Hassan A. Karimi

oGNM: online computation of structural dynamics using the Gaussian Network Model

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5–6 orders of magnitude faster than those using conventional normal mode analyses. Two cases studies illustrate the utility of oGNM. The first shows that the thermal fluctuations predicted for 1250 non-homologous proteins correlate well with X-ray crystallographic data over a broad range [7.3–15 Å] of inter-residue interaction cutoff distances and the correlations improve with increasing observation temperatures. The second study, focused on 64 oligonucleotides and oligonucleotide–protein complexes, shows that good agreement with experiments is achieved by representing each nucleotide by three GNM nodes (as opposed to one-node-per-residue in proteins) along with uniform interaction ranges for all components of the complexes. These results open the way to a rapid assessment of the dynamics of DNA/RNA-containing complexes. The server can be accessed at .

A critical evaluation of location based services and their potential

This Editorial lead article for the Journal of Location Based Services surveys this complex and multi-disciplinary field and identifies the key research issues. Although this field has produced early commercial disappointments, the inevitability that pervasive location-aware services on mobile devices will emerge means that much research is needed to inform these developments. The article reviews firstly: the science and technology of positioning, geographic information science, mobile cartography, spatial cognition and interfaces, information science, ubiquitous computing; and secondly the business, content and legal, social and ethics aspects, before synthesising the key issues for this new field.

i GNM: a database of protein functional motions based on Gaussian Network Model

MOTIVATION The knowledge of protein structure is not sufficient for understanding and controlling its function. Function is a dynamic property. Although protein structural information has been rapidly accumulating in databases, little effort has been invested to date toward systematically characterizing protein dynamics. The recent success of analytical methods based on elastic network models, and in particular the Gaussian Network Model (GNM), permits us to perform a high-throughput analysis of the collective dynamics of proteins. RESULTS We computed the GNM dynamics for 20 058 structures from the Protein Data Bank, and generated information on the equilibrium dynamics at the level of individual residues. The results are stored on a web-based system called iGNM and configured so as to permit the users to visualize or download the results through a standard web browser using a simple search engine. Static and animated images for describing the conformational mobility of proteins over a broad range of normal modes are accessible, along with an online calculation engine available for newly deposited structures. A case study of the dynamics of 20 non-homologous hydrolases is presented to illustrate the utility of the iGNM database for identifying key residues that control the cooperative motions and revealing the connection between collective dynamics and catalytic activity.

Applications of location-based services: a selected review

This article reviews a selected set of location–based services (LBS) that have been published in the research literature, focussing on mobile guides, transport support, gaming, assistive technology and health. The research needs and opportunities in each area are evaluated and the connections between each category of LBS are discussed. The review illustrates the enormous diversity of forms in which LBS are appearing and the wide range of application sectors that are represented. However, very few of these applications are implemented pervasively on a commercial basis as this is still challenging technically and economically.

Coupling methodologies for environmental models

Abstract Environmental models have been developed to address narrowly defined issues. As these issues become broader and scientific understanding grows, models become more complex. A variety of methodologies couple environmental models to address multifaceted issues, such as cross-media effects, risk analysis, and environmental justice investigations. This study analyzes, from a modelers perspective, various coupling methodologies according to their characteristics. This analysis is presented as a five-level coupling hierarchy, and includes a representation of a modeling framework for coupled environmental models requiring dynamic feedback during a simulation (e.g., multimedia modeling). The framework addresses the special needs for this type of modeling, including spatial locking for environmental data, autogeneration of simulation metadata, simulation verification, and automated recovery from system problems.

Location awareness through trajectory prediction

Abstract Location-aware computing is a type of ubiquitous computing that uses user’s location information as an essential parameter for providing services and application-related optimization. Location management plays an important role in location-aware computing because the provision of services requires convenient access to dynamic location and location-dependent information. Many existing location management strategies are passive since they rely on system capability to periodically record current location information. In contrast, active strategies predict user movement through trajectories and locations. Trajectory prediction provides richer location and context information and facilitates the means for adapting to future locations. In this paper, we present two models for trajectory prediction, namely probability-based model and learning-based model. We analyze these two models and conduct experiments to test their performances in location-aware systems.

