Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Towards a model-driven engineering approach of data mining

Nowadays, data mining is based on low-level specications of the employed techniques typically bounded to a specic analysis platform. Therefore, data mining lacks a modelling architecture that allows analysts to consider it as a truly software-engineering process. Here, we propose a model-driven approach based on (i) a conceptual modelling framework for data mining, and (ii) a set of model transformations to automatically generate both the data under analysis (via data-warehousing technology) and the analysis models for data mining (tailored to a specic platform). Thus, analysts can concentrate on the analysis problem via conceptual data-mining models instead of low-level programming tasks related to the underlying-platform technical details. These tasks are now entrusted to the model-transformations scaffolding.

Integrating the development of data mining and data warehouses via model-driven engineering

Data mining is one of the most important analysis techniques to automatically extract knowledge from large amount of data. Nowadays, data mining is based on low-level specifications of the employed techniques typically bounded to a specific analysis platform. Therefore, data mining lacks a modelling architecture that allows analysts to consider it as a truly software-engineering process. Bearing in mind this situation, we propose a model-driven approach which is based on (i) a conceptual modelling framework for data mining, and (ii) a set of model transformations to automatically generate both the data under analysis (that is deployed via data-warehousing technology) and the analysis models for data mining (tailored to a specific platform). Thus, analysts can concentrate on understanding the analysis problem via conceptual data-mining models instead of wasting efforts on low-level programming tasks related to the underlying-platform technical details. These time consuming tasks are now entrusted to the model-transformations scaffolding. The feasibility of our approach is shown by means of a hypothetical data-mining scenario where a time series analysis is required.

Development and application of sensitive genome-wide platforms to study the genetic and epigenetic (DNA methylation) makeup of gametes and early bovine embryos

Pour ce projet, nous avons développé une plateforme pour l’analyse pangénomique de la méthylation de l’ADN chez le bovin qui est compatible avec des échantillons de petites tailles. Cet outil est utilisé pour étudier les caractéristiques génétiques et épigénétiques (méthylation de l’ADN) des gamètes soumis aux procédures de procréation médicalement assisitée et des embryons précoces. Dans un premier temps, une plateforme d’analyse de biopuces spécifiques pour l’étude de la méthylation de l’ADN chez l’espèce bovine a été développée. Cette plateforme a ensuite été optimisée pour produire des analyses pangénomiques de méthylation de l’ADN fiables et reproductibles à partir d’échantillons de très petites tailles telle que les embryons précoces (≥ 10 ng d’ADN a été utilisé, ce qui correspond à 10 blastocystes en expansion). En outre, cet outil a permis d’évaluer de façon simultanée la méthylation de l’ADN et le transcriptome dans le même échantillon, fournissant ainsi une image complète des profils génétiques et épigénétiques (méthylation de l’ADN). Comme preuve de concept, les profils comparatifs de méthylation de l’ADN spermatique et de blastocystes bovins ont été analysés au niveau de l’ensemble du génome. Dans un deuxième temps, grâce à cette plateforme, les profils globaux de méthylation de l’ADN de taureaux jumeaux monozygotes (MZ) ont été analysés. Malgré qu’ils sont génétiquement identiques, les taureaux jumeaux MZ ont des descendants avec des performances différentes. Par conséquent, l’hypothèse que le profil de méthylation de l’ADN spermatique de taureaux jumeaux MZ est différent a été émise. Dans notre étude, des différences significatives entre les jumeaux MZ au niveau des caractéristiques de la semence ainsi que de la méthylation de l’ADN ont été trouvées, chacune pouvant contribuer à l’obtention de performances divergentes incongrues des filles engendrées par ces jumeaux MZ. Dans la troisième partie de ce projet, la même plateforme a été utilisée pour découvrir les impacts d’une supplémentation à forte concentration en donneur de méthyle universel sur les embryons précoces bovins. La supplémentation avec de grandes quantités d’acide folique (AF) a été largement utilisée et recommandée chez les femmes enceintes pour sa capacité bien établie à prévenir les malformations du tube neural chez les enfants. Cependant, plus récemment, plusieurs études ont rapporté des effets indésirables de l’AF utilisé à des concentrations élevées, non seulement sur le développement de l’embryon, mais aussi chez les adultes. Au niveau cellulaire, l’AF entre dans le métabolisme monocarboné, la seule voie de production de S-adénosyl méthionine (SAM), un donneur universel de groupements méthyles pour une grande variété de biomolécules, y compris l’ADN. Par conséquent, pour résoudre cette controverse, une forte dose de SAM a été utilisée pour traiter des embryons produits in vitro chez le bovin. Ceci a non seulement permis d’influencer le phénotype des embryons précoces, mais aussi d’avoir un impact sur le transcriptome et le méthylome de l’ADN. En somme, le projet en cours a permis le développement d’une plateforme d’analyse de la méthylation de l’ADN à l’échelle du génome entier chez le bovin à coût raisonnable et facile à utiliser qui est compatible avec les embryons précoces. De plus, puisque c’est l’une des premières études de ce genre en biologie de la reproduction bovine, ce projet avait trois objectifs qui a donné plusieurs nouveaux résultats, incluant les profils comparatifs de méthylation de l’ADN au niveau : i) blastocystes versus spermatozoïdes ; ii) semence de taureaux jumeaux MZ et iii) embryons précoces traités à de fortes doses de SAM versus des embryons précoces non traités.

