PDB Goodies - a web-based GUI to manipulate the Protein Data Bank file

PDB Goodies is a web-based graphical user interface (GUI) to manipulate the Protein Data Bank file containing the three-dimensional atomic coordinates of protein structures. The program also allows users to save the manipulated three-dimensional atomic coordinate file on their local client system. These fragments are used in various stages of structure elucidation and analysis. This software is incorporated with all the three-dimensional protein structures available in the Protein Data Bank, which presently holds approximately 18 000 structures. In addition, this program works on a three-dimensional atomic coordinate file (Protein Data Bank format) uploaded from the client machine. The program is written using CGI/PERL scripts and is platform independent. The program PDB Goodies can be accessed over the World Wide Web at http:// 144.16.71.11/pdbgoodies/.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X-ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra-molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. (c) 2012 Wiley Periodicals, Inc.

Foot-mounted INS for everybody - an open-source embedded implementation

We present an open-source, realtime, embedded implementation of a foot-mounted, zero-velocity-update-aided inertial navigation system. The implementation includes both hardware design and software, uses off-the-shelf components and assembly methods, and features a standard USB interface. The software is written in C and can easily be modified to run user implemented algorithms. The hardware design and the software are released under permissive open-source licenses and production files, source code, documentation, and further resources are available at www.openshoe.org. The reproduction cost for a single unit is below $800, with the inertial measurement unit making up the bulk ($700). The form factor of the implementation is small enough for it to be integrated in the sole of a shoe. A performance evaluation of the system shows a position errors for short trajectories (<;100 [m]) of ± 0.2-1% of the traveled distance, depending on the shape of trajectory.

A Vision-Based Micro-Newton Static Force Sensor Using a Displacement-Amplifying Compliant Mechanism (DaCM)

A micro-newton static force sensor is presented here as a packaged product. The sensor, which is based on the mechanics of deformable objects, consists of a compliant mechanism that amplifies the displacement caused by the force that is to be measured. The output displacement, captured using a digital microscope and analyzed using image processing techniques, is used to calculate the force using precalibrated force-displacement curve. Images are scanned in real time at a frequency of 15 frames per second and sampled at around half the scanning frequency. The sensor was built, packaged, calibrated, and tested. It has simulated and measured stiffness values of 2.60N/m and 2.57N/m, respectively. The smallest force it can reliably measure in the presence of noise is about 2 mu N over a range of 1.4mN. The off-the-shelf digital microscope aside, all of its other components are purely mechanical; they are inexpensive and can be easily made using simple machines. Another highlight of the sensor is that its movable and delicate components are easily replaceable. The sensor can be used in aqueous environment as it does not use electric, magnetic, thermal, or any other fields. Currently, it can only measure static forces or forces that vary at less than 1Hz because its response time and bandwidth are limited by the speed of imaging with a camera. With a universal serial bus (USB) connection of its digital microscope, custom-developed graphical user interface (GUI), and related software, the sensor is fully developed as a readily usable product.

Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms

Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semiautomated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of similar to 1 mu N on an individual pillar and a total average force of similar to 7.68 mu N. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4Hz applying an average force of similar to 1.58 mu N on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment. (C) 2015 AIP Publishing LLC.

Using the system dynamics paradigm in teaching and learning technological university subjets

2nd International Conference on Education and New Learning Technologies

Criterios para la aplicación de coeficientes modificativos de la curva S-N de fatiga

[ES]Este Trabajo de Fin de Grado tiene como objeto crear un programa que sirva como herramienta para los cálculos en las propiedades a fatiga de una pieza. El conjunto del trabajo se centra en su creación mediante la herramienta Excel. El programa cuenta con tres diferentes pestañas: una para los datos que debe introducir el usuario, otra correspondiente a los cálculos y por último una en la que aparecen los resultados. El usuario debe conocer las propiedades de la probeta del material a ensayar, así como el rango de ciclos en el cual se va a trabajar (siempre en un rango de ciclos medio alto). A partir de estas informaciones de la probeta, y gracias a la curva de Basquin y la ecuación de Marin, el programa será capaz de obtener la curva de resistencia a fatiga correspondiente para la pieza. Se incluyen también casos especiales en los que se realicen tratamientos mecánicos de mejora, con una tensión límite del proceso. Para obtener la curva S-N de la pieza se pedirá información en la pestaña de interfaz con el usuario sobre distintas propiedades de la pieza, que permitan así calcular los valores de los coeficientes de Marín gracias a la base de datos que contiene el programa. El usuario tiene también la opción de introducir él mismo los valores de los coeficientes para así obtener una curva que se aproxime más a sus resultados experimentales. En resumen, la función del programa es la de ser una calculadora de la resistencia fatiga de la pieza a partir de los datos que se disponen de la probeta.

Design and implementation of a cloud computing adoption decision tool: Generating a cloud road

Migrating to cloud computing is one of the current enterprise challenges. This technology provides a new paradigm based on "on-demand payment" for information and communication technologies. In this sense, the small and medium enterprise is supposed to be the most interested, since initial investments are avoided and the technology allows gradual implementation. However, even if the characteristics and capacities have been widely discussed, entry into the cloud is still lacking in terms of practical, real frameworks. This paper aims at filling this gap, presenting a real tool already implemented and tested, which can be used as a cloud computing adoption decision tool. This tool uses diagnosis based on specific questions to gather the required information and subsequently provide the user with valuable information to deploy the business within the cloud, specifically in the form of Software as a Service (SaaS) solutions. This information allows the decision makers to generate their particular Cloud Road. A pilot study has been carried out with enterprises at a local level with a two-fold objective: To ascertain the degree of knowledge on cloud computing and to identify the most interesting business areas and their related tools for this technology. As expected, the results show high interest and low knowledge on this subject and the tool presented aims to readdress this mismatch, insofar as possible. Copyright: © 2015 Bildosola et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

