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/.

Ramachandran plot on the web

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.

An efficient web cache replacement policy

Several replacement policies for web caches have been proposed and studied extensively in the literature. Different replacement policies perform better in terms of (i) the number of objects found in the cache (cache hit), (ii) the network traffic avoided by fetching the referenced object from the cache, or (iii) the savings in response time. In this paper, we propose a simple and efficient replacement policy (hereafter known as SE) which improves all three performance measures. Trace-driven simulations were done to evaluate the performance of SE. We compare SE with two widely used and efficient replacement policies, namely Least Recently Used (LRU) and Least Unified Value (LUV) algorithms. Our results show that SE performs at least as well as, if not better than, both these replacement policies. Unlike various other replacement policies proposed in literature, our SE policy does not require parameter tuning or a-priori trace analysis and has an efficient and simple implementation that can be incorporated in any existing proxy server or web server with ease.

Efficient Algorithms for Combinatorial Auctions with Volume Discounts Arising in Web Service Composition

Web services are now a key ingredient of software services offered by software enterprises. Many standardized web services are now available as commodity offerings from web service providers. An important problem for a web service requester is the web service composition problem which involves selecting the right mix of web service offerings to execute an end-to-end business process. Web service offerings are now available in bundled form as composite web services and more recently, volume discounts are also on offer, based on the number of executions of web services requested. In this paper, we develop efficient algorithms for the web service composition problem in the presence of composite web service offerings and volume discounts. We model this problem as a combinatorial auction with volume discounts. We first develop efficient polynomial time algorithms when the end-to-end service involves a linear workflow of web services. Next we develop efficient polynomial time algorithms when the end-to-end service involves a tree workflow of web services.

Geographic Resources Decision Support System – an Open Source GIS

Fully structured and matured open source spatial and temporal analysis technology seems to be the official carrier of the future for planning of the natural resources especially in the developing nations. This technology has gained enormous momentum because of technical superiority, affordability and ability to join expertise from all sections of the society. Sustainable development of a region depends on the integrated planning approaches adopted in decision making which requires timely and accurate spatial data. With the increased developmental programmes, the need for appropriate decision support system has increased in order to analyse and visualise the decisions associated with spatial and temporal aspects of natural resources. In this regard Geographic Information System (GIS) along with remote sensing data support the applications that involve spatial and temporal analysis on digital thematic maps and the remotely sensed images. Open source GIS would help in wide scale applications involving decisions at various hierarchical levels (for example from village panchayat to planning commission) on economic viability, social acceptance apart from technical feasibility. GRASS (Geographic Resources Analysis Support System, http://wgbis.ces.iisc.ernet.in/grass) is an open source GIS that works on Linux platform (freeware), but most of the applications are in command line argument, necessitating a user friendly and cost effective graphical user interface (GUI). Keeping these aspects in mind, Geographic Resources Decision Support System (GRDSS) has been developed with functionality such as raster, topological vector, image processing, statistical analysis, geographical analysis, graphics production, etc. This operates through a GUI developed in Tcltk (Tool command language / Tool kit) under Linux as well as with a shell in X-Windows. GRDSS include options such as Import /Export of different data formats, Display, Digital Image processing, Map editing, Raster Analysis, Vector Analysis, Point Analysis, Spatial Query, which are required for regional planning such as watershed Analysis, Landscape Analysis etc. This is customised to Indian context with an option to extract individual band from the IRS (Indian Remote Sensing Satellites) data, which is in BIL (Band Interleaved by Lines) format. The integration of PostgreSQL (a freeware) in GRDSS aids as an efficient database management system.

Comparative Assessment of Techniques for Bioresource Monitoring Using GIS and Remote Sensing

Growing concern over the status of global and regional bioenergy resources has necessitated the analysis and monitoring of land cover and land use parameters on spatial and temporal scales. The knowledge of land cover and land use is very important in understanding natural resources utilization, conversion and management. Land cover, land use intensity and land use diversity are land quality indicators for sustainable land management. Optimal management of resources aids in maintaining the ecosystem balance and thereby ensures the sustainable development of a region. Thus sustainable development of a region requires a synoptic ecosystem approach in the management of natural resources that relates to the dynamics of natural variability and the effects of human intervention on key indicators of biodiversity and productivity. Spatial and temporal tools such as remote sensing (RS), geographic information system (GIS) and global positioning system (GPS) provide spatial and attribute data at regular intervals with functionalities of a decision support system aid in visualisation, querying, analysis, etc., which would aid in sustainable management of natural resources. Remote sensing data and GIS technologies play an important role in spatially evaluating bioresource availability and demand. This paper explores various land cover and land use techniques that could be used for bioresources monitoring considering the spatial data of Kolar district, Karnataka state, India. Slope and distance based vegetation indices are computed for qualitative and quantitative assessment of land cover using remote spectral measurements. Differentscale mapping of land use pattern in Kolar district is done using supervised classification approaches. Slope based vegetation indices show area under vegetation range from 47.65 % to 49.05% while distance based vegetation indices shoes its range from 40.40% to 47.41%. Land use analyses using maximum likelihood classifier indicate that 46.69% is agricultural land, 42.33% is wasteland (barren land), 4.62% is built up, 3.07% of plantation, 2.77% natural forest and 0.53% water bodies. The comparative analysis of various classifiers, indicate that the Gaussian maximum likelihood classifier has least errors. The computation of talukwise bioresource status shows that Chikballapur Taluk has better availability of resources compared to other taluks in the district.