Busway platform bus capacity analysis

Bus Rapid Transit (BRT), because of its operational flexibility and simplicity, is rapidly gaining popularity with urban designers and transit planners. Earlier BRTs were bus shared lane or bus only lane, which share the roadway with general and other forms of traffic. In recent time, more sophisticated designs of BRT have emerged, such as busway, which has separate carriageway for buses and provides very high physical separation of buses from general traffic. Line capacities of a busway are predominately dependent on bus capacity of its stations. Despite new developments in BRT designs, the methodology of capacity analysis is still based on traditional principles of kerbside bus stop on bus only lane operations. Consequently, the tradition methodology lacks accounting for various dimensions of busway station operation, such as passenger crowd, passenger walking and bus lost time along the long busway station platform. This research has developed a purpose made bus capacity analysis methodology for busway station analysis. Extensive observations of kerbside bus stops and busway stations in Brisbane, Australia were made and differences in their operation were studied. A large scale data collection was conducted using the video recording technique at the Mater Hill Busway Station on the South East Busway in Brisbane. This research identified new parameters concerning busway station operation, and through intricate analysis identified the elements and processes which influence the bus dwell time at a busway station platform. A new variable, Bus lost time, was defined and its quantitative descriptions were established. Based on these finding and analysis, a busway station platform bus capacity methodology was developed, comprising of new models for busway station lost time, busway station dwell time, busway station loading area bus capacity, and busway station platform bus capacity. The new methodology not only accounts for passenger boarding and alighting, but also covers platform crowd and bus lost time in station platform bus capacity estimation. The applicability of this methodology was shown through demonstrative examples. Additionally, these examples illustrated the significance of the bus lost time variable in determining station capacities.

Appendiceal sonography in children: A retrospective analysis as a platform for potential implementation of diagnostic categories

- Background Sonography is an important diagnostic tool in children with suspected appendicitis. Reported accuracy and appendiceal visualisation rates vary significantly, as does the management of equivocal ultrasound findings. The aim of this study was to audit appendiceal sonography at a tertiary children's hospital, and provide baseline data for a future prospective study. - Summary of work Records of children who underwent ultrasound studies for possible appendicitis between January 2008 and December 2010 were reviewed. Variables included patient demographics, sonographic appendix characteristics, and secondary signs. Descriptive statistics and analysis using ANOVA, Mann-Whitney U test, and ROC curves were performed. Mater Human Research Ethic Committee approval was granted. - Summary of results There were 457 eligible children. Using a dichotomous diagnostic model (including equivocal results), sensitivity was 89.6%, specificity 91.6%, and diagnostic yield of 40.7%. ROC curve analysis of a 6mm diameter cut-off was 0.88 AUC (95% CI 0.80 to 0.95). - Discussion and conclusions Sonography is an accurate test for acute appendicitis in children, with a high sensitivity and negative predictive value. A diameter of 6mm as an absolute cut-off in a binary model can lead to false findings. Results were compared with available literature. Recent publications propose categorising diameter1 and integrating secondary signs2 to improve accuracy and provide more meaningful results to clinicians. This study will be a benchmark for future studies with multiple diagnostic categorisation.

Modelling, Design and Analysis of Low Frequency Platform for Attenuating Micro-Vibration in Spacecraft

One of the most important factors that affect the pointing of precision payloads and devices in space platforms is the vibration generated due to static and dynamic unbalanced forces of rotary equipments placed in the neighborhood of payload. Generally, such disturbances are of low amplitude, less than 1 kHz, and are termed as ‘micro-vibrations’. Due to low damping in the space structure, these vibrations have long decay time and they degrade the performance of payload. This paper addresses the design, modeling and analysis of a low frequency space frame platform for passive and active attenuation of micro-vibrations. This flexible platform has been designed to act as a mount for devices like reaction wheels, and consists of four folded continuous beams arranged in three dimensions. Frequency and response analysis have been carried out by varying the number of folds, and thickness of vertical beam. Results show that lower frequencies can be achieved by increasing the number of folds and by decreasing the thickness of the blade. In addition, active vibration control is studied by incorporating piezoelectric actuators and sensors in the dynamic model. It is shown using simulation that a control strategy using optimal control is effective for vibration suppression under a wide variety of loading conditions.

