MyDas, an Extensible Java DAS Server

BackgroundA large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still remains a problematic task. Availability of protein sequence data allows direct confirmation of protein-coding genes. Mass spectrometry has recently emerged as a powerful tool for proteomic studies. Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts. This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified.ResultsWe searched 3,967 mass spectra from 16 LC-MS/MS runs of Anopheles gambiae salivary gland homogenates against the Anopheles gambiae genome database. This allowed us to validate 23 known transcripts and 50 novel transcripts. In addition, a novel gene was identified on the basis of peptides that matched a genomic region where no gene was known and no transcript had been predicted. The amino termini of proteins encoded by two predicted transcripts were confirmed based on N-terminally acetylated peptides sequenced by tandem mass spectrometry. Finally, six sequence polymorphisms could be annotated based on experimentally obtained peptide sequences.ConclusionThe peptide sequences from this study were mapped onto the genomic sequence using the distributed annotation system available at Ensembl and can be visualized in the context of all other existing annotations. The strategy described in this paper can be used to correct and confirm genome annotations and permit discovery of novel proteins in a high-throughput manner by mass spectrometry.

Nowadays Web Services are gaining a lot of attention as a new technology, which indicate automated information services and a collection of functions packaged in a single, self-contained entity and conducted over internet for other programs to use. They use the standardized technologies and formats/protocols that simplify the exchange and integration of large amounts of data over the Internet, and as such they make it easier to conduct work across organizations regardless of the types of operating systems, hardware/software, programming languages, and databases that are being used. This paper will express the modeling of Choreography of web services; which is the process of combining different web services with intention to create interactive applications. The interconnection of web services with databases is a valuable step, because it provides backup for data. When it comes to analyzing the performance of a specific query, one of the best methods is to view the query execution plan, which provides information on how a specific DBMS query optimizer runs a specific query. This information is very valuable when we want to find out why a specific query is running slow.

This paper introduces a dependability assessment tool (WSsDAT) for Web Services monitoring and testing. It allows users to evaluate dependability of Web Services from the point of view of their clients by collecting metadata representing a number of dependability metrics. This Java-based tool can be deployed in diverse geographical locations to monitor and test the behavior of a selected set of Web Services within preset time intervals. The graphical user interface of the tool provides real-time statistical data describing dependability of the Web Services under monitoring. The tool makes it possible for the users to identify typical patterns of dependability-specific behavior depending on the time of the day, days of the week or the client locations. In addition, WSsDAT can collect and analyze service dependability measurements during long periods of time, as well as obtaining dependability-related information about current service behavior. The paper reports on a successful series of experiments using this tool for investigating the dependability of two BLAST Web Services which are widely used in the bioinformatics domain. The paper shows how the tool can be employed by e-scientists in making informed choices of the distributed services being used in an in silico experiment and thereby improving their overall dependability.KeywordsService-oriented architecturereliabilitymonitoringBLAST services

The paper describes an agent-based web service coordination framework in ubiquitous computing. It is called context-mediated web service coordination. In the framework, all service processes in ubiquitous computing environments are wrapped in web services that have standard communication protocols. The framework coordinates sensor devices wrapped in web services, web services on the Internet, and web services that manage user profile, etc. In addition, these web services are wrapped in specific types of agents. Giving a standard agent communication protocols to the heterogeneous web service processes, the framework introduces a new agent-based service coordination layer in ubiquitous computing. Coordinating these agents based on the user’s intention and their physical contexts, we can seamlessly coordinate the heterogeneous service components over the digital and real world in a human-centered manner. We also show a prototype application of the framework, context-aware information retrieval services in a museum.

The efficient cooperation of Web services is essential to applications of a Virtual Organization (VO). However, lots of challenges result from the diversity of services and the variability of business requirements. A novel approach to service cooperation based on Agile Services is proposed. The model of Agile Service is realized based on Tree Syntax. Aiming at mismatches of services existing in the cooperation, a set of operators for automatic service adaptation is also introduced. To verify the availability and efficiency of the approach to service cooperation, a real scenario and some Web services in the domain of Bioinformatics are taken. Application and experiments indicate that the proposed approach is efficient to realize more agile cooperation in a dynamic and heterogeneous services environment.

