DNAContentViewer a BioJS component to visualise GC/AT Content

Summary: Compositional GC/AT content of DNA sequences is a useful feature in genome analysis. GC/AT content provides useful information about evolution, structure and function of genomes, giving clues about their biological function and organisation. We have developed DNAContentViewer, a BioJS component for visualisation of compositional GC/AT content in raw sequences. DNAContentViewer has been integrated in the BioJS project as part of the BioJS registry of components. DNAContentViewer requires a simple configuration and installation. Its design allows potential interactions with other components via predefined events

Prioritization of Re-executable Test Cases of Activity Diagram in Regression Testing Using Model Based Environment

As we all know, software testing is of vital importance in software development life cycle (SDLC) to validate the new versions of the software and detection of faults. Regression Testing, however concentrates on generating test cases on changed part of the software to detect faults more earlier than any other testing practices. In case of model based testing approach, testing is performed using top-down method (black box method) and design models of the software, for example, UML diagrams. UML diagrams gives us requirement level representation of the software in graphical format which is now a days a standard used in software engineering. In our proposed approach, we have derived a new technique which has never been used before to prioritize the test cases in model based environment. In this technique, we have used activity diagram as an input to the system. Activity diagram is used basically because it gives us the complete flow of each and every activity involved in the system and represents its complete working. Activity diagram is further changed as the requirement changes, each time, when the changes happen, they are recorded and test cases are generated for the changed diagram, test cases are also generated for the original diagram. Test cases for both the diagrams are compared and classified as re-usable and re-executable test cases. Re-usable test cases are those that remain unchanged during requirement changes and re-executable test cases belong to the changed part of the diagram. Then re-executable test cases are prioritized using one heuristic algorithm based on ACT(Activity Connector) table. Now, the question is why to prioritize only the re-executable test cases. Because, any how we have to execute re-usable test cases, as they remain same for both the versions of the diagram and are already tested when original diagram was made. But, re-executable test cases are never been tested and may detect faults in the modified design quickly and by prioritizing them we can also reduce the execution time of the test cases which will give us effective testing performance and will evolve a better new version of the software. All the existing prioritization techniques are either code based or are using various tool supports. Code based techniques are too complex and tedious because for a small change in code, we need to test whole application repeatedly. And in case of tool support, we have multiple assumptions and constraints to be followed. This proposed technique will surely give better results and as the type of technique has never been used before will also prove very effective. DOI: 10.17762/ijritcc2321-8169.15077

Performance Evaluation and Experimental Studies on Metallised Gel Propellants

Metallised gel propellants offer higher specific impulse and volumetric loading, reduced vaporisation loss, spillage and slosh problems and easy storage in comparison to the conventional liquid propellants. Theoretical performance analysis of gel propellant containing Al in unsymmetrical dimethyl hydrazine-dinitrogen tetroxide (UDMH-N/sub 2/O/sub 4} system shows peak Isp (vacuum condition) of 316.7 s and 318.3 s at oxidiser/fuel (O/f) ratios of 1.5 and 1.0, respectively for 30 per cent and 40 per cent UDMH-Al gel propellants, under standard conditions. The effect of other parameters like area ratio and chamber pressure on performance has been brought out in view of mission oriented applications. Aluminium has been found to be a better choice over magnesium in metallised gel propellants. Experimental studies on UDMH gellation using propellant grade (15 micrometer)and pyrotechnic grade (1.5 micrometer)Al in 500g batch level show that gellant(methyl cellulose) concentration could be reduced by 50 percent using pyrotechnic grade Al. The pseudoplastic-thixotropic behaviour, flow rate through die holes, burst pressure tests and bulk density are studied. UDMH -25 to 30 per cent Al gels with both grades of Al are found to be stable, pseudoplastic (shear thinning) and thixotropic (time-dependent shear thinning), but their flow pattern through die holes differ in nature

ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Morphological Classification of Galaxies by Shapelet Decomposition in the Sloan Digital Sky Survey

