libSBOLj 2.0: A Java Library to Support SBOL 2.0

The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic desig

The Synthetic Biology Open Language (SBOL) Version 3:Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use

BBF RFC 108: Synthetic Biology Open Language (SBOL) Version 2.0.0

The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards

Synthetic Biology Open Language (SBOL) Version 2.0.0

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long deve

Synthetic biology open language (SBOL) version 3.0.0

Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints

BBF RFC 112: Synthetic Biology Open Language (SBOL) Version 2.1.0

BBF RFC 112 (the SBOL 2.1.0 standard) replaces BBF RFC 108 (the SBOL 2.0 standard), as well as the minor update SBOL 2.0.1.The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information

A standard-enabled workflow for synthetic biology

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications

Synthetic Biology Open Language (SBOL) Version 1.1.0

In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation

Monitoring quality of service in service-oriented systems : architectural design and stakeholder support

Zsfassung in dt. SpracheIn service-orientierten Systemen werden Services angeboten welche inner- und ausserbetriebliche Aufgaben hauptsächlich automatisch abarbeiten. Zwischen den Service Anbietern und den Service Konsumenten können Verträge vereinbart werden, welche Klausen über die Performanz der Services definieren. Solche Verträge werden als Service Level Agreements (SLA) bezeichnet. Ein Service Anbieter muss sicherstellen, dass die vertraglichen Vereinbarungen erfüllt werden um Pönale zu vermeiden sowie, viel schlimmer noch, seinen Ruf zu schädigen. Ein Service Konsument möchte gerne wissen, ob der Service Anbieter auch wirklich die Vereinbarungen erfüllt bzw. nach Vertrasgende erfüllt hat.Daher ist eine Überwachung der Performanz der Services bezüglich der vertraglichen Vereinbarung unabdinglich. In der Entwurfsphase einer Überwachungsinfrastruktur müssen Lösungen für Architekurentscheidungen getroffen werden, welche die betrieblichen und technischen Anforderung erfüllen . Ausserdem sind viele Akteure involviert welche unterschiedliches Hintergrundwissen und Interssen haben. Weiters sind die Anforderungen an die Überwachungsstruktur zu Beginn nicht klar definiert. Dadurch sind spätere Änderungen in der Architektur und in dessen Implementierung unumgänglich. In dieser Dissertation wird ein Modell vorgestellt um den Entwurf einer Überwachungsstruktur zu vereinfachen. Das Modell stellt Architekturlösungen für die Architekturentscheidungen vor, welche grundlegende Anforderungen erfüllen. Das vorgestellte Entwurfsmodell hilft Designern eine betriebsoptimale Überwachungsstruktur zu entwerfen.Damit die Akteure die vertraglichen Vereinbarungen spezifizieren können, werden modell-getriebene domänen-spezifische Sprachen verwendet. Die Verwendung von modell-getriebenen Sprachen ermöglicht Business-Experten die vertraglichen Vereinbarungen zu definieren ohne ein technologisches Wissen zu verfügen. Ausserdem wird ein inkrementeller Entwicklungsansatz vorgestellt welcher den Umgang mit späteren Änderungen erleichtert. Es wird eine Fallstudie präsentiert welche as Evaluationsgrundlage dient.Die Fallstudie beschäftigt sich mit Multimedia Services um Filme oder Live-Streams in einer gewünschten Sprache anzusehen.In a service-oriented system, services are utilized to perform inter- and cross-organization business tasks with few human intervention. Between a service provider and a service consumer contracts can exist containing performance-related Quality of Service (QoS) agreements, called Service Level Agreements (SLA). A services provider must prevent SLA violations in order to avoid serious financial consequences and a diminished reputation. Service consumers want to ensure that they get the service they pay for. In order to prevent and detect violations of the performance-related agreements during the SLA's validity, a monitoring infrastructure is required. To design an architecture of a QoS monitoring infrastructure, many architectural design decisions must be faced, depend on business and technical requirements. At early stages, the infrastructure's requirements are fuzzy and incomplete, making later changes inevitable. The design process and the specification of the negotiated performance-related QoS properties involve various differently skilled stakeholders, ranging from business to technical experts.In this thesis, we present an architectural design decision model that covers design decisions about measuring, storing, and evaluating performance-related QoS properties. The model proposes architectural solutions for the design decisions that fulfill the requirements.Model-driven Development (MDD) makes it possible to generate the QoS monitoring infrastructure almost automatically. To support the differently skilled stakeholders to specify the performance-related QoS agreements, we utilize Domain-specific Languages (DSL). The specified performance-related agreements are then monitored during the SLA's validity. We develop the model-driven DSLs using an incremental development approach. We evaluate our work in the scope of an industrial case study dealing with advanced multi-media services that have to comply with performance-related QoS agreements.The presented architectural design decision model guides the designers through the decision making process. Utilizing model-driven DSLs, business stakeholders can specify the performance-related agreements without technical knowledge. The stakeholders with a technical expertise describe the technological artifacts to monitor the performance-related agreements during the SLAs' validity. Developing model-driven DSLs incrementally helps the developers to deal with permanent changing requirements.14