An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

The role of network externalities in value creating process of the commercial web service for two-sided international markets

Network externalities and two-sided markets in the context of web services and value creation is not very well discussed topic in academic literature. The explosive rise of the Internet users has created a strong base for many successful web services and pushed many firms towards e-business and online service based business models. Thus the subject of this thesis, the role of network externalities in value creating process of the commer-cial web service for two-sided international markets is very current and interesting topic to examine. The objective of this Master’s Thesis is to advance the study of network externalities from the viewpoint of two-sided markets and network effects as well as describe the value creation & value co-creation process in commercial web service business models. The main proposition suggests that the larger network of customers and the bigger number of users the web service is able to attract, the more value and stronger positive net-work externalities the service is able to create for each customer group. The empirical research of this study was implemented for commercial web service, targeted to Russian consumers and Finnish business users. The findings suggest that the size of the network is highly related to the experi-enced value of the customers and the whole value creation process of commercial web targeted for two-sided international markets varies from the value creation for one-sided or pure domestic markets.

Managing Quality Properties of Web Service Compositions

Web services from different partners can be combined to applications that realize a more complex business goal. Such applications built as Web service compositions define how interactions between Web services take place in order to implement the business logic. Web service compositions not only have to provide the desired functionality but also have to comply with certain Quality of Service (QoS) levels. Maximizing the users' satisfaction, also reflected as Quality of Experience (QoE), is a primary goal to be achieved in a Service-Oriented Architecture (SOA). Unfortunately, in a dynamic environment like SOA unforeseen situations might appear like services not being available or not responding in the desired time frame. In such situations, appropriate actions need to be triggered in order to avoid the violation of QoS and QoE constraints. In this thesis, proper solutions are developed to manage Web services and Web service compositions with regard to QoS and QoE requirements. The Business Process Rules Language (BPRules) was developed to manage Web service compositions when undesired QoS or QoE values are detected. BPRules provides a rich set of management actions that may be triggered for controlling the service composition and for improving its quality behavior. Regarding the quality properties, BPRules allows to distinguish between the QoS values as they are promised by the service providers, QoE values that were assigned by end-users, the monitored QoS as measured by our BPR framework, and the predicted QoS and QoE values. BPRules facilitates the specification of certain user groups characterized by different context properties and allows triggering a personalized, context-aware service selection tailored for the specified user groups. In a service market where a multitude of services with the same functionality and different quality values are available, the right services need to be selected for realizing the service composition. We developed new and efficient heuristic algorithms that are applied to choose high quality services for the composition. BPRules offers the possibility to integrate multiple service selection algorithms. The selection algorithms are applicable also for non-linear objective functions and constraints. The BPR framework includes new approaches for context-aware service selection and quality property predictions. We consider the location information of users and services as context dimension for the prediction of response time and throughput. The BPR framework combines all new features and contributions to a comprehensive management solution. Furthermore, it facilitates flexible monitoring of QoS properties without having to modify the description of the service composition. We show how the different modules of the BPR framework work together in order to execute the management rules. We evaluate how our selection algorithms outperform a genetic algorithm from related research. The evaluation reveals how context data can be used for a personalized prediction of response time and throughput.

An EPN-based method for web service composition

Web service composition can be facilitated by an automatic process which consists of rules, conditions and actions. This research has adapted ElementaryPetri Net (EPN) to analyze and model the web services and their composition. This paper describes a set of techniques for representing transition rules, algorithm and workflow that web service composition can be automatically carried out.

Collaborative personal profiling for web service ranking and recommendation

Web service is one of the most fundamental technologies in implementing service oriented architecture (SOA) based applications. One essential challenge related to web service is to find suitable candidates with regard to web service consumer’s requests, which is normally called web service discovery. During a web service discovery protocol, it is expected that the consumer will find it hard to distinguish which ones are more suitable in the retrieval set, thereby making selection of web services a critical task. In this paper, inspired by the idea that the service composition pattern is significant hint for service selection, a personal profiling mechanism is proposed to improve ranking and recommendation performance. Since service selection is highly dependent on the composition process, personal knowledge is accumulated from previous service composition process and shared via collaborative filtering where a set of users with similar interest will be firstly identified. Afterwards a web service re-ranking mechanism is employed for personalised recommendation. Experimental studies are conduced and analysed to demonstrate the promising potential of this research.

