Data transport between visualization web services for medical image analysis

Many scientific endeavors, such as molecular biology, have become dependent on big data and its analysis. For example, precision medicine depends on molecular measurements and data analysis per patient. Data analyses supporting medical decisions must be standardized and performed consistently across patients. While perhaps not life-threatening, data analyses in basic research have become increasingly complex. RNAseq data, for example, entails a multi-step analysis ranging from quality assessment of the measurements to statistical analyses. Workflow management systems (WFMS) enable the development of data analysis workflows (WF), their reproduction, and their application to datasets of the same type. However, far more than a hundred WFMS are available, and there is no way to convert data analysis WFs among WFMS. Therefore, the initial choice of a WFMS is important as it entails a lockin to the system. The reach in their particular field (number of citations) can be used as a proxy for selecting a WFMS, but of the about 25 WFMS we mention in this work, at least 5 have a large reach in scientific data analysis. Hence other criteria are needed to delineate among WFMS. By extracting such criteria from selected studies concerning WFMS and adding additional criteria, we arrived at five critical criteria: reproducibility, reusability, FAIRness, versioning support, and security. Another five criteria (providing a graphical user interface, WF flexibility, WF scalability, WF shareability, and computational transparency) we deemed important but not critical for the assessment of WFMS. We applied the criteria to the most cited WFMS in PubMed and found none that support all criteria. We hope that suggesting these criteria will spark a discussion on what features are important for WFMS in scientific data analysis and may lead to developing WFMS that fulfill such criteria.

Service Oriented Computing (SOC) is a computing paradigm broadly pushed by vendors, utilizing services to support the rapid development of distributed applications in heterogeneous environments. The visionary promise of SOC is a world of cooperating services being loosely coupled to flexibly create dynamic business processes and agile applications that may span organizations and computing platforms and can nevertheless adapt quickly and autonomously to changes of requirements or context. Consequently, the subject of Service Oriented Computing is vast and enormously complex, spanning many concepts and technologies that find their origins in diverse disciplines like Workflow Management Systems, Component Based Computing, "classical" Web applications, and Enterprise Application Integration (EAI) including Message Oriented Middleware. In addition, there is a strong need to merge technology with an understanding of business processes and organizational structures, a combination of recognizing an enterprise's pain points and the potential solutions that can be applied to correct them. Middleware, on the other hand, is defined by the ObjectWeb consortium as the software layer in a distributed computing system that lies between the operating system and the applications on each site of the system. Middleware is the enabling technology of system and enterprise application integration (EAI) and therefore it clearly and evidently plays a key role for SOC. While the immediate need of middleware support for Service Oriented Architectures (SOA) is evident, current approaches and solutions mostly fall short by primarily providing support for the EAI aspect of SOC only and do not sufficiently address composition support, service management and monitoring. Moreover, quality properties (in particular dependability and security) need to be addressed not only by interfacing and communication standards, but also in terms of integrated middleware support. But what makes these issues so different in a SOA setting? Why - for instance - is traditional middleware support for transaction processing different to transaction processing in SOA, reflecting different types of atomicity needs? One answer lies in the administrative heterogeneity, the loose coupling between coarsegrained operations and long-running interactions, high dynamicity, and the required flexibility during run-time. Recently, massive-scale and mobility were added to the challenges for Middleware for SOC. However, loose coupling is not always the best approach to solve a particular problem. In order to temporarily allow for a stronger (traditional) form of coupling (like group membership agreement or atomic transaction), the middleware also has to provide explicit and configurable means to change between different strengths of coupling and various communication paradigms. This will enable servicebased applications to take the best from both worlds by dynamically adjusting the interactions between the composed services. The highly dynamic modularity and need for flexible integration of services (e.g. Web service implementations) may require new middleware architectures, protocols, and services. These considerations also lead to the question to what extent service-orientation at the middleware layer itself is beneficial (or not). Recently emerging "Middleware as service" offerings, from providers like Amazon or from the open source community, support this trend towards "infrastructure services" that can be purchased and consumed over the Internet. However, this model may not be suitable for all kinds of middleware functions, including those addressing dependability (availability, reliability, integrity, safety, maintainability). Providing end-to-end properties and addressing cross-cutting concerns in a crossorganizational SOA is a particular challenge and the limits and benefits thereof have still to be investigated.

