Paul Greenfield

Data-Intensive Computing in the 21st Century

The deluge of data that future applications must process—in domains ranging from science to business informatics—creates a compelling argument for substantially increased R&D targeted at discovering scalable hardware and software solutions for data-intensive problems.The deluge of data that future applications must process—in domains ranging from science to business informatics—creates a compelling argument for substantially increased R&D targeted at discoverin...

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.

Blue: correcting sequencing errors using consensus and context

MOTIVATION Bioinformatics tools, such as assemblers and aligners, are expected to produce more accurate results when given better quality sequence data as their starting point. This expectation has led to the development of stand-alone tools whose sole purpose is to detect and remove sequencing errors. A good error-correcting tool would be a transparent component in a bioinformatics pipeline, simply taking sequence data in any of the standard formats and producing a higher quality version of the same data containing far fewer errors. It should not only be able to correct all of the types of errors found in real sequence data (substitutions, insertions, deletions and uncalled bases), but it has to be both fast enough and scalable enough to be usable on the large datasets being produced by current sequencing technologies, and work on data derived from both haploid and diploid organisms. RESULTS This article presents Blue, an error-correction algorithm based on k-mer consensus and context. Blue can correct substitution, deletion and insertion errors, as well as uncalled bases. It accepts both FASTQ and FASTA formats, and corrects quality scores for corrected bases. Blue also maintains the pairing of reads, both within a file and between pairs of files, making it compatible with downstream tools that depend on read pairing. Blue is memory efficient, scalable and faster than other published tools, and usable on large sequencing datasets. On the tests undertaken, Blue also proved to be generally more accurate than other published algorithms, resulting in more accurately aligned reads and the assembly of longer contigs containing fewer errors. One significant feature of Blue is that its k-mer consensus table does not have to be derived from the set of reads being corrected. This decoupling makes it possible to correct one dataset, such as small set of 454 mate-pair reads, with the consensus derived from another dataset, such as Illumina reads derived from the same DNA sample. Such cross-correction can greatly improve the quality of small (and expensive) sets of long reads, leading to even better assemblies and higher quality finished genomes. AVAILABILITY AND IMPLEMENTATION The code for Blue and its related tools are available from http://www.bioinformatics.csiro.au/Blue. These programs are written in C# and run natively under Windows and under Mono on Linux.

Behavior and performance of message-oriented middleware systems

The middleware technology used as the foundation of Internet-enabled enterprise systems is becoming increasingly complex. In addition, the various technologies offer a number of standard architectures that can be used by designers as templates to build applications. However, there is little concrete understanding in the software industry on the strengths and weaknesses of competing technologies, and the different trade-offs that various component architectures impose. The SACT Group at CSIRO has qualitatively and quantitatively evaluated a number of commercially available Message-Oriented Middleware (MOM) systems. This paper focuses on the results obtained from the performance evaluation of the IBMs MQSeries V5.2. It presents an overview of the technology, and discusses the metric used in this study for performance measurement The test results related to the sustainable performance of the system using various test configurations are described and their implications discussed.

QoS evaluation of JMS: an empirical approach

JMS is an API specification that defines a standard way for Java applications to access messaging services. All JMS products promise good performance and to properly support the QoS attributes specified in the standard, making it hard to choose between them. Customers who want to determine which JMS product best meets their requirements need a simple, effective and fair methodology for evaluating and comparing competing implementations. This paper presents an empirical methodology for evaluating the QoS implementation of a JMS product. We present a number of test scenarios and define metrics for measuring performance and message persistence. We then illustrate this methodology by using it to evaluate two leading JMS products. Our evaluation results show differences between these products in terms of their overall performance and the impact of various QoS attributes. The case study demonstrates that our empirical methodology is an effective and practical way to test the performance of JMS and other messaging systems.

Draft Genome Sequence of Clostridium sporogenes PA 3679, the Common Nontoxigenic Surrogate for Proteolytic Clostridium botulinum

Clostridium sporogenes PA 3679 is widely used as a nontoxigenic surrogate for proteolytic strains of Clostridium botulinum in the derivation and validation of thermal processes in food. Here we report the draft assembly and annotation of the C. sporogenes PA 3679 genome. Preliminary analysis demonstrates a high degree of relatedness between C. sporogenes PA 3679 and sequenced strains of proteolytic C. botulinum.

