Related papers: semanticSBML 2.0 - A Collection of Online Services…
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Composing Web services is a convenient means of dealing with complex requests. However, the number of Web services on the Internet is increasing. This explains the growing interest in composing Web services automatically. Nevertheless, the…
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web…
In this document, we introduce a system model as a semantic domain for the Unified Modeling Language (UML) [OMG07a, OMG07b]. The system model is supposed to form a possible core and foundation of the UML semantics definition. For that…
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…
In this document we introduce a system model as the basis for a semantic model for UML 2.0. The system model is supposed to form the core and foundation of the UML semantics definition. For that purpose the basic system is targeted towards…
The purpose of this symposium, held in conjunction with MoDELS 2006, was to present the current state of research of the UML 2 Semantics Project. Equally important to receiving feedback from an audience of experts was the opportunity to…
In line with the general trend in artificial intelligence research to create intelligent systems that combine learning and symbolic components, a new sub-area has emerged that focuses on combining machine learning (ML) components with…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…
Social Network Analysis (SNA) tries to understand and exploit the key features of social networks in order to manage their life cycle and predict their evolution. Increasingly popular web 2.0 sites are forming huge social network. Classical…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
Mathematical semantic web services are very useful in practice, but only a small number of research results are reported in this area. In this paper we present a method of obtaining an approximation of a mathematical semantic web service,…
Semantic network research has seen a resurgence from its early history in the cognitive sciences with the inception of the Semantic Web initiative. The Semantic Web effort has brought forth an array of technologies that support the…
The process-based semantic composition of Web Services is gaining a considerable momentum as an approach for the effective integration of distributed, heterogeneous, and autonomous applications. To compose Web Services semantically, we need…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Semantic web services (SWS) are self-contained, self-describing, semantically marked-up software resources that can be published, discovered, composed and executed across the Web in a semi-automatic way. They are a key component of the…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
The growing proliferation of distributed information systems, allows organizations to offer their business processes to a worldwide audience through Web services. Semantic Web services have emerged as a means to achieve the vision of…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…