With the advent of distributed technologies and related Integrated Development Environments (IDEs), business collaborations across the world irrespective of the platforms in which applications were built.The underlying technology is Web Services which is based on XML standard and the architecture is SOA (Service Oriented Architecture).Many SOA frameworks came in to existence.However, their primary focus is discovering, composition of services in order to make flexible service oriented distributed enterprise applications.Such systems without human expertise may be incomplete.To overcome this problem, this paper proposes techniques to collaborate services based software with human experts thus forming a knowledgeintensive and people centric web besides sharing and reusing software components in distributed environment.To achieve this, we propose a flexible and adaptive approach which facilitates software services and humans to collaborate using Web Services and its important standards like SOAP (Simple Object Access Protocol), WSDL (Web Services Description Language) and UDDI (Universal Description Discovery Integration).This kind of human centric enterprise web has far reaching implications and it can attract the human experts to participate in rendering their best possible services.Interaction monitoring techniques that are adaptive thus realizing standards based people-centric systems.

Purpose – The purpose of this paper is to analyse the problems associated with the development of e‐government in Southern Africa Development Community (SADC) countries and propose a novel framework for adopting service orientation. This framework includes a new approach and architecture for implementing service orientation called SBA‐eGOV (Service Based Architecture for E‐Government).

Bringing white-box testing to Service Oriented Architectures through a Service Oriented Approach

Service Oriented Architecture (SOA) introduced the web services as distributed computing components that can be independently deployed and invoked by other services or software to execute composite services that represent an end-to-end business process. An important problem in the SOA is the web service selection and composition problem which involves selecting the right web services mix to construct the best service composition that achieves the consumers Service Level Agreement (SLA) requirements. In this chapter we propose different methods to solve the problem of the business processes execution engine web service selection and services composition construction in the Service Oriented Architecture (SOA).  The chapter provides different mechanisms to improve the web services selection and composition using dynamic techniques. The main goal is to satisfy the services' requirements expressed as the SLA and to enhance the services selection and composition by increasing the availability and decreasing the response time of the service compositions.

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.

Poland is characterised by a relatively high variety of living organisms attributed to terrestrial and water environments. Currently, close to 57.000 species of living organisms are described that occur in Poland (Symonides 2008), including lowland and mountain species, those attributed to oceanic and continental areas, as well as species from forested and open habitats. Poland comprehensively represents biodiversity of living organisms on a continental scale and thus, is considered to have an important role for biodiversity maintenance. The Mammal Research Institute of Polish Academy of Sciences (MRI PAS), located in Białowieża Forest, a UNESCO Heritage Site, has been collecting biodiversity data for 90 years. However, a great amount of data gathered over the years, especially old data, is gradually being forgotten and hard to access. Old catalogues and databases have never been digitalized or publicly shared, and not many Polish scientists are aware of the existence of such resources, not to mention the rest of the scientific world. Recognizing the need for an online, interoperable platform, following FAIR data principles (findable, accessible, interoperable, reusable), where biodiversity and scientific data can be shared, MRI PAS took a lead in creation of an Open Forest Data (OFD) repository. OpenForestData.pl (Fig. 1) is a newly created (2020) digital repository, designed to provide access to natural sciences data and provide scientists with an infrastructure for storing, sharing and archiving their research outcomes. Creating such a platform is a part of an ongoing development of life sciences in Poland, aiming for an open, modern science, where data are published as free-access. OFD also allows for the consolidation of natural science data, enabling the use and processing of shared data, including API (Application Programming Interface) tools. OFD is indexed by the Directory of Open Repositories (OpenDOAR) and Registry of Research Data Repositories (re3data). The OFD platform is based entirely on reliable, globally recognized open source software: DATAVERSE, an interactive database app which supports sharing, storing, exploration, citation and analysis of scientific data; GEONODE, a content management geospatial system used for storing, publicly sharing and visualising vector and raster layers, GRAFANA, a system meant for storing and analysis of metrics and large scale measurement data, as well as visualisation of historical graphs at any time range and analysis for trends; and external tools for database storage (Orthanc) and data visualisation (Orthanc plugin Osimis Web Viewer and Online 3D Viewer (https://3dviewer.net/), which were integrated with the system mechanism of Dataverse. Furthermore, according to the need for specimen description, Darwin Core (Wieczorek et al. 2012) metadata schema was decided to be the most suitable for specimen and collections description and mapped into a Dataverse additional metadata block. The use of Darwin Core is based on the same file format, the Darwin Core Archive (DwC-A) which allows for sharing data using common terminology and provides the possibility for easy evaluation and comparison of biodiversity datasets. It allows the contributors to OFD to optionally choose Darwin Core for object descriptions making it possible to share biodiversity datasets in a standardized way for users to download, analyse and compare. Currently, OFD stores more than 10.000 datasets and objects from the collections of Mammal Research Institute of Polish Academy of Sciences and Forest Science Institute of Białystok University of Technology. The objects from natural collections were digitalized, described, catalogued and made public in free-access. OFD manages seven types of collection materials: 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. In the OFD repository, researchers have the possibility to share data in standardized way, which nowadays is often a requirement during the publishing process of a scientific article. Beside scientists, OFD is designed to be open and free for students and specialists in nature protection, but also for officials, foresters and nature enthusiasts. Creation of the OFD repository supports the development of citizen science in Poland, increases visibility and access to published data, improves scientific collaboration, exchange and reuse of data within and across borders.

