WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

BackgroundSharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software.ResultsWe here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages.ConclusionsWith these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called "Smiley2png 1.0") can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu

Visual communication in urban planning and urban design

This report documents the current status of visual communication in urban design and planning. Visual communication is examined through discussion of standalone and network media, specifically concentrating on visualisation on the World Wide Web(WWW).Firstly, we examine the use of Solid and Geometric Modelling for visualising urban planning and urban design. This report documents and compares examples of the use of Virtual Reality Modelling Language (VRML) and proprietary WWW based Virtual Reality modelling software. Examples include the modelling of Bath and Glasgow using both VRML 1.0 and 2.0. A review is carried out on the use of Virtual Worldsand their role in visualising urban form within multi-user environments. The use of Virtual Worlds is developed into a case study of the possibilities and limitations of Virtual Internet Design Arenas (ViDAs), an initiative undertaken at the Centre for Advanced Spatial Analysis, University College London. The use of Virtual Worlds and their development towards ViDAs is seen as one of the most important developments in visual communication for urban planning and urban design since the development plan.Secondly, photorealistic media in the process of communicating plans is examined.The process of creating photorealistic media is documented, examples of the Virtual Streetscape and Wired Whitehall Virtual Urban Interface System are provided. The conclusion is drawn that although the use of photo-realistic media on the WWW provides a way to visually communicate planning information, its use is limited. The merging of photorealistic media and solid geometric modelling is reviewed in the creation of Augmented Reality. Augmented Reality is seen to provide an important step forward in the ability to quickly and easily visualise urban planning and urban design information.Thirdly, the role of visual communication of planning data through GIS is examined interms of desktop, three dimensional and Internet based GIS systems. The evolution to Internet GIS is seen as a critical component in the development of virtual cities which will allow urban planners and urban designers to visualise and model the complexity of the built environment in networked virtual reality.Finally a viewpoint is put forward of the Virtual City, linking Internet GIS with photorealistic multi-user Virtual Worlds. At present there are constraints on how far virtual cities can be developed, but a view is provided on how these networked virtual worlds are developing to aid visual communication in urban planning and urban design

The space physics environment data analysis system (SPEDAS)

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have “crib-sheets,” user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer’s Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its “modes of use” with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.Published versio

Functional requirements document for the Earth Observing System Data and Information System (EOSDIS) Scientific Computing Facilities (SCF) of the NASA/MSFC Earth Science and Applications Division, 1992

Five scientists at MSFC/ESAD have EOS SCF investigator status. Each SCF has unique tasks which require the establishment of a computing facility dedicated to accomplishing those tasks. A SCF Working Group was established at ESAD with the charter of defining the computing requirements of the individual SCFs and recommending options for meeting these requirements. The primary goal of the working group was to determine which computing needs can be satisfied using either shared resources or separate but compatible resources, and which needs require unique individual resources. The requirements investigated included CPU-intensive vector and scalar processing, visualization, data storage, connectivity, and I/O peripherals. A review of computer industry directions and a market survey of computing hardware provided information regarding important industry standards and candidate computing platforms. It was determined that the total SCF computing requirements might be most effectively met using a hierarchy consisting of shared and individual resources. This hierarchy is composed of five major system types: (1) a supercomputer class vector processor; (2) a high-end scalar multiprocessor workstation; (3) a file server; (4) a few medium- to high-end visualization workstations; and (5) several low- to medium-range personal graphics workstations. Specific recommendations for meeting the needs of each of these types are presented

