Papers by Ernst Oberortner
The development of Web applications involves many stakeholders with different expertise. In many ... more The development of Web applications involves many stakeholders with different expertise. In many cases, the development of Web applications provides only technical models and their implementations, making it hard for non-technical stakeholders to get involved into the development process. As a result, a permanent collaboration and communication between all participating technical and non-technical stakeholders is needed during the whole development process. This paper proposes a model-driven approach of Domain-specific Modeling Languages (DSML) to separate the technical details from the non-technical ones. Non-technical stakeholders, also called domain experts, can assist the technical experts to map not well-known domain problems to the appropriate technological models. This leads to an intense collaboration between the different stakeholders and lowers the possibility of misunderstandings. These concepts improve the collaboration and, as a consequence, lowers the possibility of misunderstandings. Also, the modeldriven approach leads to a better maintainability and reusability of the resulting Web application.
Proceedings of the 17th Conference on Pattern Languages of Programs - PLOP '10, 2010
In distributed systems, clients can access a server's objects via a network. Service Level Agreem... more In distributed systems, clients can access a server's objects via a network. Service Level Agreements (SLA) can exist, which specify -among other things -performance-related Quality of Service (QoS) properties between the client and the server, such as round-trip time, processing time, or availability. For a provider, i.e., the server's host, serious financial consequences or other penalties can follow in case of not fulfilling the SLAs. The consumer, i.e., the client, wants to evaluate that the provider complies with the guaranteed SLAs. Designing and developing a QoSaware distributed system means facing many design challenges, such as where and how to measure the performance-related QoS properties. This paper presents design practices and patterns for measuring such QoS properties by extending existing patterns. The pattern's implementations are exemplified in a web service-oriented distributed system. The focus of the pattern lies on the QoS measuring impact on the client's or server's performance, the extend of separation of concerns, the property of reusability, the preciseness of the measured QoS properties, and the vulnerability to forgery by the server or the client. This paper's patterns should help software architects and developers in building an efficient solution for measuring performance-related QoS properties in a distributed system.
Monitoring performance-related QoS properties in service-oriented systems
Proceedings of the 16th European Conference on Pattern Languages of Programs - EuroPLoP '11, 2011
A Rule-Based Design Specification Language for Synthetic Biology
ACM Journal on Emerging Technologies in Computing Systems, 2014
Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems
ACS Synthetic Biology, 2014
miniEugene provides computational support for solving combinatorial design problems, enabling use... more miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).
Lecture Notes in Computer Science, 2010
In response to recent financial scandals (e.g. those involving Enron, Fortis, Parmalat), new regu... more In response to recent financial scandals (e.g. those involving Enron, Fortis, Parmalat), new regulations for protecting the society from financial and operational risks of the companies have been introduced. Therefore, companies are required to assure compliance of their operations with those new regulations as well as those already in place. Regulations are only one example of compliance sources modern organizations deal with every day. Other sources of compliance include licenses of business partners and other contracts, internal policies, and international standards. The diversity of compliance sources introduces the problem of compliance governance in an organization. In this paper, we propose an integrated solution for runtime compliance governance in Service-Oriented Architectures (SOAs). We show how the proposed solution supports the whole cycle of compliance management: from modeling compliance requirements in domain-specific languages through monitoring them during process execution to displaying information about the current state of compliance in dashboards. We focus on the runtime part of the proposed solution and describe it in detail. We apply the developed framework in a real case study coming from EU FP7 project COMPAS, and this case study is used through the paper to illustrate our solution.
2010 12th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, 2010
It is significant for companies to ensure their businesses conforming to relevant policies, laws,... more It is significant for companies to ensure their businesses conforming to relevant policies, laws, and regulations as the consequences of infringement can be serious. Unfortunately, the divergence and frequent changes of different compliance sources make it hard to systematically and quickly accommodate new compliance requirements due to the lack of an adequate methodology for system and compliance engineering. In addition, the difference of perception and expertise of multiple stakeholders involving in system and compliance engineering further complicates the analyzing, implementing, and assessing of compliance. For these reasons, in many cases, business compliance today is reached on a per-case basis by using ad hoc, hand-crafted solutions for specific rules to which they must comply. This leads in the long run to problems regarding complexity, understandability, and maintainability of compliance concerns in a SOA. To address the aforementioned challenges, we present in this invited paper a comprehensive SOA business compliance software framework that enables a business to express, implement, monitor, and govern compliance concerns.
Nature Biotechnology, 2014
The re-use of previously validated designs is critical to the evolution of synthetic biology from... more The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a communitydriven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.
Proposed Data Model for the Next Version of the Synthetic Biology Open Language
ACS Synthetic Biology, 2015
While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several... more While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.