Personalised routing for wheelchair navigation

Wheelchair users are confronted with many outdoor obstacles in everyday travel that can make the task arduous and unsafe, especially in unfamiliar environments. However, if wheelchair users are provided with routes that can safely, accurately and efficiently guide them to their destinations, then the difficulty and danger associated with traveling might be significantly reduced. In this article, we present a routing method suitable for wheelchair users by taking into account sidewalk obstacles such as slope, steps, sidewalk condition and sidewalk traffic as are preferred by users. Our method calculates impedance scores for each sidewalk segment, which are then used to determine an optimal route between any given pair of origin-destination addresses in a sidewalk network. We first discuss sidewalk network parameters and a spatial database suitable for wheelchair navigation. Then we discuss our personalised routing approach. We also describe three methods to weight the impedance level of each sidewalk segment and compare the effectiveness of each method through experimentation using the sidewalk network for the University of Pittsburgh campus area.

An ontological engineering approach for integrating CAD and GIS in support of infrastructure management

Infrastructure managers rely on capabilities of Computer-Aided Design (CAD) and Geospatial Information Systems (GIS) for making decisions during the implementation of engineering tasks. However, despite the fact that there are domains in which both CAD and GIS are used and despite the overlaps between the data and operations they support, CAD and GIS have been developed independently over many years resulting in platforms that are not easily integrated. Engineers in infrastructure management must gain knowledge and skills in both CAD and GIS to perform infrastructure management tasks. In most cases, they need to manually transfer data queried from one system to another, due to the heterogeneous nature, such as data and operations heterogeneity, of CAD and GIS. Interoperability is seen as a solution to overcome the problems associated with heterogeneous environments and may occur at different levels and for different purposes. In this paper, we discuss the need for semantic interoperability between GIS and CAD and present an ontological engineering methodology as a possible means to enable this interoperability. This methodology uses ontological-based techniques for resolving the semantic differences in queries requiring CAD and GIS data and operations.

Comparative evaluation and analysis of online geocoding services

Geocoding is an uncertain process that associates an address or a place name with geographic coordinates. Traditionally, geocoding is performed locally on a stand-alone computer with the geocoding tools usually bundled in GIS software packages. The use of such tools requires skillful operators who know about the issues of geocoding, that is, reference databases and complicated geocoding interpolation techniques. These days, with the advancement in the Internet and Web services technologies, online geocoding provides its functionality to the Internet users with ease; thus, they are often unaware of such issues. With an increasing number of online geocoding services, which differ in their reference databases, the geocoding algorithms, and the strategy for dealing with inputs and outputs, it is crucial for the service requestors to realize the quality of the geocoded results of each service before choosing one for their applications. This is primarily because any errors associated with the geocoded addresses will be propagated to subsequent decisions, activities, modeling, and analysis. This article examines the quality of five online geocoding services: Geocoder.us, Google, MapPoint, MapQuest, and Yahoo!. The quality of each geocoding service is evaluated with three metrics: match rate, positional accuracy, and similarity. A set of addresses from the US Environmental Protection Agency (EPA) database were used as a baseline. The results were statistically analyzed with respect to different location characteristics. The outcome of this study reveals the differences among the online geocoding services on the quality of their geocoding results and it can be used as a general guideline for selecting a suitable service that matches an applications needs.

ONALIN: Ontology and Algorithm for Indoor Routing

Much research has recently been devoted to developing approaches, techniques, and technologies which assist people with navigation within buildings. Routing is an essential technique often requested by users prior to real-time navigation, providing them with appropriate routes within buildings. A survey of the literature reveals indoor routing approaches primarily based on shortest distance or fastest travel time as the main criteria. However, such routing criteria that are common in outdoor navigation may not be as applicable to indoor navigation. Presenting users with appropriate indoor routes could be beneficial to many users in various situations. For example, people with physical, cognitive, or sensory impairments may need routes that take into account their special needs as well as preferences rather than ones that are shortest or fastest. In this paper, we present a new ontology and an algorithm (ONALIN) that provides routing for individuals with various needs and preferences. To this end, ONALIN takes the ADA (American Disability Act) standards, among other requirements, into consideration. An indoor routing algorithm based on this ontology is presented and analyzed in detail where it first finds feasible routes with respect to the special needs of the users and then from those will select the comfortable routes.