BACKGROUND: Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome. RESULTS: To face these challenges, a new version of Metavir was developed. First, all Metavir tools have been adapted to support comparative analysis of viromes in order to improve the analysis of multiple datasets. In addition to the sequence comparison previously provided, viromes can now be compared through their k-mer frequencies, their taxonomic compositions, recruitment plots and phylogenetic trees containing sequences from different datasets. Second, a new section has been specifically designed to handle assembled viromes made of thousands of large genomic fragments (i.e. contigs). This section includes an annotation pipeline for uploaded viral contigs (gene prediction, similarity search against reference viral genomes and protein domains) and an extensive comparison between contigs and reference genomes. Contigs and their annotations can be explored on the website through specifically developed dynamic genomic maps and interactive networks. CONCLUSIONS: The new features of Metavir 2 allow users to explore and analyze viromes composed of raw reads or assembled fragments through a set of adapted tools and a user-friendly interface.

SUMMARY: Metavir is a web server dedicated to the analysis of viral metagenomes (viromes). In addition to classical approaches for analyzing metagenomes (general sequence characteristics, taxonomic composition), new tools developed specifically for viral sequence analysis make it possible to: (i) explore viral diversity through automatically constructed phylogenies for selected marker genes, (ii) estimate gene richness through rarefaction curves and (iii) perform cross-comparison against other viromes using sequence similarities. Metavir is thus unique as a platform that allows a comprehensive virome analysis. AVAILABILITY: Metavir is freely available online at: http://metavir-meb.univ-bpclermont.fr. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Design solutions have been proposed to implement generic data structures, however such techniques dedicated to algorithms are not well known. This article discusses various recurrent problems encountered when designing reusable, extensible algorithms for operations research. It explains how to use object-oriented concepts and the notion of genericity to design algorithms that are independent of the data structures and the algorithms they use, but that can still interact deeply with them. An object-oriented design is sometimes considered to be less efficient than a classical one, and operations research is one of these scientific fields where efficiency really matters. Hence, the main goal of this article is to explain how to design algorithms that are both generic and efficient. It also discusses specific recurring design issues for operations research software and proposes solutions that improve the genericity of the algorithms. Copyright © 2005 John Wiley & Sons, Ltd.

We study an original scheme based on distributed feedforward neural networks, aimed at modelling several queueing systems in cascade fed with bursty traffic. For each queueing system, a neural network is trained to anticipate the average number of waiting packets, the packet loss rate and the coefficient of variation of the packet inter-departure time, given the mean rate, the peak rate and the coefficient of variation of the packet inter-arrival time. The latter serves for the calculation of the coefficient of variation of the cell inter-arrival time of the aggregated traffic which is fed as input to the next neural network along the path. The potential of this method is successfully illustrated on several single server FIFO (First In, First Out) queues and on small queueing networks made up from a combination of queues in tandem and in parallel fed by a superposition of ideal sources. Our long-term goal is the design of preventive control strategy in a multiservice communication network.

We discuss a scheme based on distributed feedforward neural networks (NN), aimed at modelling several queueing systems in cascade fed with bursty traffic. For each queueing system, a neural network is trained to anticipate the average number of waiting packets, the packet loss rate and the coefficient of variation of the packet inter-departure time, given the mean rate, the peak rate and the coefficient of variation of the packet inter-arrival time. The latter serves for the calculation of the coefficient of variation of the cell inter-arrival time of the aggregated traffic which is fed as input to the next NN along the path. The potential of this method was sucessfully illustrated on several single server FIFO queues in Aussem et al. (1999). We now apply this technique to model a small queueing network made up from a combination of queues in tandem and in parallel fed by a superimposition of OnOff sources. Our long-term goal is the design of preventive control strategy in a multiservice communication network.