Setting the basis of best practices and standards for curation and annotation of logical models in biology

International audienceThe fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here,we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field. Scientists from different systems biology fields have long been developing community-driven guidelines and best practices for annotation, interoperability and reusability of computational models in biology. However, the parallel work, grounded on shared needs and similar aims, of separate communities creates a need for exchange and alignment of the different efforts to harmonise best practices. Hence, members of the Consortium for Logical Models and Tools (CoLoMoTo, http://colomoto.org) and the Computational Modelling of Biological Systems community of the International Society for Computational Biology (SysMod, https:// sysmod.info/) organised aworkshop to discusscommunitydriven guidelines and efforts for the curation and annotation of computational models during [BC]2 2021. The workshop grew from a previous edition organised during [BC]2 2019 focused on logical modelling [1]. The second edition brought together scientists with various research backgrounds and from different working groups such as BioModels [2], a central repository of mathematical models of biological/biomedical processes; the Computational Modelling in Biology Network initiative (COMBINE) [3]; CoLoMoTo, [4]; SysMod, [5]; the Systems Biology Graphical Notation (SBGN) project [6]; the systems biology markup language (SBML) [7] and simulation experiment description markup language (SED-ML) [8], to exchange and expand on several key topics of common interest (Figure 1). While the modelling approaches across these communities differ, several critical points are shared, such as (i) the importance of annotations for reproducibility, (ii) the use of community standards for exchange and annotation encoding, (iii) the need to implement standards in tools and platforms to boost reusability and interoperability, (iv) the importance of transparency of modelling frameworks in publications and (v) the use of shared repositories to enhance model accessibility (Figure 2). We use the term annotation to describe ‘a computeraccessible metadata item that captures, entirely or in part, the meaning of a model, model component or data element’. We borrow this definition from [9] which is in accordance with its use in [1]. We discuss the identified needs in the following sections

Conceptional Design of a Digital Twin to Predict the Useful Lifetime of a Gearbox

In figure 1 the schematic approach of this thesis is summarized. The outcome can be categorized in four sections with similar extent. In the first section, "Service", the digital twin concept is elaborated on the basis of investigated requirements which are defined via the identification of the system stakeholder for the realization of MoL applications. The focus on service provision is enabled via the system-protagonist interaction analysis which is represented by the aggregation of use cases. The development procedure is accompanied by SysML diagrams which are part of the section "Representation". For the modeling of the interactions between the protagonists and the digital twin, sequence diagrams are created. The static system structure is represented by block diagrams which are generated in the software "Enterprise Architect". The third section, "Analysis", includes the related gearbox investigation which is summarized in a simulationmodel that is comprising besides a diagnostics part with load-based (damage accumulation) and vibration-based (IAS signal analysis) approaches, a prognostics part, which is presenting a similarity and degradation estimation. The data input to the simulationmodel is established by HCP-Sense bearings and magnetoresistive sensors which are applied for monitoring the gearbox components, namely the bearings and the gear wheels with their toothing. Based on the data input from the sensors the subsequent information transmission within the system structure is described in the fourth section, "Communication". In this section, interfaces which are categorized by OSI-layers and the specification of objects, transferred between the system elements, are defined. The modularity of the system structure is achieved by the definition of adaption nodes

Leveraging Circular Economy through a Methodology for Smart Service Systems Engineering

Product Service Systems (PSS) and Smart Services are powerful means for deploying Circular Economy (CE) goals in industrial practices, through dematerialization, extension of product lifetime and efficiency increase by digitization. Within this article, approaches from PSS design, Smart Service design and Model-based Systems Engineering (MBSE) are combined to form a Methodology for Smart Service Architecture Definition (MESSIAH). First, analyses of present system modelling procedures and systems modelling notations in terms of their suitability for Smart Service development are presented. The results indicate that current notations and tools do not entirely fit the requirements of Smart Service development, but that they can be adapted in order to do so. The developed methodology includes a modelling language system, the MESSIAH Blueprinting framework, a systematic procedure and MESSIAH CE, which is specifically designed for addressing CE strategies and practices. The methodology was validated on the example of a Smart Sustainable Street Light System for Cycling Security (SHEILA). MESSIAH proved useful to help Smart Service design teams develop service-driven and robust Smart Services. By applying MESSIAH CE, a sustainable Smart Service, which addresses CE goals, has been developed