Chapter {1} - Web Services Overview

Simple object access protocol (SOAP) is the communication protocol used by web services to communicate between systems. Since SOAP messages have the ability to bypass firewalls and directly get processed by web servers, their security is critical to the security of the web servers. Secure transit of SOAP messages plays a critical role for the applicability of web services. At present, internet users authenticate themselves using credential are vulnerable to security threats in presence of active attackers. This imposes a burden on users to manage their credentials in different ways. Along with the thorough development and application for web services, the security of it has taken people's attention more and more. While web services security (WSS) can exchange safe SOAP message and enhance the security of web services, it will also have certain influence to the performance of web services. This paper explore the security vulnerability of SOAP message transaction and taking advantage of the existing technologies and solutions related to SOAP and web services, we developing a highly developed security model. This model is useful for solving the problem between security and performance contradiction.

A web service is a standards-based, language-agnostic software entity, that it accepts specially formatted requests from other software entities on remote machines via vendor and transport neutral communication protocols, producing application specific responses. Web services are used in every nook and corner of the world. The main strategy of web service is the availability of web service to all and its security over a distributed architecture. To ensure customer satisfaction web services must be available to all the users without any hindrance. The intrusion of attackers may be in any form such as a person or a program to cease the availability of the server. The Distributed Denial of Service attack is one of the severe attacks. The proposed system is an entropy based system which prevents the web service from the denial of service attack.

Web services – a new breed of self-contained, self-describing, modular applications published, located, and invoked across the Web – handle functions, from simple requests to complicated business processes. They are defined as network-based application components with a services-oriented architecture (SOA) using standard interface description languages and uniform communication protocols. SOA enables organizations to grasp and respond to changing trends and to adapt their business processes rapidly without major changes to the IT infrastructure. The Inaugural International Conference on Next-Generation Web Services Practices (NWeSP'05) attracted researchers who are also the world's most respected authorities on the semantic Web, Web-based services, and Web applications and services. NWeSP'05 was held in cooperation with the IEEE Computer Society Task Force on Electronic Commerce, the Technical Committee on Internet, and the Technical Committee on Scalable Computing. This special issue presents eight papers focused on different aspects of Web services and their applications. Papers were selected based on fundamental ideas and concepts rather than the thoroughness of techniques employed. Papers are organized as follows: <I>Taher et al.</I> present the first paper, on a Quality of Service Information and Computational framework (QoS-IC) supporting QoS-based service selection for SOA. The framework's functionality is expanded using a QoS constraints model that establishes an association relationship between different QoS properties and is used to govern QoS-based service selection in the underlying algorithm. Using a prototype implementation, the authors demonstrate how QoS constraints improve QoS-based service selection and save consumers valuable time. Due to the complex infrastructure of web applications, response times perceived by clients may be significantly longer than desired. To overcome some of the current problems, <I>Vilas et al.</I>, in the second paper, propose a cache-based extension of the architecture that enhances the current web services architecture, which is mainly based on program-logic or protocol-dependent optimization. In the third paper, Jo and Yoo present authorization for securing XML sources on the Web. One of the disadvantages of existing access control is that the DOM tree must be loaded into memory while all XML documents are parsed to generate the DOM tree, such that a lot of memory is used in repetitive search for tree to authorize access to all nodes in the DOM tree. The complex authorization evaluation process required thus lowers system performance. Existing access control fails to consider information structure and semantics sufficiently due to basic HTML limitations. The authors overcome some of these limitations in the proposed model. In the fourth paper, Jung and Cho propose a novel behavior-network-based method for Web service composition. The behavior network selects services automatically through internal and external links with environmental information from sensors and goals. An optimal service is selected at each step, resulting in a globally optimal service sequence for achieving preset goals. The authors detail experimental results for the proposed model by comparing them with rule-based system and user tests. <I>Kong et al.</I> present an efficient method in the fifth paper for merging heterogeneous ontologies – no ontology building standard currently exists – and the many ontology-building tools available are based on different ontology languages, mostly focusing on how to create, edit and infer the ontology efficiently. Even ontologies about the same domain differ because ontology experts hold different view points. For these reasons, interoperability between ontologies is very low. The authors propose merging heterogeneous domain ontologies by overcoming some of the above limitations. In the sixth paper, Chen and Che provide polynomial-time tree pattern query minimization algorithm whose efficiency stems from two key observations: (i) Inherent redundant "components" usually exist inside the rudimentary query provided by the user, and (ii) nonedundant nodes may become redundant when constraints such as co-occurrence and required child/descendant are given. They show that the algorithm obtained by first augmenting the input tree pattern using constraints, then applying minimization, invariably finds a unique minimal equivalent to the original query. Chen and Che present a polynomial-time algorithm for tree pattern query (TPQ) minimization without XML constraints in the seventh paper. The two-part algorithm is a dynamic programming strategy for finding all matching subtrees within a TPQ. The algorithm consists of one for subtree recognization and a second for subtree deletion. In the last paper, <I>Bagchi et al.</I> present the mobile distributed virtual memory (MDVM) concept and architecture for cellular networks containing server-groups (SG). They detail a two-round randomized distributed algorithm to elect a unique leader and co-leader of the SG that is free of any assumption about network topology, and buffer space limitations and is based on dynamically elected coordinators eliminating single points of failure. As guest editors, we thank all authors featured in this special issue for their contributions and the referees for critically evaluating the papers within the short time allotted. We sincerely believe that readers will share our enjoyment of this special issue and find the information it presents both timely and useful.

