SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

SOCR Analyses: Implementation and Demonstration of a New Graphical Statistics Educational Toolkit

The web-based, Java-written SOCR (Statistical Online Computational Resource) tools have been utilized in many undergraduate and graduate level statistics courses for seven years now (Dinov 2006; Dinov et al. 2008b). It has been proven that these resources can successfully improve students' learning (Dinov et al. 2008b). Being first published online in 2005, SOCR Analyses is a somewhat new component and it concentrate on data modeling for both parametric and non-parametric data analyses with graphical model diagnostics. One of the main purposes of SOCR Analyses is to facilitate statistical learning for high school and undergraduate students. As we have already implemented SOCR Distributions and Experiments, SOCR Analyses and Charts fulfill the rest of a standard statistics curricula. Currently, there are four core components of SOCR Analyses. Linear models included in SOCR Analyses are simple linear regression, multiple linear regression, one-way and two-way ANOVA. Tests for sample comparisons include t-test in the parametric category. Some examples of SOCR Analyses' in the non-parametric category are Wilcoxon rank sum test, Kruskal-Wallis test, Friedman's test, Kolmogorov-Smirnoff test and Fligner-Killeen test. Hypothesis testing models include contingency table, Friedman's test and Fisher's exact test. The last component of Analyses is a utility for computing sample sizes for normal distribution. In this article, we present the design framework, computational implementation and the utilization of SOCR Analyses.

Frameworks for enhancing temporal interface behaviour through software architectural design

The work reported in this thesis is concerned with understanding aspects of temporal behaviour. A large part of the thesis is based on analytical studies of temporal properties and interface and architectural concerns. The main areas covered include: i. analysing long-term human processes and the impact of interruptions and delays ii. investigating how infrastructures can be designed to support synchronous fast pace activity iii.design of the Getting-to-Know (GtK) experimental notification server The work is motivated by the failure of many collaborative systems to effectively manage the temporal behaviour at the interface level, as they often assume that the interaction is taking place over fast, reliable local area networks. However, the Web has challenged this assumption and users are faced with frequent network-related delays. The nature of cooperative work increases the importance of timing issues. Collaborative users require both rapid feedback of their own actions and timely feedthrough of other actions. Although it may appear that software architectures are about the internals of system design and not a necessary concern for the user interface, internal details do show up at the surface in non-functional aspects, such as timing. The focus of this work is on understanding the behavioural aspects and how they are influenced by the infrastructure. The thesis has contributed to several areas of research: (a)the study of long-term work processes generated a trigger analysis technique for task decomposition in HCI (b)the analysis of architectures was later applied to investigate architectural options for mobile interfaces (c)the framework for notification servers commenced a design vocabulary in CSCW for the implementation of notification services, with the aim of improving design (d)the impedance matching framework facilitate both goal-directed feedthrough and awareness In particular, (c) and (d) have been exercised in the development of the GtK separable notification server

ClassRank subject recommendations

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2008.Includes bibliographical references (p. 51).Undergraduate students at M.I.T. typically utilize three resources when selecting subjects: course specific evaluations, faculty advisors, and peers. While these resources have distinct advantages, they are all limited in scope. The ClassRank web application has been developed to bridge the gap between these resources by providing a simple institute-wide system for undergraduate students to evaluate and rate subjects. The application also provides a solid platform to build new tools utilizing subject evaluation data. To extend the initial core functionality of the ClassRank system, a rating-based subject recommendation algorithm was added to offer students an unbiased perspective on potential subjects of interest. Developed as a Ruby on Rails plugin and then integrated into ClassRank, the recommendation algorithm analyzes subject ratings and provides personalized suggestions to students about subjects that would likely fit their interests and educational goals. The ClassRank web application and recommendation algorithm will provide the M.I.T. undergraduate student body with a unique and invaluable resource for subject selection.by William G. Tetler.M.Eng

EsaCake: a semantic software enviroment for sharing software proyects knowledge based on the ESA software methodology

Proceedings of: The Third International Conference on Internet and Web Applications and Services (ICIW 2008), 8-13 June 2008, Athens, GreeceThere is an increasing need of defining standards at the beginning of any engineering project. The correct specification of standards has become essential in software development in order to handle correctly the development of projects. Nowadays the need to define standards at the outset of any engineering project is more evident than ever. The specification of standards has become an essential topic which universities try to teach to software engineering students. In fact, software creation processes are required intrinsically to be produced according to a systematic methodology to enable constant control during the project life cycle. This paper presents a new environment that enables semantic and social interaction of documentation produced during software development processes.This work is supported by the Spanish Ministry of Industry, Tourism, and Commerce under the project GODO (FIT-340000-2007-134), under the PIBES project of the Spanish Committee of Education & Science (TEC2006-12365-C02-01) and the MID-CBR project of the Spanish Committee of Education & Science (TIN2006-15140-C03-02).Publicad

E-MDAV: A Framework for Developing Data-Intensive Web Applications

The ever-increasing adoption of innovative technologies, such as big data and cloud computing, provides significant opportunities for organizations operating in the IT domain, but also introduces considerable challenges. Such innovations call for development processes that better align with stakeholders needs and expectations. In this respect, this paper introduces a development framework based on the OMG's Model Driven Architecture (MDA) that aims to support the development lifecycle of data-intensive web applications. The proposed framework, named E-MDAV (Extended MDA-VIEW), defines a methodology that exploits a chain of model transformations to effectively cope with both forward- and reverse-engineering aspects. In addition, E-MDAV includes the specification of a reference architecture for driving the implementation of a tool that supports the various professional roles involved in the development and maintenance of data-intensive web applications. In order to evaluate the effectiveness of the proposed E-MDAV framework, a tool prototype has been developed. E-MDAV has then been applied to two different application scenarios and the obtained results have been compared with historical data related to the implementation of similar development projects, in order to measure and discuss the benefits of the proposed approach