The Synthetic Biology Open Language
Methods in Molecular Biology, 2014
The design and construction of engineered organisms is an emerging new discipline called syntheti... more The design and construction of engineered organisms is an emerging new discipline called synthetic biology and holds considerable promise as a new technological platform. The design of biologically engineered systems is however nontrivial, requiring contributions from a wide array of disciplines. One particular issue that confronts synthetic biologists is the ability to unambiguously describe novel designs such that they can be reengineered by a third-party. For this reason, the synthetic biology open language (SBOL) was developed as a community wide standard for formally representing biological designs. A design created by one engineering team can be transmitted electronically to another who can then use this design to reproduce the experimental results. The development and the community of the SBOL standard started in 2008 and has since grown in use with now over 80 participants, including international, academic, and industrial interests. SBOL has stimulated the development of repositories and software tools to help synthetic biologists in their design efforts. This chapter summarizes the latest developments and future of the SBOL standard and its supporting infrastructure.
Process-driven service-oriented architectures (SOA) need to cope with constant changing requireme... more Process-driven service-oriented architectures (SOA) need to cope with constant changing requirements of various compliance requirements, such as quality of service (QoS) constraints within service level agreements (SLA). To the best of our knowledge, only little evidence is available if and in how far process-driven SOAs deal with the evolution of the requirements. In this work, we evaluate an incremental and model-driven development approach on the evolution of the requirements and the domain model in the context of an industrial case study. The case study focuses on advanced telecom services that need to be compliant to QoS constraints. This paper answers questions about the applicability of the incremental development approach, the impact of requirement changes, possible drawbacks of using a non-incremental development approach, and general recommendations based on the findings. Our results provide guidelines for dealing with the evolution of model-driven service-oriented systems.
Domain-specific languages (DSLs) are an important software development approach for many service-... more Domain-specific languages (DSLs) are an important software development approach for many service-oriented architectures (SOAs). They promise to model the various SOA concerns in a suitable way for the various technical and non-technical stakeholders of a SOA. However, so far the research on SOA DSLs concentrates on novel technical contributions, and not much evidence or counter-evidence for the claims associated to SOA DSLs has been provided. In this paper, we present a qualitative, explorative study that provides an initial analysis of a number of such claims through a series of three prototyping experiments in which each experiment has developed, analyzed, and compared a set of DSLs for process-driven SOAs. Our result is to provide initial evidence for a number of popular claims about SOA DSLs which follow the model-driven software development (MDSD) approach, as well as a list of design trade-offs to be considered in the design decisions that must be made when developing a SOA DSL.
Many service-oriented business systems have to comply to various contracts and agreements. Multip... more Many service-oriented business systems have to comply to various contracts and agreements. Multiple technical and non-technical stakeholders with different background and knowledge are involved in modeling such business concerns. In many cases, these concerns are only encoded in the technical models and implementations of the systems, making it hard for non-technical stakeholders to get involved in the modeling process. In this paper we propose to tackle this problem by providing model-driven Domain-specific Languages (DSL) for specifying the contracts and agreements, as well as an approach to separate these DSLs into sub-languages at different abstraction levels, where each sub-language is tailored for the appropriate stakeholders. We exemplify our approach by describing a Quality-of-Service (QoS) DSL which can be used to describe Service Level Agreements (SLA). This work provides insights into how DSLs can be utilized to model and enrich service-oriented business systems with concerns defined in contracts and agreements.
Towards Patterns to Enhance the Communication in Distributed Software Development Environments
ABSTRACT Distributed Software Development (DSD) is an emerging research area in software engineer... more ABSTRACT Distributed Software Development (DSD) is an emerging research area in software engineering. Several conducted research studies identified similar communication problems among DSD teams and tried to solve them. In this paper we present patterns that we have identified while surveying state of the art research studies. The patterns can help to organize DSD teams better in order to enhance their communication. We also highlight some potential future research challenges.
Context: Ensuring software systems conforming to multiple sources of relevant policies, laws, and... more Context: Ensuring software systems conforming to multiple sources of relevant policies, laws, and regulations is significant because the consequences of infringement can be serious. Unfortunately, this goal is hardly achievable due to the divergence and frequent changes of compliance sources and the differences in perception and expertise of the involved stakeholders. In the long run, these issues lead to problems regarding complexity, understandability, maintainability, and reusability of compliance concerns. Objective: In this article, we present a model-driven and view-based approach for addressing problems related to compliance concerns. Method: Compliance concerns are represented using separate view models. This is achieved using domain-specific languages (DSLs) that enable non-technical and technical experts to formulate only the excerpts of the system according to their expertise and domain knowledge. The compliance implementations, reports, and documentation can be automatically generated from the models. The applicability of our approach has been validated using an industrial case study. Results: Our approach supports stakeholders in dealing with the divergence of multiple compliance sources. The compliance controls and relevant reports and documentation are generated from the models and hence become traceable, understandable, and reusable. Because the generated artifacts are associated with the models, the compliance information won't be lost as the system evolves. DSLs and view models convey compliance concerns to each stakeholder in a view that is most appropriate for his/her current work task. Conclusions: Our approach lays a solid foundation for ensuring conformance to relevant laws and regulations. This approach, on the one hand, aims at addressing the variety of expertise and domain knowledge of stakeholders. On the other hand, it also aims at ensuring the explicit links between compliance sources and the corresponding implementations, reports, and documents for conducting many important tasks such as root cause analysis, auditing, and governance.
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Papers by Ernst Oberortner