BackgroundAs genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques. The gap between protein sequence and structure continues to enlarge rapidly as the throughput of genome sequencing techniques is much higher than that of protein structure determination techniques. Computational software tools for predicting protein structure and structural features from protein sequences are crucial to make use of this vast repository of protein resources.ResultsTo meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map prediction, disulfide bond prediction, beta-sheet topology prediction, fold recognition, multiple template combination and alignment, template-based tertiary structure modeling, protein model quality assessment, and mutation stability prediction.ConclusionsThese tools have been rigorously tested by many users in the last several years and/or during the last three rounds of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7-9) from 2006 to 2010, achieving state-of-the-art or near performance. In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and scientific research. It is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.

A configuration space of homologous protein sequences (or CSHP) has been recently constructed based on pairwise comparisons, with probabilities deduced from Z-value statistics (Monte Carlo methods applied to pairwise comparisons) and following evolutionary assumptions. A Z-value cut-off is applied so as proteins are placed in the CSHP only when the similarity of pairs of sequences is significant following the Theorem of the Upper Limit of a score Probability (TULIP theorem). Based on the positions of similar protein sequences in the CSHP, a classification can be deduced, which can be visualized as trees, called TULIP trees. In previous case studies, TULIP trees where shown to be consistent with phylogenetic trees. To date, no tool has been made available to allow the computation of TULIP trees following this model. The availability of methods to cluster proteins based on pairwise comparisons and following evolutionary assumptions should be useful for evaluation and for the future improvements they might inspire. We developed a web server allowing the local or online computation of TULIP trees based on the CSHP probabilities. The input is a set of homologous protein sequences in multi-FASTA format. Pairwise comparisons are conducted using the Smith-Waterman method, with 100-1,000 sequence shuffling to estimate pairwise Z-values. Obtained Z-value matrix is used to infer a tree which is then written to a file. Output consists therefore of a Z-value matrix, a distance matrix, a TULIP treefile in NEWICK format, and a TULIP tree visualisation. The TULIP server provides an easy-to-use interface to the TULIP software, and allows a classification of protein sequences based on pairwise alignments and following evolutionary assumptions. TULIP trees are consistent with phylogenies in numerous cases, but they can be inconsistent for multi-domain proteins in which some domains have been conserved in all branches. Thus TULIP trees cannot be considered as conventional phylogenetic trees, following the MIAPA (Minimum Information About a Phylogenetic Analysis) recommendations. A major strength of the TULIP classification is its statistical validity when analysing samples including compositionally unbiased and biased sequences (i.e. with biased amino acid distributions), like sequences from Plasmodium falciparum. The TULIP web server is a service of the Malaria Portal of the University of Pretoria, South Africa, and is available at http://malport.bi.up.ac.za/TULIP/.

