SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information.

Twenty one fully sequenced and well annotated insect genomes were used to construct genome content matrices for phylogenetic analysis and functional annotation of insect genomes. To examine the role of e-value cutoff in ortholog determination we used scaled e-value cutoffs and a single linkage clustering approach.. The present communication includes (1) a list of the genomes used to construct the genome content phylogenetic matrices, (2) a nexus file with the data matrices used in phylogenetic analysis, (3) a nexus file with the Newick trees generated by phylogenetic analysis, (4) an excel file listing the Core (CORE) genes and Unique (UNI) genes found in five insect groups, and (5) a figure showing a plot of consistency index (CI) versus percent of unannotated genes that are apomorphies in the data set for gene losses and gains and bar plots of gains and losses for four consistency index (CI) cutoffs.

BeagleBone Black is a low-cost, open hardware computer uniquely suited to interact with sensors and actuators directly and over the Web. Introduced in April 2013 by BeagleBoard.org, a community of developers first established in early 2008, BeagleBone Black is used frequently to build vision-enabled robots, home automation systems, artistic lighting systems, and countless other do-it-yourself and professional projects. BeagleBone variants include the original BeagleBone and the newer BeagleBone Black, both hosting a powerful 32-bit, super-scalar ARM Cortex A8 processor capable of running numerous mobile and desktop-capable operating systems, typically variants of Linux including Debian, Android, and Ubuntu. Yet, BeagleBone is small enough to fit in a small mint tin box. The may be used in a wide variety of projects from middle school science fair projects to senior design projects to first prototypes of very complex systems. Novice users may access the power of the Bone through the user-friendly BoneScript software, experienced through a Web browser in most major operating systems, including Microsoft Windows, Apple Mac OS X, or the Linux operating systems. Seasoned users may take full advantage of the Bone's power using the underlying Linux-based operating system, a host of feature extension boards (Capes) and a wide variety of Linux community open source libraries. This book provides an introduction to this powerful computer and has been designed for a wide variety of users including the first time novice through the seasoned embedded system design professional. The book contains background theory on system operation coupled with many well-documented, illustrative examples. Examples for novice users are centered on motivational, fun robot projects while advanced projects follow the theme of assistive technology and image-processing applications.

Halichondrida is a pivotal demosponge order of which the classification underwent major changes in the recent history. The monophyly of this order and its intra-ordinal phylogeny cannot be reliably determined on the basis of morphology. Here we present a 28Sr RNA gene tree of selected halichondrids, which supports the hypothesis of halichondrid non-monophyly and elucidates further inter-ordinal relationships. We enlarged the analysis by previously published sequences, discuss how previous analyses suffer from taxon bias and analyse the resulting phylogenetic implications. Most halichondrid families (in particular Axinellidae und Dictyonellidae) cluster polyphyletic and the molecular classification of several genera does not agree with the current (morphological) system. Zusammenfassung Die Systematik der Ordnung Halichondrida ist von Bedeutung fur die Phylogenie aller Demospongien und hat in den letzten Jahren grose Veranderungen vollzogen. Dennoch konnte die Monophylie dieser Ordnung und ihrer Familien noch nicht mit morphologischen Merkmalen deutlich gemacht werden. Hier prasentieren und diskutieren wir eine 28SrDNA-Phylogenie reprasentativer Halichondrien. Teils wurde diese Stammbaumrekonstruktion durch Sequenzen aus anderen Arbeiten erweitert und der Einfluss des Taxonsets auf das Resultat analysiert. Die Monophylie der Ordnung wird durch diese Fragmentanalyse nicht gestutzt, und mehrere Familien (insbesondere Axinellidae und Dictyonellidae) gruppieren polyphyletisch. Die Position mehrerer Gattungen, insbesondere Axinyssa und Stylissa, ist nicht im Einklang mit dem aktuellen (morphologischen) System.

concatenator is a simple and user-friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice-versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.

When modeling electronic devices of complex geometry and their systems using finite element analysis software packages, several problems related to the modeling duration emerge. With the increase of the variety of modeling software packages dedicated both to “Microsoft Windows” and “Apple Mac OS X” operating systems, it is important to determine the dependency of modeling performance in respect of operating system which is used to control the modeling environment. The modeling performance investigation was accomplished using COMSOL software. The algorithm used to analyse the finite element mesh generation and differential equation system solution duration was created and it was implemented during the computational experiment during which the modeling performance was analysed. The obtained analysis results are provided. Ill. 8, bibl. 5 (in English; abstracts in English and Lithuanian).DOI: http://dx.doi.org/10.5755/j01.eee.119.3.1362

This article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

Cloud computing is evolving as a new paradigm of computing in which dynamically scalable and often virtualized resources are provided as a service over the Internet. The confluence of hardware virtualization, cloud and mobile computing drives the new era of mobile cloud computing. Platforms such as android, iOS, Windows 7 erodes the power of computing platforms like Microsoft Windows and Apple Mac OS and is creating cross platform app centric environment in which end-users and in particular the consumer marketplace will drive developments in business computing. There are endless possibilities that can be brought about with the mobile cloud in the near future. This paper discusses the current state of mobile cloud computing and the services provided by cloud providers like Amazon and how easy it is to build a mobile application on top of Amazon S3 with their APIs. Open challenges in mobile cloud computing are also discussed to highlight the future research directions.

The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.