Both Academia and Industry have intensified their efforts to realize the potential of Service Oriented Computing and Service Oriented Architecture (SOA). There are many obstacles yet to overcome in the com-mercial adoption, design and implementation of SOA. This workshop seeks insight from academia and industry to de-scribe the problems encountered and formulate theoretical and propose practical solutions for their resolution from industry and academia perspectives. This workshop is a continuation of a highly successful series of workshops at OOPSLA 2007, OOPSLA 2006, OOPSLA 2005, OOPSLA 2004 and OOPSLA 2003.

Service Oriented Architecture (SOA) has been widely used during the past decade due to its ability to seamlessly integrate various applications developed using different technologies. Web services based on open standards are the most commonly used technology to realize an SOA. Business processes are executed by appropriate orchestration of various services from different departments that belong to a single organization or from multiple organizations. Security is an important quality attribute that has to be built into any application that is developed using SOA. XML is the underlying technology for Web Service Description Language (WSDL), SOAP protocol and Business Process Execution Language (BPEL). It is highly probable that an attacker could inject malicious information into these XML files to modify the flow of the business process. Further, SOAP was not designed with security in mind, it is possible to tamper the SOAP messages while they are in transit. There exist a number of such potential vulnerabilities which lead to possible security breach in the individual services. In an orchestrated business process, there are possibilities of more vulnerabilities. One of the existing tools namely WS-Attacker is only capable of testing the security of individual web services alone. In spite of the widespread usage of SOA, currently there is limited automatic tool support for testing the security provided by an entire SOA application involving service orchestration. In this context, this paper focuses on designing and implementing a plug-in for WS-Attacker to analyze a few security vulnerabilities present in SOA business processes.

Nowadays, a Service Oriented Architecture (SOA) seems to be one of the most promising paradigms for leveraging enterprise information systems. SOA creates opportunities for enterprises to provide value added service tailored for on demand enterprise collaboration. With the emergence and rapid development of Web services technologies, SOA is being paid increasing attention and has become widespread. In spite of the popularity of SOA, a standardized framework for modeling and implementing business services are still in progress. For the purpose of supporting these service-oriented solutions, we adopt a model driven development approach. This paper outlines the Contextual Service Oriented Modeling and Analysis (CSOMA) methodology and presents UML profiles for the PIM level service-oriented architectural modeling, as well as its corresponding meta-models. The proposed PIM (Platform Independent Model) describes the business SOA at a high level of abstraction regardless of techniques involved in the application employment. In addition, all essential service-specific concerns required for delivering quality and context-aware service are covered. Some of the advantages of this approach are that it is generic and thus not closely allied with Web service technology as well as specifically treating the service adaptability during the design stage.

14 - Web Services and SOA for DBA, Data Architects, and Others

Today, the B2B E-business systems in most enterprises usually have multiple heterogeneous and independent systems which are based on different platforms and operate in different functional departments. To deal with the increased services in future, an enterprise needs to expand its system continuously. This, however, will cause great inconvenience to the future system maintenance. To implement E-business successfully, a unified internal E-business integration environment must be established to integrate the internal system and thus realize a unified internal mechanism within the enterprise E-business system. The SOA (Service Oriented Architecture) architecture, however, can well meet the above requirements. The integration of SOA- architecture-based applications can reduce the dependency of different types of IT systems, reduce the cost of system maintenance and the complexity of the IT system operation, increase the flexibility of the system deployment, and at the same time exclude the barrier of service innovation. Research and application of SOA-architecture-based enterprise application systems has become a very important research project at present. As an important SOA implementation, Web services is a relatively new technology widely accepted by people. This is because Web services provides a distributed computing method for the heterogene- ous applications integrated in the Internet. It can integrate the applications running on the distributed servers which are connected through Intranet, Extranet, and Internet together. Based on SOA, this document designs an enterprise E-business application model and realizes a flexible and expandable E-business platform.