The tremendous growth in the amount of available web services (WS) impulses many researchers on proposing recommender systems to help users discover services. Most of the proposed solutions analyzed query strings and web service descriptions to generate recommendations. However, text based recommendations approaches depend mainly on user's perspective, languages and notations which easily decrease recommendation's efficiency. Moreover, new published web services often have lower priorities to be selected for recommendations.\\In this paper, we propose to take into account user's behaviors instead of text based analysis. We apply collaborative filtering technique on user's interactions. We propose and implement three algorithms (user-based, operation-based and priority-based) to validate our approach. We also provide evaluation methods which indicate that our approach produces high quality recommendations in case users have stable behavior.

Nowadays, web services are one of the most fashionable technology. Their simplicity of use and interoperability make them used in several fields such as web sites,widgets, classical applications and so on. There exists many technologies linked to this paradigm: SOAP (a communication protocol), WSDL (a description language)and UDDI (a yellow pages system) are among the most known. Some works proposed enhanced UDDI servers which only publish fully reliable web service. This reliability is generally evaluated using tests. In those works, only web services for which every tests are positive are published.In this paper, we introduce why we consider that this kind of approach is too binary. We also present examples of web services that could be used by customers even if some tests fails. Then, we introduce a new approach for web services publication. This approach relies on test categorization based on the Common Criteria norm. Then, we present how this marking system is implemented in iTaC-QoS, our validation framework based on UDDI.

Web service tags, terms annotated by users to describe the functionality or other aspects of Web services, are being treated as collective user knowledge for Web service mining. However, the tags associated with a Web service generally are listed in a random order or chronological order without considering the relevance information, which limits the effectiveness of tagging data. In this paper, we propose a novel tag ranking approach to automatically rank tags according to their relevance to the target Web service. In particular, service-tag network information is utilized to compute the relevance scores of tags by employing HITS model. Furthermore, we apply tag ranking approach in Web service clustering. Comprehensive experiments based on 15,968 real Web services demonstrate the effectiveness of the proposed tag ranking approach.

The overuse of antibiotics has led to emergence of antimicrobial resistance, and as a result, antibacterial peptides (ABPs) are receiving significant attention as an alternative. Identification of effective ABPs in lab from natural sources is a cost-intensive and time-consuming process. Therefore, there is a need for the development of in silico models, which can identify novel ABPs in protein sequences for chemical synthesis and testing. In this study, we propose a deep learning classifier named Deep-ABPpred that can identify ABPs in protein sequences. We developed Deep-ABPpred using bidirectional long short-term memory algorithm with amino acid level features from word2vec. The results show that Deep-ABPpred outperforms other state-of-the-art ABP classifiers on both test and independent datasets. Our proposed model achieved the precision of approximately 97 and 94% on test dataset and independent dataset, respectively. The high precision suggests applicability of Deep-ABPpred in proposing novel ABPs for synthesis and experimentation. By utilizing Deep-ABPpred, we identified ABPs in the tail protein sequences of Streptococcus bacteriophages, chemically synthesized identified peptides in lab and tested their activity in vitro. These ABPs showed potent antibacterial activity against selected Gram-positive and Gram-negative bacteria, which confirms the capability of Deep-ABPpred in identifying novel ABPs in protein sequences. Based on the proposed approach, an online prediction server is also developed, which is freely accessible at https://abppred.anvil.app/. This web server takes the protein sequence as input and provides ABPs with high probability (>0.95) as output.