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.

A combinatorial procurement auction for QoS-aware web services

Business processes and application functionality are becoming available as internal web services inside enterprise boundaries as well as becoming available as commercial web services from enterprise solution vendors and web services marketplaces. Typically there are multiple web service providers offering services capable of fulfilling a particular functionality, although with different Quality of Service (QoS). Dynamic creation of business processes requires composing an appropriate set of web services that best suit the current need. This paper presents a novel combinatorial auction approach to QoS aware dynamic web services composition. Such an approach would enable not only stand-alone web services but also composite web services to be a part of a business process. The combinatorial auction leads to an integer programming formulation for the web services composition problem. An important feature of the model is the incorporation of service level agreements. We describe a software tool QWESC for QoS-aware web services composition based on the proposed approach.

PRUNE and PROBE-two modular web services for protein-protein docking

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

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.

DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Federated Search Service for OAI-compliant, Open-Access Repositories in India

Many of the research institutions and universities across the world are facilitating open-access (OA) to their intellectual outputs through their respective OA institutional repositories (IRs) or through the centralized subject-based repositories. The registry of open access repositories (ROAR) lists more than 2850 such repositories across the world. The awareness about the benefits of OA to scholarly literature and OA publishing is picking up in India, too. As per the ROAR statistics, to date, there are more than 90 OA repositories in the country. India is doing particularly well in publishing open-access journals (OAJ). As per the directory of open-access journals (DOAJ), to date, India with 390 OAJs, is ranked 5th in the world in terms of numbers of OAJs being published. Much of the research done in India is reported in the journals published from India. These journals have limited readership and many of them are not being indexed by Web of Science, Scopus or other leading international abstracting and indexing databases. Consequently, research done in the country gets hidden not only from the fellow countrymen, but also from the international community. This situation can be easily overcome if all the researchers facilitate OA to their publications. One of the easiest ways to facilitate OA to scientific literature is through the institutional repositories. If every research institution and university in India set up an open-access IR and ensure that copies of the final accepted versions of all the research publications are uploaded in the IRs, then the research done in India will get far better visibility. The federation of metadata from all the distributed, interoperable OA repositories in the country will serve as a window to the research done across the country. Federation of metadata from the distributed OAI-compliant repositories can be easily achieved by setting up harvesting software like the PKP Harvester. In this paper, we share our experience in setting up a prototype metadata harvesting service using the PKP harvesting software for the OAI-compliant repositories in India.

e-SURAKSHAK: A Cyber-Physical Healthcare System with Service Oriented Architecture

In this paper we present the design of ``e-SURAKSHAK,'' a novel cyber-physical health care management system of Wireless Embedded Internet Devices (WEIDs) that sense vital health parameters. The system is capable of sensing body temperature, heart rate, oxygen saturation level and also allows noninvasive blood pressure (NIBP) measurement. End to end internet connectivity is provided by using 6LoWPAN based wireless network that uses the 802.15.4 radio. A service oriented architecture (SOA) 1] is implemented to extract meaningful information and present it in an easy-to-understand form to the end-user instead of raw data made available by sensors. A central electronic database and health care management software are developed. Vital health parameters are measured and stored periodically in the database. Further, support for real-time measurement of health parameters is provided through a web based GUI. The system has been implemented completely and demonstrated with multiple users and multiple WEIDs.