Reanalysis and Simulation Suggest a Phylogenetic Microarray Does Not Accurately Profile Microbial Communities

The second generation (G2) PhyloChip is designed to detect over 8700 bacteria and archaeal and has been used over 50 publications and conference presentations. Many of those publications reveal that the PhyloChip measures of species richness greatly exceed statistical estimates of richness based on other methods. An examination of probes downloaded from Greengenes suggested that the system may have the potential to distort the observed community structure. This may be due to the sharing of probes by taxa; more than 21% of the taxa in that downloaded data have no unique probes. In-silico simulations using these data showed that a population of 64 taxa representing a typical anaerobic subterranean community returned 96 different taxa, including 15 families incorrectly called present and 19 families incorrectly called absent. A study of nasal and oropharyngeal microbial communities by Lemon et al (2010) found some 1325 taxa using the G2 PhyloChip, however, about 950 of these taxa have, in the downloaded data, no unique probes and cannot be definitively called present. Finally, data from Brodie et al (2007), when re-examined, indicate that the abundance of the majority of detected taxa, are highly correlated with one another, suggesting that many probe sets do not act independently. Based on our analyses of downloaded data, we conclude that outputs from the G2 PhyloChip should be treated with some caution, and that the presence of taxa represented solely by non-unique probes be independently verified.

Expressing and Reasoning about Service Contracts in Service-Oriented Computing

The Web services and service-oriented architectures (SOA) vision by Helland, P. (2005) is about building large-scale distributed applications by composing coarse-grained autonomous services in a flexible architecture that can adapt to changing business requirements. These services interact by exchanging one-way messages through standardized message processing and transport protocols. This vision is being driven by economic imperatives for integration and automation across administrative and organizational boundaries. This paper presents a concise yet expressive model for service contracts to describe messaging behavior. The idea is simple: we use Boolean conditions to specify when a message can be sent and received, where the conditions refer only to other messages in the service contract - that is, conditions only refer to a services externalized messaging state and not to internal state

Aspergillus hancockii sp. Nov., a biosynthetically talented fungus endemic to southeastern Australian soils

Aspergillus hancockii sp. nov., classified in Aspergillus subgenus Circumdati section Flavi, was originally isolated from soil in peanut fields near Kumbia, in the South Burnett region of southeast Queensland, Australia, and has since been found occasionally from other substrates and locations in southeast Australia. It is phylogenetically and phenotypically related most closely to A. leporis States and M. Chr., but differs in conidial colour, other minor features and particularly in metabolite profile. When cultivated on rice as an optimal substrate, A. hancockii produced an extensive array of 69 secondary metabolites. Eleven of the 15 most abundant secondary metabolites, constituting 90% of the total area under the curve of the HPLC trace of the crude extract, were novel. The genome of A. hancockii, approximately 40 Mbp, was sequenced and mined for genes encoding carbohydrate degrading enzymes identified the presence of more than 370 genes in 114 gene clusters, demonstrating that A. hancockii has the capacity to degrade cellulose, hemicellulose, lignin, pectin, starch, chitin, cutin and fructan as nutrient sources. Like most Aspergillus species, A. hancockii exhibited a diverse secondary metabolite gene profile, encoding 26 polyketide synthase, 16 nonribosomal peptide synthase and 15 nonribosomal peptide synthase-like enzymes.

Compensation is not enough [fault-handling and compensation mechanism]

An important problem in designing infrastructure to support business-to-business integration (B2Bi) is how to cancel a long-running interaction (either because the user has changed their mind, or in response to an unrecoverable failure). We review the fault-handling and compensation mechanism that is now used in most workflow products and business process modeling standards. We then use an e-procurement case-study to extract a set of requirements for an effective cancellation mechanism, and we show that the standard approach using fault-handling, and compensation transactions is not adequate to meet these requirements.