Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Pinocchio: Bringing Reflection to Life with First-Class Interpreters

To support development tools like debuggers, runtime systems need to provide a meta-programming interface to alter their semantics and access internal data. Reflective capabilities are typically fixed by the Virtual Machine (VM). Unanticipated reflective features must either be simulated by complex program transformations, or they require the development of a specially tailored VM. We propose a novel approach to behavioral reflection that eliminates the barrier between applications and the VM by manipulating an explicit tower of first-class interpreters. Pinocchio is a proof-of-concept implementation of our approach which enables radical changes to the interpretation of programs by explicitly instantiating subclasses of the base interpreter. We illustrate the design of Pinocchio through non-trivial examples that extend runtime semantics to support debugging, parallel debugging, and back-in-time object-flow debugging. Although performance is not yet addressed, we also discuss numerous opportunities for optimization, which we believe will lead to a practical approach to behavioral reflection.

Copyright, Interfaces, and a Possible Atlantic Divide

Recent copyright cases on both sides of the Atlantic focused on important interoperability issues. While the decision by the Court of Justice of the European Union in SAS Institute, Inc.v. World Programming Ltd. assessed data formats under the EU Software Directive, the ruling by the Northern District of California Court in Oracle America, Inc. v. Google Inc. dealt with application programming interfaces. The European decision is rightly celebrated as a further important step in the promotion of interoperability in the EU. This article argues that, despite appreciable signs of convergence across the Atlantic, the assessment of application programming interfaces under EU law could still turn out to be quite different, and arguably much less pro-interoperability, than under U.S. law.

Customer training, oriented toward the customer in the spanish affiliate

On that date , the Spanish affiliate offered for the 1st. time to its customers courses oriented toward the user, not the product, within the area of programming, in the subarea of application programming

Introducción a la informática para estudiantes de enseñanza secundaria mediante programación de aplicaciones móviles

Este trabajo contiene el diseño y análisis de dos modalidades de docencia de programación de aplicaciones móviles, con el objetivo de aumentar el interés de los estudiantes de enseñanza secundaria por la Ingeniería Informática. Primeramente se analizó la estructura y el contenido de las diferentes materias relacionadas con la informática que existen actualmente en la educación secundaria en España, con el fin de localizar las carencias del currículo. Estas carencias principales son: la falta de reconocimiento de la Ingeniería informática al mismo nivel que el resto de ingenierías y una falta de contenidos relacionados con el desarrollo de software, tanto a nivel de programación como de diseño. A continuación, una vez analizados diferentes posibilidades de entornos con los que desarrollar dichos cursos, se diseñaron los dos modelos de docencia utilizando App Inventor como herramienta conductora, con los que poder cubrir esos conocimientos. El primer modelo consiste en un curso de cuatro semanas a impartir directamente en el centro, mientras que el segundo se trata de un taller de una mañana a impartir en la Escuela Técnica Superior de Ingenieros Informáticos de la Universidad Politécnica de Madrid. De los resultados de esos modelos se han obtenidos resultados muy positivos en cuanto al incremento de los conocimientos de los alumnos sobre informática, además de aumentar su interés por la Ingeniería Informática y obtener una visión más ajustada a la realidad de la misma.---ABSTRACT---This work details the design and realization of a workshop and a course for teaching mobile application programming to Spanish high school students, with the aim of increasing their interest in Computing. In order to locate the shortcomings of the curriculum, the structure and contents of various subjects related to Computing in currently secondary education in Spain were analyzed. The results show a lack of recognition of computer engineering at the same level as the rest of engineering disciplines and a lack of content related to software development, both in terms of programming and design. Then, after analyzing existing programming environments available for covering the basic programming objectives, App Inventor was chosen as mobile programming environment for both teaching activities (the workshop and the course). The first activity consists of a four-week course to teach directly in the high school, while the second one is a 4-hour workshop to be held at the university. The workshop and the course were carried out with students of two secondary schools, obtaining very positive results in terms of increasing students’ knowledge about computers, increasing their interest in Computing, and making them get a more accurate vision of the discipline.

SimuMap: a computational system for spatial modelling

The paper presents a computational system based upon formal principles to run spatial models for environmental processes. The simulator is named SimuMap because it is typically used to simulate spatial processes over a mapped representation of terrain. A model is formally represented in SimuMap as a set of coupled sub-models. The paper considers the situation where spatial processes operate at different time levels, but are still integrated. An example of such a situation commonly occurs in watershed hydrology where overland flow and stream channel flow have very different flow rates but are highly related as they are subject to the same terrain runoff processes. SimuMap is able to run a network of sub-models that express different time-space derivatives for water flow processes. Sub-models may be coded generically with a map algebra programming language that uses a surface data model. To address the problem of differing time levels in simulation, the paper: (i) reviews general approaches for numerical solvers, (ii) considers the constraints that need to be enforced to use more adaptive time steps in discrete time specified simulations, and (iii) scaling transfer rates in equations that use different time bases for time-space derivatives. A multistep scheme is proposed for SimuMap. This is presented along with a description of its visual programming interface, its modelling formalisms and future plans. (C) 2003 Elsevier Ltd. All rights reserved.

