Hawkeye: An interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. © 2007 Schatz et al.; licensee BioMed Central Ltd

Surface correlations for two-dimensional Coulomb fluids in a disc

After a brief review of previous work, two exactly solvable two-dimensional models of a finite Coulomb fluid in a disc are studied. The charge correlation function near the boundary circle is computed. When the disc radius is large compared to the bulk correlation length, a correlation function of the surface charge density can be defined. It is checked, on the solvable models, that this correlation function does have the generic long-range behaviour, decaying as the inverse square distance, predicted by macroscopic electrostatics. In the case of a two-component plasma (Coulomb fluid made of two species of particles of opposite charges), the density correlation function on the boundary circle itself is conjectured to have a temperature-independent behaviour, decaying as the -4 power of the distance.Comment: 15 pages, Latex, submitted to J.Phys.:Condens.Matte

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

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

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

Improving effectiveness of honeypots: predicting targeted destination port numbers during attacks using J48 algorithm

During recent years, there has been an increase in cyber-crime and cybercriminal activities around the world and as countermeasures, effective attack prevention and detection mechanisms are needed. A popular tool to augment existing attack detection mechanisms is the Honeypot. It serves as a decoy for luring attackers, with the purpose to accumulate essential details about the intruder and techniques used to compromise systems. In this endeavor, such tools need to effectively listen and keep track of ports on hosts such as servers and computers within networks. This paper investigates, analyzes and predicts destination port numbers targeted by attackers in order to improve the effectiveness of honeypots. To achieve the purpose of this paper, the J48 decision tree classifier was applied on a database containing information on cyber-attacks. Results revealed insightful information on key destination port numbers targeted by attackers, in addition to how these targeted ports vary within different regions around the world

A Generalization of the Stillinger-Lovett Sum Rules for the Two-Dimensional Jellium

In the equilibrium statistical mechanics of classical Coulomb fluids, the long-range tail of the Coulomb potential gives rise to the Stillinger-Lovett sum rules for the charge correlation functions. For the jellium model of mobile particles of charge $q$ immersed in a neutralizing background, the fixing of one of the $q$-charges induces a screening cloud of the charge density whose zeroth and second moments are determined just by the Stillinger-Lovett sum rules. In this paper, we generalize these sum rules to the screening cloud induced around a pointlike guest charge $Z q$ immersed in the bulk interior of the 2D jellium with the coupling constant $\Gamma=\beta q^2$ ($\beta$ is the inverse temperature), in the whole region of the thermodynamic stability of the guest charge $Z>-2/\Gamma$. The derivation is based on a mapping technique of the 2D jellium at the coupling $\Gamma$ = (even positive integer) onto a discrete 1D anticommuting-field theory; we assume that the final results remain valid for all real values of $\Gamma$ corresponding to the fluid regime. The generalized sum rules reproduce for arbitrary coupling $\Gamma$ the standard Z=1 and the trivial Z=0 results. They are also checked in the Debye-H\"uckel limit $\Gamma\to 0$ and at the free-fermion point $\Gamma=2$. The generalized second-moment sum rule provides some exact information about possible sign oscillations of the induced charge density in space.Comment: 16 page

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-term results of simplified frozen elephant trunk technique in complicated acute type A aortic dissection: A case–control study

Aim: To describe the long-term experience of a simplified frozen elephant trunk technique (sFETT) used in complicated acute type A aortic dissection (AAAD) treatment. Methods and results: Between January 2001 and December 2012, 34 patients (mean age 59.9 ± 11.0 years) with complicated AAAD (DeBakey I) underwent an emergency surgery including sFETT. sFETT consisted in gluing the dissected aortic arch wall layers with gelatine-resorcinol adhesive and video-assisted antegrade open arch aortic stent-graft deployment in the arch or proximal descending aorta. In addition to sFETT, the aortic root was addressed with standard techniques. A 30-day mortality was 14.7% (five patients) due to bleeding (1), multiple organ failure (2), and colon ischemia (2). Postoperative morbidity included neurological (2), renal (1) and cardio-pulmonary complications (4), as well as wound infection (1). Mean follow-up was 74.4 ± 45.0 months. Actual survival rates were 73.5% at 1 year, 70.2% at 5 years, and 58.5% at 13 years of follow-up. Six patients died during long-term follow-up from heart failure (1) and unknown reasons (5). Five patients required reoperation for aortic arch (3) or aorto-iliac (2) progression of aneurysm during the mid- and long-term follow-up. The remaining patients showed favorable evolution of the dissected aorta with false lumen occlusion in most cases and stable aortic diameters. Conclusions: In AAAD patients, sFETT as used in our series is an easy and safe technique to repair the aortic arch. Long-term results after sFETT showed false lumen occlusion and stable aortic diameter in up to 13 years of follow-up