Distributed multi-display systems often require high-end servers and/or linux operating systems. These requirements are not familiar to intermediate PC users, therefore making it difficult for those users to take advantage of multidisplay applications such as multi-user cooperative work. To alleviate this situation we developed Tenmads, a software multi-display implementation that runs on the most prevalent PC operating system – Microsoft Windows. Tenmads focuses on cost effectiveness and simplicity in configuration so that most PC users can set up multi-display environments without any help from computer experts. This paper describes how Tenmads is designed while maintaining a fair performance for low- and middle- range computer/network resources. It also describes Tenmads' support for multiple input devices which enables mixed local/remote real-time multi-user cooperative work.

Both hardware and software play important roles in computers.On the hardware front, in the first generation of modern computers, magnetic tapes and disks were developed and used for storage, and printers appeared and were used for output.On the software side, simple operating systems (OSs) were developed and used, and over 100 high-level programming languages were developed.During the second generation of computers, the Universal Automatic Computer (UNIVAC I), the first computer for commercial use, was introduced to the public (1951).The International Business Machines Corporation (IBM) also brought their IBM650 and IBM700 series computers to the computer world (1953).Since 1963, the beginning of the third generation of modern computers, advances in hardware have made computers smaller and smaller but much more powerful, with a higher speed of CPU and a bigger memory with faster throughput.In 1980, Microsoft developed MS-DOS, short for Microsoft Disk Operating System, and in 1981, IBM introduced the first personal computer (PC) for home and office use.In 1984, Apple brought its Macintosh computer with its icondriven interface to the world, and in the 1990s, Microsoft brought the world the Windows operating system.Billions of computer users around the world have enjoyed both Microsoft Windows and Apple's macOS.

RNA secondary structure comparison is one of the important analyses for elucidating individual functions of RNAs since it is widely accepted that their functions and structures are strongly correlated. However, although the RNA secondary structures with pseudoknot play important roles in vivo, it is difficult to deal with such structures in silico due to their structural complexity, which is a major obstacle to the analysis of RNA functions.Here, we introduce an algorithm and a metric for comparing pseudoknotted RNA secondary structures based on topological centroid identification and tree edit distance and describe the usage protocol of a software enabling us to run the comparison. This software is publicly available and works on both Microsoft Windows and Apple macOS.

Chapter 7 - Interfacing Software to the PC

Since January 2011, IPv4 address space has exhausted and IPv6 is taking up the place as successor. Coexistence of IPv4 and IPv6 bears problem of incompatibility, as IPv6 and IPv4 headers are different from each other, thus, cannot interoperate with each other directly. The IPv6 transitioning techniques are still not mature, causing hindrance in the deployment of IPv6 and development of next generation Internet. Until IPv6 completely takes over from IPv4, they will both coexist. For IPv4-IPv6 coexistence, three solutions are possible: a) making every device dual stack, b) translation, c) tunneling. Tunneling stands out as the best possible solution. Among the IPv6 tunneling techniques, this paper evaluates the impact of three recent IPv6 tunneling techniques: 6to4, Teredo, and ISATAP, in cloud virtualization environment. In virtual networks, these protocols were implemented on Microsoft Windows (MS Windows 7 and MS Windows Server 2008) and Linux operating system. Each protocol was implemented on the virtual network. UDP audio streaming, video streaming and ICMP-ping traffic was run. Multiple runs of traffic were routed over the setup for each protocol. The average of the data was taken to generate graphs and final results. The performance of these tunneling techniques has been evaluated on eight parameters, namely: throughput, end to end delay (E2ED), jitter, round trip time (RTT), tunneling overhead, tunnel setup delay, query delay, and auxiliary devices required. This evaluation shows the impact of IPv4-IPv6 coexistence in virtualization environment for cloud computing.

Coexistence of IPv4 and IPv6 bears problem of incompatibility, as IPv6 and IPv4 headers are different from each other. To counter this problem, three solutions are possible: a) making every device dual stack, b) translation, c) tunneling. Tunneling stands out as the best possible solution. Among the IPv6 tunneling techniques, this paper evaluates the performance of two recent IPv6 tunneling techniques: 6to4 and ISATAP. These protocols were implemented on real test bed setup, on Microsoft Windows (MS Windows XP and MS Windows Server 2003) and Linux operating systems. Five to six devices were used to setup the whole test bed. Each protocol was then implemented on the setup using specific configuration commands, available online at various sources. UDP based audio streaming, video streaming, and TCP based ICMP-ping traffic was run. Four different runs of IPv6 traffic were routed over the setup for both IPv6 tunneling protocols. The average of the data was taken to generate graphs and final results. The performance of these tunneling techniques has been evaluated through certain parameters, namely: throughput, end to end delay (E2ED), round trip time (RTT), and jitter.

Although Microsoft Windows is being deployed in mission-critical applications, little quantitative data has been published about its robustness. We present the results of executing over two million Ballista-generated exception handling tests across 237 functions and system calls involving six Windows variants, as well as similar tests conducted on the Linux operating system. Windows 95, Windows 98 and Windows CE were found to be vulnerable to complete system crashes caused by very simple C programs for several different functions. No system crashes were observed on Windows NT, Windows 2000 or Linux. Linux was significantly more graceful at handling exceptions from system calls in a program-recoverable manner than Windows NT and Windows 2000, but those Windows variants were more robust than Linux (with glibc) at handling C library exceptions. While the choice of operating systems cannot be made solely on the basis of one set of tests, it is hoped that such results will form a starting point for comparing dependability across heterogeneous platforms.