Solar energy potential assessment using GIS

Renewable energy resources are those having a cycling time less than 100 years and are renewed by the nature and their supply exceeds the rate of consumption. Renewable energy systems use resources that are constantly replaced in nature and are usually less polluting. In order to tap the potential of renewable energy sources, there is a need to assess the availability of resources spatially as well as temporally. Geographic Information Systems (GIS) along with Remote Sensing (RS) helps in mapping on spatial and temporal scales of the resources and demand. The spatial database of resource availability and the demand would help in the regional energy planning. This paper discusses the application of geographical information system (GIS) to map the solar potential in Karnataka state, India. Regions suitable for tapping solar energy are mapped on the basis of global solar radiation data, and this analysis provides a picture of the potential. The study identifies that Coastal parts of Karnataka with the higher global solar radiation is ideally suited for harvesting solar energy. The potential analysis reveals that, maximum global solar radiation is in districts such as Uttara Kannada and Dakshina Kannada. Global solar radiation in Uttara Kannada during summer, monsoon and winter are 6.31, 4.40 and 5.48 kWh/sq.m, respectively. Similarly, Dakshina Kannada has 6.16, 3.89 and 5.21 kWh/sq.m during summer, monsoon and winter.

Vegetation Analysis in Uttara Kannada District Using GIS and Remote Sensing Techniques

Uttara Kannada is the only district in Karnataka, which has a forested area of about 80% and falls in the region of the Western Ghats. It is considered to be a very resourceful in terms of abundant natural resources and constitutes an important district in Karnataka. The forest resources of the district are under pressure as a large portion of the forested area has been converted to non-forestry activities since independence owing to the increased demands from human and animal population resulting in degradation of the forest ecosystem. This has led to poor productivity and regenerative capacity which is evident in the form of barren hill tops, etc in Coastal taluks of Uttara Kannada, entailing regular monitoring of the forest resources very essential. The classification of forest is a prerequisite for managing forest resources. Geographical Information System (GIS), allows the spatial and temporal analysis of the features of interest, and helps in solving the problem of deforestation and associated environmental and ecological problems. Spatial and temporal tools such as GIS and remotely sensed data helps the planners and decision makers in evolving the sustainable strategies for management and conservation of natural resources. Uttara Kannada district was classified on the basis of the land-use using supervised hard classifiers. The land use categories identified were urban area, water bodies, agricultural land, forest cover, and waste land. Further classification was carried out on the basis of forest type. The types of forest categorised were semi-evergreen, evergreen, moist deciduous, dry deciduous, plantations and scrub, thorny and non-forested area. The identified classes were correlated with the ground data collected during field visits. The observed results were compared with the historic data and the changes in the forest cover were analysed. From the assessment made it was clear that there has been a considerable degree of forest loss in certain areas of the district. It was also observed that plantations and social forests have increased drastically over the last fifteen years,and natural forests have declined.

Quality Assurance and Assessment in Technical Education System: A Web Based Approach

Engineering education quality embraces the activities through which a technical institution satisfies itself that the quality of education it provides and standards it has set are appropriate and are being maintained. There is a need to develop a standardised approach to most aspects of quality assurance for engineering programmes which is sufficiently well defined to be accepted for all assessments.We have designed a Technical Educational Quality Assurance and Assessment (TEQ-AA) System, which makes use of the information on the web and analyzes the standards of the institution. With the standards as anchors for definition, the institution is clearer about its present in order to plan better for its future and enhancing the level of educational quality.The system has been tested and implemented on the technical educational Institutions in the Karnataka State which usually host their web pages for commercially advertising their technical education programs and their Institution objectives, policies, etc., for commercialization and for better reach-out to the students and faculty. This helps in assisting the students in selecting an institution for study and to assist in employment.

Bidding Dynamics of Rational Advertisers in Sponsored Search Auctions on the Web

In this paper, we address a key problem faced by advertisers in sponsored search auctions on the web: how much to bid, given the bids of the other advertisers, so as to maximize individual payoffs? Assuming the generalized second price auction as the auction mechanism, we formulate this problem in the framework of an infinite horizon alternative-move game of advertiser bidding behavior. For a sponsored search auction involving two advertisers, we characterize all the pure strategy and mixed strategy Nash equilibria. We also prove that the bid prices will lead to a Nash equilibrium, if the advertisers follow a myopic best response bidding strategy. Following this, we investigate the bidding behavior of the advertisers if they use Q-learning. We discover empirically an interesting trend that the Q-values converge even if both the advertisers learn simultaneously.

An intelligent procurement marketplace for web services composition

This paper presents an intelligent procurement marketplace for finding the best mix of web services to dynamically compose the business process desired by a web service requester. We develop a combinatorial auction approach that leads to an integer programming formulation for the web services composition problem. The model takes into account the Quality of Service (QoS) and Service Level Agreements (SLA) for differentiating among multiple service providers who are capable of fulfilling a functionality. An important feature of the model is interface aware composition.