We describe application of the `shapelet' linear decomposition of galaxy images to morphological classification using images of $\sim$ 3000 galaxies from the Sloan Digital Sky Survey. After decomposing the galaxies we perform a principal component analysis to reduce the number of dimensions of the shapelet space to nine. We find that each of these nine principal components contains unique morphological information, and give a description of each principal component's contribution to a galaxy's morphology. We find that galaxies of differing Hubble type separate cleanly in the shapelet space. We apply a Gaussian mixture model to the 9-dimensional space spanned by the principal components and use the results as a basis for classification. Using the mixture model, we separate galaxies into seven classes and give a description of each class's physical and morphological properties. We find that several of the mixture model classes correlate well with the traditional Hubble types both in their morphology and their physical parameters (e.g., color, velocity dispersions, etc.). In addition, we find an additional class of late-type morphology but with high velocity dispersions and very blue color; most of these galaxies exhibit post-starburst activity. This method provides an objective and quantitative alternative to traditional and subjective visual classification.Comment: 21 pages, 16 figures, accepted by AJ, minor changes per the referee's comment

Anatomy of BioJS, an open source community for the life sciences

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects

GGE biplot based assessment of yield stability, adaptability and mega-environment characterization for hybrid pigeonpea (Cajanus cajan)

GGE biplot methodology is a powerful tool to study relationship among test environments (E), genotypes (G) and genotype-by-environment interaction (GE). Present study was conducted on 10 short-duration genotypes in five test environments for two years, and 16 medium-duration genotypes in six test locations for three years in randomized complete block design with two replications. In short-maturity group three mega-environments (ME) were found—ME1 comprised of Phaltan, Patancheru and Hyderabad1; ME2 and 3 constituted Jalna and Aurangabad, respectively. In scenario of limited resources, Patancheru may be a good testing location for general adaptability of short-duration hybrids, while Aurangabad and Hyderabad1 may be right environments for testing specific adaptation of short-duration cultivars in pigeonpea. ICPH 2433 was a winning genotype in ME1 in terms of high yield and stability. In medium-maturity group, two MEs were observed. Jalna, Jalna 1, Parbhani and Hyderabad grouped together as ME1, while Patancheru and Phaltan formed the second mega-environment (ME2). Parbhani was found to be most representative of all the six test locations. Jalna (ME1) and Phaltan (ME2) produced longest environment vectors, and hence may be regarded as highly discriminating. In mediummaturity group ICPH 2673 was found to be stable and high-yielding genotype for ME

Development of ‘super-early’ pigeonpeas with good yield potential from early × early crosses

To enhance the adaptability of pigeonpea at higher latitude and altitude, a breeding program was initiated at ICRISAT involving different sources of early-maturity. A full diallel mating design involving 11 early-maturing lines were used as parents. In F2–F5 generations, selection was followed for early flowering and maturity, grain yield and 100-seed weight by pedigree method. Four brown seeded (ICPX 060064-4-6-10, ICPX 060077-6-5-14, ICPX 060064-4-6-2 and ICPX 060063-11-8-4) and one cream seeded (ICPX 060036-13-4-8) F4/F5 indeterminate super-early progenies that matured, respectively 25 and 23 days earlier than the control cultivar ICPL 88039 were recovered. ICPX 060036-13-4-8 recorded 107% and 34% grain yield advantage over the checks ICPL 86022 and ICPL 88039, respectively. These super-early lines were derived from crosses involving AL 1518-2 × ICPL 85010, AL 1621 × MN 5, AL 1518-2 × MN 8 and MN 8 × AL 1518-2. Other super-early progenies [ICPX 060016-10-8-1 (from MN 1 × AL 1518-2 cross) and ICPX 060017-12-12-20 (from MN 1 × AL 1621 cross)] with greater 100-seed weight were also recovered. Besides serving as excellent donors for earliness, these lines may be photo/thermo insensitive. These super-early pigeonpea lines may open new niches for this crop and help in intensification of farming system

The InterPro protein families and domains database: 20 years on

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan

The spatio-relational nature of urban innovation systems: Universities, knowledge intensive business service firms, and collaborative networks

The need to better identify the spatio-relational nature of urban innovation systems and spaces is increasingly acknowledged. The aim of this paper, therefore, is to provide an enhanced understanding of the knowledge networks existing between urban Knowledge Intensive Business Services firms (KIBS) and universities, which are often key components of such systems and spaces. Drawing on an analysis of urban KIBS firms and universities in the UK, it is found that the nature of firms, the location in which they are based, and the research intensity of their university partners are important determinants of the spatiality and localisation of the networks they form. The results show that the smallest urban KIBS firms have the highest propensity to engage in local links with universities, suggesting that they rely most significantly on their own urban innovation system for collaborative network ties. Keywords : innovation systems; urban innovation spaces; knowledge-based development; proximity; networks; KIBS; universities