Finite Element Analysis of Deformed Legs of Offshore Platform Structures

The element stiffness matrix of the equivalent beam or pipe element of the deformed leg of the platform is derived by the finite element method. The stresses and displacements of some damaged components are calculated, and the numeri-cal solutions agree well with those obtained by the fine mesh finite element method. Finally, as an application of this method, the stresses of some platform structures are calculated and analyzed.

Hill Instability Analysis Of Tlp Tether Subjected To Combined Platform Surge And Heave Motions

This paper presents the Hill instability analysis of Tension Leg Platform (TLP) tether it, deep sea. The 2-D nonlinear beam model which is Undergoing Coupled axial and transverse vibrations, is applied. The governing equations are reduced to nonlinear Hill equation by use of the Galerkin's method and the modes superposition principle. The Hill instability charted Lip to large parameters is obtained. An important parameter M is defined and can he expressed as the functions of tether length, the platform surge and heave motion amplitudes. Some example studies are performed for various environmental conditions. The results demonstrate that the nonlinear coupling between the axial and transverse vibrations has a significant effect on the response of structure.. It needs to be considered for the accurate dynamic analysis of long TLP tether subjected to the combined platform surge and heave motions.

Nonlinear analysis of pile foundation jacket platform

In this paper, the nonlinear collapse of the BOHAI-8 pile foundation jacket platform has been analyzed. The ultimate load and collapse process of two computational models of the structure are given. One model is of fixed support whose length is eight times the pile leg diameter and the other considers the nonlinearity of the soil-pile interaction.

World Cultures in English(es) at the School of Arts and Humanities Library, University of Lisbon: the Communication Platform Architecture and Its Critical Analysis

We will consider the architecture of the communication platform prototype, "World Cultures in English(es)" (WCE), in relation to the interaction among different types of media and audiences. Such an architecture has emphasized the need for an interdisciplinary team of scholars, librarians, and Information Technology experts who have conceived the prototype. This prototype was developed using PHP and MySQL, and is based on the University of Lisbon server. The "World Cultures in English(es)" is an Open Access platform bringing together different types of documents—written, audio, visual, multimedia, and electronic—and aims at educational, cultural, social, and economic inclusiveness, namely in terms of users with special needs. The WCE platform strongly implies social commitment through reliable information and forms of communication adequate to different kinds of audiences. The "World Cultures in English(es)" prototype will be tested by different audiences from different schools and universities, leading to the necessary adjustments.

Business model analysis of Mobitto: How to solve the chicken and egg problem of a multi-sided platform?

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform

The availability of crop specimens archived in herbaria and old seed collections represent valuable resources for the analysis of plant genetic diversity and crop domestication. The ability to extract ancient DNA (aDNA) from such samples has recently allowed molecular genetic investigations to be undertaken in ancient materials. While analyses of aDNA initially focused on the use of markers which occur in multiple copies such as the internal transcribed spacer region (ITS) within ribosomal DNA and those requiring amplification of short DNA regions of variable length such as simple sequence repeats (SSRs), emphasis is now moving towards the genotyping of single nucleotide polymorphisms (SNPs), traditionally undertaken in aDNA by Sanger sequencing. Here, using a panel of barley aDNA samples previously surveyed by Sanger sequencing for putative causative SNPs within the flowering-time gene PPD-H1, we assess the utility of the Kompetitive Allele Specific PCR (KASP) genotyping platform for aDNA analysis. We find KASP to out-perform Sanger sequencing in the genotyping of aDNA samples (78% versus 61% success, respectively), as well as being robust to contamination. The small template size (≥46 bp) and one-step, closed-tube amplification/genotyping process make this platform ideally suited to the genotypic analysis of aDNA, a process which is often hampered by template DNA degradation and sample cross-contamination. Such attributes, as well as its flexibility of use and relatively low cost, make KASP particularly relevant to the genetic analysis of aDNA samples. Furthermore, KASP provides a common platform for the genotyping and analysis of corresponding SNPs in ancient, landrace and modern plant materials. The extended haplotype analysis of PPD-H1 undertaken here (allelic variation at which is thought to be important for the spread of domestication and local adaptation) provides further resolution to the previously identified geographic cline of flowering-time allele distribution, illustrating how KASP can be used to aid genetic analyses of aDNA from plant species. We further demonstrate the utility of KASP by genotyping ten additional genetic markers diagnostic for morphological traits in barley, shedding light on the phenotypic traits, alleles and allele combinations present in these unviable ancient specimens, as well as their geographic distributions.