Log-based middleware server recovery with transaction support

Abstract Providing enterprises with reliable and available Web-based application programs is a challenge. Applications are traditionally spread over multiple nodes, from user (client), to middle tier servers, to back end transaction systems, e.g. databases. It has proven very difficult to ensure that these applications persist across system crashes so that "exactly once" execution is produced, always important and sometimes essential, e.g., in the financial area. Our system provides a framework for exactly once execution of multitier Web applications, built on a commercially available Web infrastructure. Its capabilities include low logging overhead, recovery isolation (independence), and consistency between mid-tier and transactional back end. Good application performance is enabled via persistent shared state in the middle tier while providing for private session state as well. Our extensive experiments confirm both the desired properties and the good performance

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

<p>Abstract</p> <p>Background</p> <p>In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL.</p> <p>Results</p> <p>To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available.</p> <p>Conclusion</p> <p>This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.</p

Long-range interactions and non-extensivity in ferromagnetic spin models

The Ising model with ferromagnetic interactions that decay as $1/r^\alpha$ is analyzed in the non-extensive regime $0\leq\alpha\leq d$, where the thermodynamic limit is not defined. In order to study the asymptotic properties of the model in the $N\rightarrow\infty$ limit ($N$ being the number of spins) we propose a generalization of the Curie-Weiss model, for which the $N\rightarrow\infty$ limit is well defined for all $\alpha\geq 0$. We conjecture that mean field theory is {\it exact} in the last model for all $0\leq\alpha\leq d$. This conjecture is supported by Monte Carlo heat bath simulations in the $d=1$ case. Moreover, we confirm a recently conjectured scaling (Tsallis\cite{Tsallis}) which allows for a unification of extensive ($\alpha>d$) and non-extensive ($0\leq\alpha\leq d$) regimes.Comment: RevTex, 12 pages, 1 eps figur

Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species

A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R2

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

BACKGROUND: The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. RESULTS: We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. CONCLUSIONS: Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species

BACKGROUND: The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. RESULTS: By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. CONCLUSIONS: The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank

The field theoretic derivation of the contact value theorem in planar geometries and its modification by the Casimir effect

The contact value theorem for Coulomb gases in planar or film-like geometries is derived using a Hamiltonian field theoretic representation of the system. The case where the film is enclosed by a material of different dielectric constant to that of the film is shown to contain an additional Casimir-like term which is generated by fluctuations of the electric potential about its mean-field value.Comment: Link between Sine-Gordon and Coulomb gas pressures via subtraction of self interaction terms included. Discussion of results within Debye-Huckel approximation included. Added reference

Perturbation and Variational Methods in Nonextensive Tsallis Statistics

A unified presentation of the perturbation and variational methods for the generalized statistical mechanics based on Tsallis entropy is given here. In the case of the variational method, the Bogoliubov inequality is generalized in a very natural way following the Feynman proof for the usual statistical mechanics. The inequality turns out to be form-invariant with respect to the entropic index $q$. The method is illustrated with a simple example in classical mechanics. The formalisms developed here are expected to be useful in the discussion of nonextensive systems.Comment: revte