11,348 research outputs found
TinkerCell: Modular CAD Tool for Synthetic Biology
Synthetic biology brings together concepts and techniques from engineering
and biology. In this field, computer-aided design (CAD) is necessary in order
to bridge the gap between computational modeling and biological data. An
application named TinkerCell has been created in order to serve as a CAD tool
for synthetic biology. TinkerCell is a visual modeling tool that supports a
hierarchy of biological parts. Each part in this hierarchy consists of a set of
attributes that define the part, such as sequence or rate constants. Models
that are constructed using these parts can be analyzed using various C and
Python programs that are hosted by TinkerCell via an extensive C and Python
API. TinkerCell supports the notion of a module, which are networks with
interfaces. Such modules can be connected to each other, forming larger modular
networks. Because TinkerCell associates parameters and equations in a model
with their respective part, parts can be loaded from databases along with their
parameters and rate equations. The modular network design can be used to
exchange modules as well as test the concept of modularity in biological
systems. The flexible modeling framework along with the C and Python API allows
TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is
a free and open-source project under the Berkeley Software Distribution
license. Downloads, documentation, and tutorials are available at
www.tinkercell.com.Comment: 23 pages, 20 figure
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies
Forum Session at the First International Conference on Service Oriented Computing (ICSOC03)
The First International Conference on Service Oriented Computing (ICSOC) was held in Trento, December 15-18, 2003. The focus of the conference ---Service Oriented Computing (SOC)--- is the new emerging paradigm for distributed computing and e-business processing that has evolved from object-oriented and component computing to enable building agile networks of collaborating business applications distributed within and across organizational boundaries. Of the 181 papers submitted to the ICSOC conference, 10 were selected for the forum session which took place on December the 16th, 2003. The papers were chosen based on their technical quality, originality, relevance to SOC and for their nature of being best suited for a poster presentation or a demonstration. This technical report contains the 10 papers presented during the forum session at the ICSOC conference. In particular, the last two papers in the report ere submitted as industrial papers
Semantic business process management: a vision towards using semantic web services for business process management
Business process management (BPM) is the approach to manage the execution of IT-supported business operations from a business expert's view rather than from a technical perspective. However, the degree of mechanization in BPM is still very limited, creating inertia in the necessary evolution and dynamics of business processes, and BPM does not provide a truly unified view on the process space of an organization. We trace back the problem of mechanization of BPM to an ontological one, i.e. the lack of machine-accessible semantics, and argue that the modeling constructs of semantic Web services frameworks, especially WSMO, are a natural fit to creating such a representation. As a consequence, we propose to combine SWS and BPM and create one consolidated technology, which we call semantic business process management (SBPM
LODE: Linking Digital Humanities Content to the Web of Data
Numerous digital humanities projects maintain their data collections in the
form of text, images, and metadata. While data may be stored in many formats,
from plain text to XML to relational databases, the use of the resource
description framework (RDF) as a standardized representation has gained
considerable traction during the last five years. Almost every digital
humanities meeting has at least one session concerned with the topic of digital
humanities, RDF, and linked data. While most existing work in linked data has
focused on improving algorithms for entity matching, the aim of the
LinkedHumanities project is to build digital humanities tools that work "out of
the box," enabling their use by humanities scholars, computer scientists,
librarians, and information scientists alike. With this paper, we report on the
Linked Open Data Enhancer (LODE) framework developed as part of the
LinkedHumanities project. With LODE we support non-technical users to enrich a
local RDF repository with high-quality data from the Linked Open Data cloud.
LODE links and enhances the local RDF repository without compromising the
quality of the data. In particular, LODE supports the user in the enhancement
and linking process by providing intuitive user-interfaces and by suggesting
high-quality linking candidates using tailored matching algorithms. We hope
that the LODE framework will be useful to digital humanities scholars
complementing other digital humanities tools
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Benefits and challenges of applying Semantic Web Services in the e-Government domain
Joining up services in e-Government usually implies governmental agencies acting in concert without a central control regime. This requires the sharing of scattered and heterogeneous data. Semantic Web Service (SWS) technology can help to integrate, mediate and reason between these datasets. However, since few real-world applications have been developed, it is still unclear which are the actual benefits and issues of adopting such a technology in the e-Government domain. In this paper, we contribute to raising awareness of the potential benefits in the e-Government community by analyzing motivations, requirements, and expected results, before proposing a reusable SWS-based framework. We demonstrate the application of this framework by a compelling use case: a GIS-based emergency planning system. We illustrate the obtained benefits and the key challenges which remain to be addressed
A Model-Driven Engineering Approach for ROS using Ontological Semantics
This paper presents a novel ontology-driven software engineering approach for
the development of industrial robotics control software. It introduces the
ReApp architecture that synthesizes model-driven engineering with semantic
technologies to facilitate the development and reuse of ROS-based components
and applications. In ReApp, we show how different ontological classification
systems for hardware, software, and capabilities help developers in discovering
suitable software components for their tasks and in applying them correctly.
The proposed model-driven tooling enables developers to work at higher
abstraction levels and fosters automatic code generation. It is underpinned by
ontologies to minimize discontinuities in the development workflow, with an
integrated development environment presenting a seamless interface to the user.
First results show the viability and synergy of the selected approach when
searching for or developing software with reuse in mind.Comment: Presented at DSLRob 2015 (arXiv:1601.00877), Stefan Zander, Georg
Heppner, Georg Neugschwandtner, Ramez Awad, Marc Essinger and Nadia Ahmed: A
Model-Driven Engineering Approach for ROS using Ontological Semantic
Towards a service-oriented e-infrastructure for multidisciplinary environmental research
Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures
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