Linking de novo assembly results with long DNA reads by dnaasm-link application

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, a result of \textit{de novo} assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions, as presented in the paper. Finally, our implementation outperforms other state-of-the-art tools in terms of speed and memory requirements, which may enable the usage of the presented application for organisms with a large genome, which is not possible in~existing applications. The presented application has many advantages as (i) significant memory optimization and reduction of computation time (ii) filling the gaps through the appropriate fragment of a specified long DNA read (iii) reducing number of spanned and unspanned gaps in the existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, docker image and source code are available at http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure

Interests Diffusion in Social Networks

Understanding cultural phenomena on Social Networks (SNs) and exploiting the implicit knowledge about their members is attracting the interest of different research communities both from the academic and the business side. The community of complexity science is devoting significant efforts to define laws, models, and theories, which, based on acquired knowledge, are able to predict future observations (e.g. success of a product). In the mean time, the semantic web community aims at engineering a new generation of advanced services by defining constructs, models and methods, adding a semantic layer to SNs. In this context, a leapfrog is expected to come from a hybrid approach merging the disciplines above. Along this line, this work focuses on the propagation of individual interests in social networks. The proposed framework consists of the following main components: a method to gather information about the members of the social networks; methods to perform some semantic analysis of the Domain of Interest; a procedure to infer members' interests; and an interests evolution theory to predict how the interests propagate in the network. As a result, one achieves an analytic tool to measure individual features, such as members' susceptibilities and authorities. Although the approach applies to any type of social network, here it is has been tested against the computer science research community. The DBLP (Digital Bibliography and Library Project) database has been elected as test-case since it provides the most comprehensive list of scientific production in this field.Comment: 30 pages 13 figs 4 table

Complex networks and public funding: the case of the 2007-2013 Italian program

In this paper we apply techniques of complex network analysis to data sources representing public funding programs and discuss the importance of the considered indicators for program evaluation. Starting from the Open Data repository of the 2007-2013 Italian Program Programma Operativo Nazionale 'Ricerca e Competitivit\`a' (PON R&C), we build a set of data models and perform network analysis over them. We discuss the obtained experimental results outlining interesting new perspectives that emerge from the application of the proposed methods to the socio-economical evaluation of funded programs.Comment: 22 pages, 9 figure

Finding statistics and newspapers workbook

This resource supports the Understanding Educational Enquiry module DET050 of the PG Cert at the University of Birmingham. It details how to find statistics and newspapers, and could be used by participants as part of their action research. It also stands alone for any user wanting to find statistics or newspapers for their studies. It outlines resources and guidance specifically for the University of Birmingham, but it may be adapted for use elsewhere

Network Kriging

Network service providers and customers are often concerned with aggregate performance measures that span multiple network paths. Unfortunately, forming such network-wide measures can be difficult, due to the issues of scale involved. In particular, the number of paths grows too rapidly with the number of endpoints to make exhaustive measurement practical. As a result, it is of interest to explore the feasibility of methods that dramatically reduce the number of paths measured in such situations while maintaining acceptable accuracy. We cast the problem as one of statistical prediction--in the spirit of the so-called `kriging' problem in spatial statistics--and show that end-to-end network properties may be accurately predicted in many cases using a surprisingly small set of carefully chosen paths. More precisely, we formulate a general framework for the prediction problem, propose a class of linear predictors for standard quantities of interest (e.g., averages, totals, differences) and show that linear algebraic methods of subset selection may be used to effectively choose which paths to measure. We characterize the performance of the resulting methods, both analytically and numerically. The success of our methods derives from the low effective rank of routing matrices as encountered in practice, which appears to be a new observation in its own right with potentially broad implications on network measurement generally.Comment: 16 pages, 9 figures, single-space

Using data network metrics, graphics, and topology to explore network characteristics

Yehuda Vardi introduced the term network tomography and was the first to propose and study how statistical inverse methods could be adapted to attack important network problems (Vardi, 1996). More recently, in one of his final papers, Vardi proposed notions of metrics on networks to define and measure distances between a network's links, its paths, and also between different networks (Vardi, 2004). In this paper, we apply Vardi's general approach for network metrics to a real data network by using data obtained from special data network tools and testing procedures presented here. We illustrate how the metrics help explicate interesting features of the traffic characteristics on the network. We also adapt the metrics in order to condition on traffic passing through a portion of the network, such as a router or pair of routers, and show further how this approach helps to discover and explain interesting network characteristics.Comment: Published at http://dx.doi.org/10.1214/074921707000000058 in the IMS Lecture Notes Monograph Series (http://www.imstat.org/publications/lecnotes.htm) by the Institute of Mathematical Statistics (http://www.imstat.org