Model-Based Systems Engineering for the Design of an Intermodal High-Speed Freight Train Terminal

Since rail traffic is the mode of mass transport with minimal transportation-related greenhouse gas emissions, it plays a key role in achieving the sustainability targets of the transportation sector. To enable a modal shift from road to rail the German Aerospace Center has developed the Next Generation Train CARGO, a high-speed freight train concept targeted to ship so-called Low-Density High Value goods on existing railway infrastructure. Studies have revealed that an intermodal transshipment terminal is key to a successful integration of the concept in current logistics networks. Driven by high requirements regarding handling, reliability, and time, the terminal is a complex intralogistics system strongly depending on the particular good that shall be handled. This work uses the principles and methods of Model-Based Systems Engineering in a tailored modeling approach to specify a generic terminal system architecture. Based on this generic architecture an exemplary good-specific variant of the terminal is derived with focus on intralogistics freight handling. The chosen design approach is further evaluated regarding its suitability in context of intralogistics system design. The results of this work demonstrate that Model-Based Systems Engineering is capable of successfully guiding architecture specification in the novel application domain of complex intralogistics facilities and further contributes to a consistent and comprehensive terminal design

Systems Engineering and Its Application to Industrial Product Development

PREFACE : Mastering the complexity of innovative systems currently looks a challenging goal of design and product development as well as embedding a suitable degree of smartness in devices, machines and equipment to make them able of adapting their operation to variable conditions or effects of a harsh environment. This goal is achieved through a continuous monitoring of the system in service, an effec-tive control of its behavior and a wide connectivity towards many other systems. Only an effective system design and manufacture, able to cover all the required actions, can assure this kind of assessment overall the life cycle since a very ear-ly concept of the product to a full disposal and service. Complexity makes hard managing the product development, because of the number of functions, subsystems, components and related interfaces usually in-volved, like in motor vehicles, robots, railways systems, aircrafts and spacecrafts as well as in large industrial manufacturing systems or very innovative microsys-tems and bioinspired devices. A crucial issue in this activity is performing a bright and complete elicitation of requirements, which need to be fully and suit-ably allocated to the system components, through a clear traceability, especially in systems produced as a result of material processing and assembling of parts. Moreover, the product must fit the requirements associated to some customer needs, innovation targets, and technical standards and be compatible with the manufacturer’s capabilities. As it looks clear from the current state–of–art, since several years the Systems Engineering assures a suitable answer to the needs above mentioned. It provides a methodology to drive the product lifecycle assessment that is implemented through a well defined process, being based on some specific and graphical lan-guages and even formalized in several tools enabling the required analyses, tak-ing advantage of the capabilities of some dedicated commercial software. Those contents lead to create a platform, consisting of a sort of tools chain, which might be used and shared among different industrial and professional partners to digitalize both the information and even the whole industrial product develop-ment, as far as the current strategy referred to as “Industry 4.0 / The Factory of the Future” brightly suggests and supports. The so–called Model Based Systems Engineering (MBSE) is then successfully proposing an effective and modern al-ternative to the document-based approach, using data models as a main element of the design process. Some technical standards already drive the user in imple-menting the Systems Engineering, thus leading to develop a systematic approach the design aimed at satisfying the customer needs. Suitable capabilities in the manufactured system are assured by the so–called architectural frameworks, which support the system development and integration. The Model Based Systems Engineering allows proceeding with a modeling activity which investigates requirements, behavior and architecture through a combined operational, functional and logical analysis, being linked and interop-erated with a mathematical and physical modeling, which is typically more known and widely used within the industrial engineering. A full integration of all the activities of the Product Lifecycle Management (PLM) is currently going on, to include the system architecture definition and its Application Lifecycle Man-agement (ALM) as well as the Product Data Management (PDM), i.e. the design activity together with the tasks of production, testing, homologation and service. A recognized standard certification to qualify the Systems Engineer is even available as the International Council on Systems Engineering (INCOSE) pro-vides. The scenario above described is strongly integrated with the increasing devel-opment of both the network and the cyber–physical systems, for a fully distribut-ed connectivity, to be exploited in advanced smart systems and devices as well as in intelligent manufacturing, according to the most recent strategies of innova-tion as the “Industry 4.0” initiative and the “Lean manufacturing” idea. Simulta-neously, the system smartness and connectivity together increase the demand of data transmission and elaboration, thus linking this topic to the technology of big data management, whilst they benefit of the progress in information technology, through a secure cloud based on the network. The context just described motivates the fast diffusion of the Model Based Systems Engineering as a tool for innovating all the production processes. The increasing demand of specialized software and of educational activities as well as the number of workshops and conferences focused on this topic confirm this trend. However, it might be remarked that several contributions to the literature about the Systems Engineering widely grew up during the last years, thus making the Reader sometimes confused, especially when approaching this topic at first. The Systems Engineering topics are so many that it looks rather difficult mas-tering its skills, without a preliminary classification of contents. Technical do-mains involved are mainly those of engineering and computer science, although many other ones play the role of a daily user of this methodology. According to the most recent development of the Systems Engineering, whose typical applica-tion fields were the software and electronic systems even for space missions, the current focus consists of several industrial systems, being gradually innovated by introducing the tailored solutions of mechatronics. It is worthy noticing that a significant advancement was introduced between the very early implementation of the Systems Engineering and its recent evolution, since several new applica-tions are focused on the production of systems, which need to be manufactured through a material processing. Usually, they exhibit some attributes related both to their physical nature and to the functions performed, thus requiring to model both their functional and physical behaviors together. This need is changing the scenario of the typical applications of the Systems Engineering as software de-sign. This handbook expressively avoids to cover all the typical contents of the spe-cialized literature of the Model Based Systems Engineering, whilst is aimed at making easier a first approach to this topic and sharing a preliminary experience performed by the authors within some industrial domains, by proceeding in the modeling activity in a real industrial environment. The main goal is drawing a sort of simple and hopefully clear roadmap in modeling and developing the in-dustrial and material systems and in implementing the Systems Engineering, par-ticularly in the design activity. Therefore, the target audience of this handbook includes professional engineers, scientists and students dealing with the Applica-tion Lifecycle Management and the system architecture assessment, more than the Product Data Management or the whole Product Lifecycle Management. The approach followed is that of introducing some examples of implementa-tion of the Systems Engineering, by proceeding step by step from the screening of needs and the elicitation of requirements till a synthesis of the system design. Each action will be referred to the literature, related to the implementation of the Systems Modeling Language or SysML and to the use of some tools available on market, thus highlighting benefits, drawbacks and current limitations of some dedicated software or even of some proposed methodologies. Several comments will be provided to describe the troubles shared among some users of the Sys-tems Engineering as they were detected in daily practice by the authors. They wish that this handbook could briefly and gradually provide the Reader with a preliminary guideline to approach professionally the Model Based Systems En-gineering, by understanding its main contents and applying it to the industrial environment. As a desired result, this work might be considered as an integration of some textbooks of Machine Design, and it is aimed at completing the education within Engineering Design or at simply providing a friendly introduction to the Systems Engineerin

