication libraries used by distributed systems, such as SSL, TLS, and Kerberos, fail to make a clear distinction between the authentication, session, and communication layers. In this paper we introduce CEDAR, the secure communication library used by the Condor High Throughput Computing software, and present the advantages to a distributed computing system resulting from CEDAR's separation of these layers. Regardless of the authentication method used, CEDAR establishes a secure session key, which has the flexibility to be used for multiple capabilities. We demonstrate how a layered approach to security sessions can avoid round-trips and latency inherent in network authentication. The creation of a distinct session management layer allows for optimizations to improve scalability by way of delegating sessions to other components in the system. This session delegation creates a chain of trust that reduces the overhead of establishing secure connections and enables centralized enforcement of system-wide security policies. Additionally, secure channels based upon UDP datagrams are often overlooked by existing libraries; we show how CEDAR's structure accommodates this as well. As an example of the utility of this work, we show how the use of delegated security sessions and other techniques inherent in CEDAR's architecture enables US CMS to meet their scalability requirements in deploying Condor over large-scale, wide-area grid systems