1 IntroductionDuring its evolution, humanity always looked for instruments and innovative solutions that ensure maximum comfort from the perspective of human universe dimensions: familial, social, cultural, economic, religious etc. Many times during this social development, the individual had to resort to various association forms with others in order to achieve these goals, thus laying the foundation for what we call today collaboration. Current forms of association transcend the original goals and the individual aspirations have been altered and transposed into mercantile organization objectives. Unconditional support of these considerations is reflected by the capitalist system and largely by the industrial system, where the aim of earning money through all means outweighs any attempt of collaboration in the original meaning. Unfortunately the mercantilism is not only an economic doctrine of 15th-18th centuries, but it is still fully manifest in the digital society.Beyond these considerations, thinking of the social and economic status quo we must notice a change in the business paradigm. The traditional models defined through the goal of maximizing the profit adapt to modern management doctrines, oriented towards the individuals. Current society is not only information and knowledge based; it is also a society of technology and artificial intelligence. Transposing the business in the digital environment is no longer a caprice but a need. Additionally, the simple presence in virtual environment is not the premise for the success of modern business, the advantages provided by technology must also be fully exploited.Orientation towards exploiting individual abilities and ensuring business processes flexibility has led to what specialists call business agility. Ensuring a certain level of agility for the business requires more and more relying on information and communications technology. Additionally, the agile business status implies redefining the human resource as primary production factor. The anthropocentric paradigm is evidence to this. In the context of modern agile business collaboration and team work are more than ever necessary. Through the prism of dedicated agility technologies, the essence of collaboration as instrument for founding and unfolding economic activities dissolves into the business itself, becoming visible on the level of business processes and work tasks. The individuals, activities, processes and work tasks are vertices of informational graphs representing the functioning of modern businesses. The edges of these graphs are merely informational flows (later translated into workflows) that ensure communication and cooperation on business level for reaching its goals.For technological and economic reasons (meaning resource economy), the need to share resources, skills, competencies, market shares and experience overlays on top of these modern business architecture. In many occasions this was a premise for development of virtual organizations that take advantage of concrete market opportunities. The modern technological solutions is now provided by cloud computing. Together with a workflow management system (WfMS), cloud computing comes to ensure scalability, reutilization of technological capabilities, reliability, improvement of business processes, minimization of information and communications technology (ICT) investment.Thus, exploitation of cloud services may generate an intensified use of workflows, mainly for collaborative environments. On the other hand, business agility built on service-oriented architecture (SOA) and complex event processing (CEP) solutions may ensure real time collaboration between business processes through processing heterogeneous data extracted from business connected information flows. A solution of workflow management system based on cloud for real time collaboration will provide the capabilities for multi-criterion analyses for business processes, while considering their interdependence with the environment. …

This tutorial explains how to implement a Service-Oriented Architecture (SOA) for reliable systems using an Enterprise Service Bus (ESB) and the Ada Web Server (AWS). The first part of the tutorial describes terms of Service-Oriented Architectures (SOA) including service, service registry, service provider, service consumer, Service Oriented Architecture Protocol (SOAP), and Web Service Description Language (WSDL). This tutorial also presents principles of SOA including loose coupling, encapsulation, composability of web services, and statelessness of web services. The tutorial also covers the benefits of SOA and organizations that are supporting SOA infrastructure. The second part of the tutorial covers the Enterprise Service Bus (ESB) including definitions, capabilities, benefits and drawbacks. The tutorial discusses the difference between SOA and an ESB, as well as some of the commercially available ESB solutions on the market. The Mule ESB is explored in more detail and several examples are given. In the third part, the tutorial covers the Ada Web Server (AWS) built using the Ada programming language. The tutorial covers the capabilities of AWS and explains how to build and install AWS. The tutorial explains how to build an AWS server and include the server in an Ada application. The tutorial demonstrates how to build a call back function in AWS and build a response to a SOAP message. Finally, the tutorial explains how to connect an AWS server to an ESB endpoint. AWS is a key component to building a SOA for a reliable system. This capability allows the developer to expose services in a high-integrity system using the Ada and SPARK programming languages.