The R Commander: A Basic-Statistics Graphical User Interface to R

Unlike S-PLUS, R does not incorporate a statistical graphical user interface (GUI), but it does include tools for building GUIs. Based on the tcltk package (which furnishes an interface to the Tcl/Tk GUI toolkit), the Rcmdr package provides a basic-statistics graphical user interface to R called the "R Commander." The design objectives of the R Commander were as follows: to support, through an easy-to-use, extensible, cross-platform GUI, the statistical functionality required for a basic-statistics course (though its current functionality has grown to include support for linear and generalized-linear models, and other more advanced features); to make it relatively difficult to do unreasonable things; and to render visible the relationship between choices made in the GUI and the R commands that they generate. The R Commander uses a simple and familiar menu/dialog-box interface. Top-level menus include File, Edit, Data, Statistics, Graphs, Models, Distributions, Tools, and Help, with the complete menu tree given in the paper. Each dialog box includes a Help button, which leads to a relevant help page. Menu and dialog-box selections generate R commands, which are recorded in a script window and are echoed, along with output, to an output window. The script window also provides the ability to edit, enter, and re-execute commands. Error messages, warnings, and some other information appear in a separate messages window. Data sets in the R Commander are simply R data frames, and can be read from attached packages or imported from files. Although several data frames may reside in memory, only one is "active" at any given time. There may also be an active statistical model (e.g., an R lm or glm ob ject). The purpose of this paper is to introduce and describe the use of the R Commander GUI; to describe the design and development of the R Commander; and to explain how the R Commander GUI can be extended. The second part of the paper (following a brief introduction) can serve as an introductory guide for students who will use the R Commander.

Viability of commercial depth sensors for the REX medical exoskeleton : a thesis presented in partial fulfilment of the requirements for the degree of Master of Engineering in Mechatronics at Massey University, Albany, New Zealand

Closing the feedback loop of machine control has been a known method for gaining stability. Medical exoskeletons are no exception to this phenomenon. It is proposed that through machine vision, their stability control can be enhanced in a commercially viable manner. Using machines to enhance human’s capabilities has been a concept tried since the 19th century, with a range of successful demonstrations since then such as the REX platform. In parallel, machine vision has progressed similarly, and while applications that could be considered to be synonymous have been researched, using computer vision for traversability analysis in medical exoskeletons still leaves a lot of questions unanswered. These works attempt to understand better this field, in particular, the commercial viability of machine vision system’s ability to enhance medical exoskeletons. The key method to determine this will be through implementation. A system is designed that considers the constraints of working with a commercial product, demonstrating integration into an existing system without significant alterations. It shows using a stereo vision system to gather depth information from the surroundings and amalgamate these. The amalgamation process relies on tracking movement to provide accurate transforms between time-frames in the threedimensional world. Visual odometry and ground plane detection is employed to achieve this, enabling the creation of digital elevation maps, to efficiently capture and present information about the surroundings. Further simplification of this information is accomplished by creating traversability maps; that directly relate the terrain to whether the REX device can safely navigate that location. Ultimately a link is formed between the REX device and these maps, and that enables user movement commands to be intercepted. Once intercepted, a binary decision is computed whether that movement will traverse safe terrain. If however the command is deemed unsafe (for example stepping backwards off a ledge), this will not be permitted, hence increasing patient safety. Results suggest that this end-to-end demonstration is capable of improving patient safety; however, plenty of future work and considerations are discussed. The underlying data quality provided by the stereo sensor is questioned, and the limitations of macro vs. micro applicability to the REX are identified. That is; the works presented are capable of working on a macro level, but in their current state lack the finer detail to improve patient safety when operating a REX medical exoskeleton considerably

A Prototype Lisp-Based Soft Real-Time Object-Oriented Graphical User Interface for Control System Development

A prototype Lisp-based soft real-time object-oriented Graphical User Interface for control system development is presented. The Graphical User Interface executes alongside a test system in laboratory conditions to permit observation of the closed loop operation through animation, graphics, and text. Since it must perform interactive graphics while updating the screen in real time, techniques are discussed which allow quick, efficient data processing and animation. Examples from an implementation are included to demonstrate some typical functionalities which allow the user to follow the control system's operation

3D User Interface for a File Management System

Two-dimensional graphical user interface (GUI) is now firmly established as the preferred interface for most applications. The purpose of this work was to develop a three-dimensional user interface as a front end for a file management system and to evaluate the efficiency of a practical 3D application. In order to create this software, a previously defined 3D graphics engine, called Valve Software’s Half-Life, was extended to provide a directory traversal and the basic file management functions (cut, copy, paste, delete). The project was divided into two basic components: generating the 3D “world”, and altering the Half-Life engine to provide some features of file management