Multi-threaded parallel numerical modelling of femtosecond pulse propagation in laser machining

Femtosecond laser microfabrication has emerged over the last decade as a 3D flexible technology in photonics. Numerical simulations provide an important insight into spatial and temporal beam and pulse shaping during the course of extremely intricate nonlinear propagation (see e.g. [1,2]). Electromagnetics of such propagation is typically described in the form of the generalized Non-Linear Schrdinger Equation (NLSE) coupled with Drude model for plasma [3]. In this paper we consider a multi-threaded parallel numerical solution for a specific model which describes femtosecond laser pulse propagation in transparent media [4, 5]. However our approach can be extended to similar models. The numerical code is implemented in NVIDIA Graphics Processing Unit (GPU) which provides an effitient hardware platform for multi-threded computing. We compare the performance of the described below parallel code implementated for GPU using CUDA programming interface [3] with a serial CPU version used in our previous papers [4,5]. © 2011 IEEE.

Semantikos: proposta de interfaces para aplicativo mediador de técnica de diferencial semântico em mobile tablet

This research aims to systematize a proposal of developing a mobile tablet application in order to help implementing the Semantic Differential technique – SD, under the approach of Participatory Design. In 1975, Osgood et al. created the Semantic Differential technique. Since then, many experiments use it to measure the affective perception of individuals concerning objects and concepts by means of compounded scales of bipolar adjectives, based on the theoretical models that support the technique: the conductible, spatial and metric models. During the application of the technique with potential users, the researcher must simultaneously manage several contexts, that is, audio recorder, when authorized, and observe and record spontaneous reports of the respondent. It is noticeable that often occurs a cognitive overload during this event. Thus, the use of a single application whose interface is assigned to its users and respondents could assist researchers in applying the SD technique. This research aimed to understand the processes inherent to the task of implementing the Semantic Differential technique and obeyed the following steps: a) training of users, b) background questionnaire c) interview with Focus Group, and d) cooperative evaluation. Besides these procedures, one can also observe the degrees of facilitation or difficulty concerning the use of the conventional model, which is the development and application of scales with the aid of printed material, pencil, pens, clipboards, and recorder software for editing the document and data analysis. This paper comprises reactions and impressions from the experiences of users of SD technique. Considering the data recollected from the user’s observation, the hypothesis of the experiment proved to be right. It means that the development of the application for mobile tablet employing the technique of Semantic Differential is viable, since it assembles all the steps in one only tool, increases the accomplishment of the task between user/researcher and user/respondent resulting in their mutual satisfaction.

Usability and Security in Medication Administration Applications

The traditional process of filling the medicine trays and dispensing the medicines to the patients in the hospitals is manually done by reading the printed paper medicine chart. This process can be very strenuous and error-prone, given the number of sub-tasks involved in the entire workflow and the dynamic nature of the work environment. Therefore, efforts are being made to digitalise the medication dispensation process by introducing a mobile application called Smart Dosing application. The introduction of the Smart Dosing application into hospital workflow raises security concerns and calls for security requirement analysis. This thesis is written as a part of the smart medication management project at Embedded Systems Laboratory, A° bo Akademi University. The project aims at digitising the medicine dispensation process by integrating information from various health systems, and making them available through the Smart Dosing application. This application is intended to be used on a tablet computer which will be incorporated on the medicine tray. The smart medication management system include the medicine tray, the tablet device, and the medicine cups with the cup holders. Introducing the Smart Dosing application should not interfere with the existing process carried out by the nurses, and it should result in minimum modifications to the tray design and the workflow. The re-designing of the tray would include integrating the device running the application into the tray in a manner that the users find it convenient and make less errors while using it. The main objective of this thesis is to enhance the security of the hospital medicine dispensation process by ensuring the security of the Smart Dosing application at various levels. The methods used for writing this thesis was to analyse how the tray design, and the application user interface design can help prevent errors and what secure technology choices have to be made before starting the development of the next prototype of the Smart Dosing application. The thesis first understands the context of the use of the application, the end-users and their needs, and the errors made in everyday medication dispensation workflow by continuous discussions with the nursing researchers. The thesis then gains insight to the vulnerabilities, threats and risks of using mobile application in hospital medication dispensation process. The resulting list of security requirements was made by analysing the previously built prototype of the Smart Dosing application, continuous interactive discussions with the nursing researchers, and an exhaustive stateof- the-art study on security risks of using mobile applications in hospital context. The thesis also uses Octave Allegro method to make the readers understand the likelihood and impact of threats, and what steps should be taken to prevent or fix them. The security requirements obtained, as a result, are a starting point for the developers of the next iteration of the prototype for the Smart Dosing application.