A framework for monitoring and runtime recovery of web service-based applications

Service provisioning is a challenging research area for the design and implementation of autonomic service-oriented software systems. It includes automated QoS management for such systems and their applications. Monitoring, Diagnosis and Repair are three key features of QoS management. This work presents a self-healing Web service-based framework that manages QoS degradation at runtime. Our approach is based on proxies. Proxies act on meta-level communications and extend the HTTP envelope of the exchanged messages with QoS-related parameter values. QoS Data are filtered over time and analysed using statistical functions and the Hidden Markov Model. Detected QoS degradations are handled with proxies. We experienced our framework using an orchestrated electronic shop application (FoodShop).

Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

A formal model of the Semantic Web Service Ontology (WSMO)

Semantic Web Service, one of the most significant research areas within the Semantic Web vision, has attracted increasing attention from both the research community and industry. The Web Service Modelling Ontology (WSMO) has been proposed as an enabling framework for the total/partial automation of the tasks (e.g., discovery, selection, composition, mediation, execution, monitoring, etc.) involved in both intra- and inter-enterprise integration of Web services. To support the standardisation and tool support of WSMO, a formal model of the language is highly desirable. As several variants of WSMO have been proposed by the WSMO community, which are still under development, the syntax and semantics of WSMO should be formally defined to facilitate easy reuse and future development. In this paper, we present a formal Object-Z formal model of WSMO, where different aspects of the language have been precisely defined within one unified framework. This model not only provides a formal unambiguous model which can be used to develop tools and facilitate future development, but as demonstrated in this paper, can be used to identify and eliminate errors present in existing documentation.

True real-time change data capture with web service database encapsulation

This research is investigating the claim that Change Data Capture (CDC) technologies capture data changes in real-time. Based on theory, our hypothesis states that real-time CDC is not achievable with traditional approaches (log scanning, triggers and timestamps). Traditional approaches to CDC require a resource to be polled, which prevents true real-time CDC. We propose an approach to CDC that encapsulates the data source with a set of web services. These web services will propagate the changes to the targets and eliminate the need for polling. Additionally we propose a framework for CDC technologies that allow changes to flow from source to target. This paper discusses current CDC technologies and presents the theory about why they are unable to deliver changes in real-time. Following, we discuss our web service approach to CDC and accompanying framework, explaining how they can produce real-time CDC. The paper concludes with a discussion on the research required to investigate the real-time capabilities of CDC technologies. © 2010 IEEE.

Desenvolupament d'aplicacions web en Django sobre servidor apache, gestionades amb mòdul WSGI i relacionades amb base de dades Postgresql

Desenvolupament d'aplicacions web en Django per al Segon Concurs de fotografia matemàtica FotoMath 2011. Allotjades en servidor Apachez, gestionades amb mòdul wsgi i relacionades amb una base de dades postgresql.

The Purdue University Research Repository (PURR): An institutional data management service with a virtual research environment, data publication, and archiving

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Web Service Composition Systems for the Web Service Challenge - A Detailed Review

This report gives a detailed discussion on the system, algorithms, and techniques that we have applied in order to solve the Web Service Challenges (WSC) of the years 2006 and 2007. These international contests are focused on semantic web service composition. In each challenge of the contests, a repository of web services is given. The input and output parameters of the services in the repository are annotated with semantic concepts. A query to a semantic composition engine contains a set of available input concepts and a set of wanted output concepts. In order to employ an offered service for a requested role, the concepts of the input parameters of the offered operations must be more general than requested (contravariance). In contrast, the concepts of the output parameters of the offered service must be more specific than requested (covariance). The engine should respond to a query by providing a valid composition as fast as possible. We discuss three different methods for web service composition: an uninformed search in form of an IDDFS algorithm, a greedy informed search based on heuristic functions, and a multi-objective genetic algorithm.