Ashraf Memon

A Web service composition and deployment framework for scientific workflows

The article presents the Web services framework in the Kepler scientific workflow system and illustrates them with a real-world example.

GEONGrid portal: design and implementations

We have developed the GEONGrid system for coordinating and managing naturally distributed computing, data, and cluster resources on the cyberinfrastructure. Recently, since the use of Grid technology is still very complex for researchers and scientists, the area of Grid Portals has made excellent progress. The Grid portal system is an emerging open Grid computing environment that promises to provide users with uniform seamless access to remote computing and data resources by providing an easy to use interface to cover over the complexity of more sophisticated Grid technologies. In this paper, we present our initial efforts in the design and implementation of service components in the GEONGrid portal. These service components may be implemented as Web services that follow the conventions of service‐oriented architecture design. In this approach, service components are self‐contained, have a well‐defined programming interface defined in WSDL, and communicate using SOAP messaging. In building a GEONGrid portal, we also use a component‐based user interface design. Portlets provide the desired component model for user interfaces in the same way as Web services. Using this approach, which allows Grid portals to be built out of reusable components, has the obvious advantages of reusability and modularity. Copyright

A three tier architecture for LiDAR interpolation and analysis

Emerging Grid technologies enable solving scientific problems that involve large datasets and complex analyses. Coordinating distributed Grid resources and computational processes requires adaptable interfaces and tools that provide a modularized and configurable environment for accessing Grid clusters and executing high performance computational tasks. In addition, it is beneficial to make these tools available to the community in a unified framework through a shared cyberinfrastructure, or a portal, so scientists can focus on their scientific work and not be concerned with the implementation of the underlying infrastructure. In this paper we describe a scientific workflow approach to coordinate various resources as data analysis pipelines. We present a three tier architecture for LiDAR interpolation and analysis, a high performance processing of point intensive datasets, utilizing a portal, a scientific workflow engine and Grid technologies. Our proposed solution is available through the GEON portal and, though focused on LiDAR processing, is applicable to other domains as well.

Screening for HIV among tuberculosis patients: a cross-sectional study in Sindh, Pakistan

Objective To describe feasibility and results of systematic screening of tuberculosis (TB) patients for HIV. Design Cross-sectional study. Setting Six selected sentinel sites (public DOTS clinics) in the province of Sindh, Pakistan. Participants All TB patients aged 16–60 years registered for treatment from April 2008 to March 2012. Measurement Demographic information of registered TB patients, screening for HIV through rapid testing and confirmation by referral lab of Sindh AIDS Control Program, according to national guidelines. Results Of a total of 18 461 registered TB patients, 12 882 fulfilled the inclusion criteria and were given education and counselling. Of those counselled 12 552 (97.4%) were screened for HIV using a rapid test. Men made up 48% of the sample and 76.5% of patients had pulmonary TB. Of the total patients tested, 42 (0.34%) were HIV-positive after confirmatory testing at the Sindh AIDS Control Program Laboratory. Prevalence of HIV among male patients was 0.67% whereas prevalence among female patients was 0.03% (p value <0.001). Prevalence of HIV among pulmonary TB patients was 0.29% and among extrapulmonary TB patients was 0.48% (p value=0.09). Conclusion In public DOTS clinics in Pakistan it is feasible to test TB patients for HIV. Prevalence of HIV is three times higher among TB patients as compared with the general population in Pakistan. Although the results are not representative of Pakistan or Sindh province they cover a large catchment area and closely match WHO estimate for the country. Routinely screening all TB patients for HIV infection, especially targeting men and ensuring antiretroviral therapy, can significantly improve TB/HIV collaborative activities in Pakistan and identify many cases of HIV, improve health outcomes and save lives.

The GEON service-oriented architecture for Earth Science applications

Abstract The Geosciences Network (GEON) project has been developing cyberinfrastructure for data sharing in the Earth Science community based on a service-oriented architecture. The layered architecture consists of Core, Middleware, and Applications services. Core services provide system-level functions (e.g. user authentication), Middleware services provide generic capabilities (e.g. catalog search), and Application services provide functions that users directly interact with, including applications that are specific to Earth Sciences. The GEON ‘service stack’ includes a standardized set of these services and the corresponding software modules. The GEON Portal provides Web-based access to these services via a set of portlets. This service-oriented approach has enabled GEON to expand to new partner sites and leverage GEON services for other projects. To facilitate interoperation in a distributed geoinformatics environment, GEON is focusing on standards for distributed search across federated catalogs.

A three tier architecture applied to LiDAR processing and monitoring

Emerging Grid technologies enable solving scientific problems that involve large datasets and complex analyses, which in the past were often considered difficult to solve. Coordinating distributed Grid resources and computational processes requires adaptable interfaces and tools that provide modularized and configurable environments for accessing Grid clusters and executing high performance computational tasks. Computationally intensive processes are also subject to a high risk of component failures and thus require close monitoring. In this paper we describe a scientific workflow approach to coordinate various resources via data analysis pipelines. We present a three tier architecture for LiDAR interpolation and analysis, a high performance processing of point intensive datasets, utilizing a portal, a scientific workflow engine and Grid technologies. Our proposed solution is available to the community in a unified framework through a shared cyberinfrastructure, the GEON portal, enabling scientists to focus on their scientific work and not be concerned with the implementation of the underlying infrastructure.