一种笔式用户界面软件领域模型及其应用

笔式用户界面软件以其自然、高效的交互方式，在很多领域中有着广泛的应用笔式用户界面软件具有以交互为中心、用户个性化需求高的特点，由此也决定了用户在软件设计中的主导地位“用户为中心的设计的关键问题在于，如何使用户的思想如实地反映到设计中通过建立笔式用户界面软件特征模型PUIDM(the domain model for pen—based user interface software)，构造了一个连接用户与软件设计的平台．从上下文、软件实体、界面特征、体系结构等角度，对该模型的建立进行分析．并给出了相应的XML描述在此基础上，描述了用户使用该模型进行软件设计的过程实例表明，PUIDM能够正确引导用户进行设计，将用户意图充分地引入到软件设计和最终实现中，使软件满足可用性要求。

基于场景方法的笔式界面软件设计工具

为缩短的笔式用户界面软件的开发周期,让设计人员对软件的整体构思在开发过程中得以保持,提高团队人员的交流效率,提出了有关笔式界面软件的文档描述规范PUIML(pen-based user interface modeling language),并设计实现了一个笔交互的笔式用户界面软件设计工具。以笔式操作平台为软件平台,以PUIML为数据模型,采用基于场景设计的开发方法,为设计人员和用户提供自然的纸笔交互方式,设计结果形成PUIML形式的文档,通过主控程序执行。实践结果表明,使用PUI Maker可以解决笔式用户界面开发中存在的以开发人员为中心,原始设计与开发结果不一致等问题,提高了笔式界面软件的开发效率。

基于知网的文本推理

文本推理在自然语言处理的应用中占有极为重要的位置,本文介绍了基于知网的一种推理方法,该方法以语义网络的形式表示知网中的知识,利用“标记传递”实现推理。其特点是引入构造-融合模型的思想,动态生成知识结构,有引导地在文本词汇间建立推理路径。利用16种推理类的实例对其进行测试,结果表明在有足够上下文的条件下,该方法能够得出较为理想的推理,并且代价不高。

笔式界面软件快速开发工具

笔式界面软件快速开发工具Visual PBAP(pen-based application)Creator可以根据用户的个性化需求快速设计和开发相应软件,缩短开发周期。一方面,Visual PBAP Creator通过场景和UI编辑方便开发人员和用户确定需求;另一方面,自动生成代码可以缩短开发周期。Visual PBAP Creator以笔式操作平台为软件平台,采用基于场景设计的开发方法,设计结果形成XML格式的文档,通过解析这些XML文档最终生成C代码。实践表明,VisualPBAP Creator可以提高笔式界面软件的开发效率。

井间地震速度层析成像方法与软件系统

Crosshole Seismic tomography has been broadly studied and applied in the fields of resource exploration and engineering exploration because of its special observing manner and better resolution than normal seismic exploration. This thesis will state the theory and method of Crosshole Seismic tomography. Basing on the previous studies，the thesis studied the initial velocity model，ray-tracing method, and developed the three-dimension tomography software. All the cells that a ray passes through are of the same velocities if the paths from transmitters to receivers are straight. The cells that the each ray passes through are recorded, and rays that pass through each cell are calculated. The ray average velocity which passes through a cell is set as the cell velocity. Analogously we can make a initial node velocity model because the velocity sum is calculated on the all cells which own to a certain node, and the cell number is summed about each nodes，the ratio of the velocity sum to the all cells number is set as the node velocity. The inversion result from the initial node velocity model is better than that of the average velocity model. Ray-bending and Shortest Path for Rays (SPR) have shortcomings and limitations respectively. Using crooked rays obtained from SPR rather than straight lines as the starting point can not only avoid ray bending converging to the local minimum travel time path, but also settle the no smooth ray problem obtained by SPR. The hybrid method costs much computation time, which is roughly equal to the time that SPR expends. The Delphi development tool based on the Object Pascal language standard has an advantage of object-oriented. TDTOM (Three Dimensions Tomography) was developed by using Delphi from the DOS version. Improvement on the part of inversion was made, which bring faster convergence velocity. TDTOM can be used to do velocity tomography from the first arrival travel time of the seismic wave, and it has the good qualities of friendly user interface and convenient operation. TDTOM is used to reconstruct the velocity image for a set of crosshole data from Karamay Oil Field. The geological explanation is then given by comparing the inversion effects of different ray-tracing methods. High velocity zones mean the cover of oil reservoir, and low velocity zones correspond to the reservoir or the steam flooding layer.

地震勘探三维可视化方法研究与实现

This thesis mainly studies the technologies of 3-D seismic visualization and Graphic User Interface of seismic processing software. By studying Computer Graphics and 3-D geological modeling, the author designs and implements the visualization module of seismic data processing software using OpenGL and Motif. Setting seismic visualization flow as the subject, NURBS surface approximation and Delaunay Triangulation as the two different methods, the thesis discusses the key algorithms and technologies of seismic visualization and attempts to apply Octree Space Partitioning and Mip Mapping to enhance system performance. According to the research mentioned above, in view of portability and scalability, the author adopts Object-oriented Analysis and Object-oriented Design, uses standard C++ as programming language, OpenGL as 3-D graphics library and Motif as GUI developing tool to implement the seismic visualization framework on SGI Irix platform. This thesis also studies the solution of fluid equations in porous media. 2-D alternating direction implicit procedure has been turned into 3-D successive over relaxation iteration, which possesses such virtues as faster computing speed, faster convergence rate, better adaptability to heterogeneous media and less memory demanding.