Scripting Interface Research Articles

Visualization of the Differential Transition State Stabilization within the Active Site Environment

Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5) is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.

The RUMBA software: tools for neuroimaging data analysis.

The enormous scale and complexity of data sets in functional neuroimaging makes it crucial to have well-designed and flexible software for image processing, modeling, and statistical analysis. At present, researchers must choose between general purpose scientific computing environments (e.g., Splus and Matlab), and specialized human brain mapping packages that implement particular analysis strategies (e.g., AFNI, SPM, VoxBo, FSL or FIASCO). For the vast majority of users in Human Brain Mapping and Cognitive Neuroscience, general purpose computing environments provide an insufficient framework for a complex data-analysis regime. On the other hand, the operational particulars of more specialized neuroimaging analysis packages are difficult or impossible to modify and provide little transparency or flexibility to the user for approaches other than massively multiple comparisons based on inferential statistics derived from linear models. In order to address these problems, we have developed open-source software that allows a wide array of data analysis procedures. The RUMBA software includes programming tools that simplify the development of novel methods, and accommodates data in several standard image formats. A scripting interface, along with programming libraries, defines a number of useful analytic procedures, and provides an interface to data analysis procedures. The software also supports a graphical functional programming environment for implementing data analysis streams based on modular functional components. With these features, the RUMBA software provides researchers programmability, reusability, modular analysis tools, novel data analysis streams, and an analysis environment in which multiple approaches can be contrasted and compared. The RUMBA software retains the flexibility of general scientific computing environments while adding a framework in which both experts and novices can develop and adapt neuroimaging-specific analyses.

Generative and incremental implementation for a scripting interface

Many systems may benefit from scripting support, but the implementation of it is seldom trivial, especially if the system has not originally been developed with scripting support in mind. In this paper we describe a generative, incremental process for creating an intuitive Python interface to a large, hierarchic COM library. The approach is illuminated with the original, real-life case study.

A web-enabled PDM system in a collaborative design environment

For manufacturers, profitability always depends upon the orderly and efficient development, production and distribution of their products. Product Data Management (PDM) is a unique technology, which integrates and manages all applications, information and processes that define a product, from design to manufacture, and to end-user support. The recent advance in Web-based technologies has the potential to greatly enhance PDM's functionality and capability, and to overcome the obstacles that many traditional PDM systems are confronted. It is found in this research that a multi-tiered, collaborative environment with advanced Web technologies is well suited for a PDM system to operate in. In this research, the overall architecture of a Web-enabled PDM system in the Collaborative Design environment is proposed. The architecture is based on the use of open data standards to allow users on a wide variety of platforms to access the product data and other related information. It enables product visualisation using interactive 3-D graphics by the disparate members of a collaborative PDM team. Integral elements of the proposed architecture include object-oriented database (OODB), object-oriented DataBase management system, common gateway interface script and visualisation applications. The use of standard for the exchange of product model data standard effectively integrates different CAD and PDM systems. The advantage of OODB is its efficiency and effectiveness in handling complex data structures often found in engineering applications. Virtual reality modelling language provides a 3-D dynamic visualisation capability. The system, which is implemented using Microsoft Visual Basic, runs in the Windows environment with the basic Internet connections.

An object-oriented scripting interface to a legacy electronic structure code

The authors have created an object-oriented scripting interface to a mature density functional theory code. The interface gives users a high-level, flexible handle on the code without rewriting the underlying number-crunching code. The authors also discuss the design issues and advantages of homogeneous interfaces.

A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via Internet.

Proteome analysis by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry, in combination with protein chemical methods, is a powerful approach for the analysis of the protein composition of complex biological samples. Data organization is imperative for efficient handling of the vast amount of information generated. Thus we have constructed a 2-D PAGE database to store and compare protein patterns of cell-associated and culture-supernatant proteins of different mycobacterial strains. In accordance with the guidelines for federated 2-DE databases, we developed a program that generates a dynamic 2-D PAGE database for the World-Wide-Web to organise and publish, via the internet, our results from proteome analysis of different Mycobacterium tuberculosis as well as Mycobacterium bovis BCG strains. The uniform resource locator for the database is http://www.mpiib-berlin.mpg.de/2D-PAGE and can be read with a Java compatible browser. The interactive hypertext markup language documents displayed are generated dynamically in each individual session from a rational data file, a 2-D gel image file and a map file describing the protein spots as polygons. The program consists of common gateway interface scripts written in PERL, minimizing the administrative workload of the database. Furthermore, the database facilitates not only interactive use, but also worldwide active participation of other scientific groups with their own data, requiring only minimal computer hardware and knowledge of information technology.

Web seismic Un ∗x: making seismic reflection processing more accessible

Web Seismic Un ∗x is a browser-based user interface for the Seismic Un ∗x freeware developed at Colorado School of Mines. The interface allows users to process and display seismic reflection data from any remote platform that runs a graphical Web browser. Users access data and create processing jobs on a remote server by completing form-based Web pages whose Common Gateway Interface scripts are written in Perl. These scripts supply parameters, manage files, call Seismic Un ∗x routines and return data plots. The interface was designed for undergraduate commuter students taking geophysics courses who need to: (a) process seismic data and other time series as a class using computers in campus teaching labs and (b) complete course assignments at home. Students from an undergraduate applied geophysics course tested the Web user interface while completing laboratory assignments in which they acquired and processed common-depth-point seismic reflection data into a subsurface image. This freeware, which will be publicly available by summer 1999, was developed and tested on a Solaris 2.5 server and will be ported to other versions of Unix, including Linux.

Peer Support on the Web

SUMMARY While independent learning is an increasingly important part of university experience, students are often unaware of what it fully involves. Acquiring such an understanding through experiential learning facilitated by student mentors is one channel offered by London Guildhall University Students’ Union. This case study considers the reasons for its limited success and the appropriateness of introducing a peer support website to broaden student interest in learning independently. The website, still in its pilot stage, is being developed as an active learning exercise by and for peer supporters. Attendant problems discussed in this paper include: 1. constraints on developing a website for promoting learning and study skills, which is non‐tutorial in character; 2. technical constraints, including the absence of dynamic interface scripts; and 3. developing channels for student feedback and further contact. An evaluation of the website by students suggests that its development as a student‐led, student‐centred forum for independent learning is especially pertinent to the needs of less confident students seeking to improve their academic performance.

A multi-robot teleoperation system utilizing the Internet

The paper describes a human interface system for multi-robot teleoperation using the WWW system. We discuss how to issue operation commands effectively through a human interface to let multiple robots work for plant maintenance tasks. Based on the discussions, an interface system utilizing WWW technology is constructed on the workstation on which our WWW server runs. When the WWW clients require tasks to the robot, the WWW server calls up the interface programs by using Common Gateway Interface scripts. It is confirmed that the operator can carry out inspection tasks from a distant place by teleoperating actual mobile robots using this system.