Usability and Security in Medication. Administration Applications

The traditional process of filling the medicine trays and dispensing the medicines to the patients in the hospitals is manually done by reading the printed paper medicinechart. This process can be very strenuous and error-prone, given the number of sub-tasksinvolved in the entire workflow and the dynamic nature of the work environment.Therefore, efforts are being made to digitalise the medication dispensation process byintroducing a mobile application called Smart Dosing application. The introduction ofthe Smart Dosing application into hospital workflow raises security concerns and callsfor security requirement analysis. This thesis is written as a part of the smart medication management project at EmbeddedSystems Laboratory, A˚bo Akademi University. The project aims at digitising the medicine dispensation process by integrating information from various health systems, and making them available through the Smart Dosing application. This application is intended to be used on a tablet computer which will be incorporated on the medicine tray. The smart medication management system include the medicine tray, the tablet device, and the medicine cups with the cup holders. Introducing the Smart Dosing application should not interfere with the existing process carried out by the nurses, and it should result in minimum modifications to the tray design and the workflow. The re-designing of the tray would include integrating the device running the application into the tray in a manner that the users find it convenient and make less errors while using it. The main objective of this thesis is to enhance the security of the hospital medicine dispensation process by ensuring the security of the Smart Dosing application at various levels. The methods used for writing this thesis was to analyse how the tray design, and the application user interface design can help prevent errors and what secure technology choices have to be made before starting the development of the next prototype of the Smart Dosing application. The thesis first understands the context of the use of the application, the end-users and their needs, and the errors made in everyday medication dispensation workflow by continuous discussions with the nursing researchers. The thesis then gains insight to the vulnerabilities, threats and risks of using mobile application in hospital medication dispensation process. The resulting list of security requirements was made by analysing the previously built prototype of the Smart Dosing application, continuous interactive discussions with the nursing researchers, and an exhaustive state-of-the-art study on security risks of using mobile applications in hospital context. The thesis also uses Octave Allegro method to make the readers understand the likelihood and impact of threats, and what steps should be taken to prevent or fix them. The security requirements obtained, as a result, are a starting point for the developers of the next iteration of the prototype for the Smart Dosing application.

Uma arquitetura de referência para o processamento distribuído de stream de dados em soluções analíticas de near real-time

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Elétrica, 2015.

DistributedCL: middleware de processamento distribuído em GPU com interface da API OpenCL.

Este trabalho apresenta a proposta de um middleware, chamado DistributedCL, que torna transparente o processamento paralelo em GPUs distribuídas. Com o suporte do middleware DistributedCL uma aplicação, preparada para utilizar a API OpenCL, pode executar de forma distribuída, utilizando GPUs remotas, de forma transparente e sem necessidade de alteração ou nova compilação do seu código. A arquitetura proposta para o middleware DistributedCL é modular, com camadas bem definidas e um protótipo foi construído de acordo com a arquitetura, onde foram empregados vários pontos de otimização, incluindo o envio de dados em lotes, comunicação assíncrona via rede e chamada assíncrona da API OpenCL. O protótipo do middleware DistributedCL foi avaliado com o uso de benchmarks disponíveis e também foi desenvolvido o benchmark CLBench, para avaliação de acordo com a quantidade dos dados. O desempenho do protótipo se mostrou bom, superior às propostas semelhantes, tendo alguns resultados próximos do ideal, sendo o tamanho dos dados para transmissão através da rede o maior fator limitante.

Design and Verification of the Programming Circuit in an Application-Specific FPGA

In this paper we present a methodology and its implementation for the design and verification of programming circuit used in a family of application-specific FPGAs that share a common architecture. Each member of the family is different either in the types of functional blocks contained or in the number of blocks of each type. The parametrized design methodology is presented here to achieve this goal. Even though our focus is on the programming circuitry that provides the interface between the FPGA core circuit and the external programming hardware, the parametrized design method can be generalized to the design of entire chip for all members in the FPGA family. The method presented here covers the generation of the design RTL files and the support files for synthesis, place-and-route layout and simulations. The proposed method is proven to work smoothly within the complete chip design methodology. We will describe the implementation of this method to the design of the programming circuit in details including the design flow from the behavioral-level design to the final layout as well as the verification. Different package options and different programming modes are included in the description of the design. The circuit design implementation is based on SMIC 0.13-micron CMOS technology.

Hammer: an Android based application for end-user industrial robot programming

This paper presents a novel tablet based end-user interface for industrial robot programming (called Hammer). This application makes easier to program tasks for industrial robots like polishing, milling or grinding. It is based on the Scratch programming language, but specifically design and created for Android OS. It is a visual programming concept that allows non-skilled programmer operators to create programs. The application also allows to monitor the tasks while it is being executed by overlapping real time information through augmented reality. The application includes a teach pendant screen that can be customized according to the operator needs at every moment.