An Approach to Complement Model-Based Vehicle Development by Implementing Future Scenarios

Today, vehicle development is already in a process of substantial transformation. Mobility trends can be derived from global megatrends and have a significant influence on the requirements of the developed vehicles. The sociological, technological, economic, ecological, and political developments can be determined by using the scenario technique. The results are recorded in the form of differently shaped scenarios; however, they are mainly document-based. In order to ensure a holistic approach in the sense of model-based systems engineering and to be able to trace the interrelationships of the fast-changing trends and requirements, it is necessary to implement future scenarios in the system model. For this purpose, a method is proposed that enables the consideration of future scenarios in model-based vehicle development. The procedure of the method is presented, and the location of the future scenarios within the system architectures is named. The method is applied and the resulting system views are derived based on the application example of an autonomous people mover. With the help of the described method, it is possible to show the effects of a change of scenario (e.g., best-case and worst-case) and the connections with the highest level of requirements: stakeholder need

Análise da concepção de sistemas de sistemas com a notação SysML

Mestrado em Engenharia InformáticaNos últimos anos, a existência de sistema de sistemas é considerada como uma banalidade, algo que aceitamos como um dado adquirido. Um exemplo deste tipo de sistemas é o automóvel, composto por vários sistemas secundários, que entre si permitem criar um sistema único, capaz de nos mover de um local A para um local B. No entanto, a projecção de tais sistemas envolve um elevado número de equipas, cada uma delas com os seus próprios recursos, metodologias e conhecimentos, levando a que a inter-comunicação seja seriamente afectada. A notação SysML, derivada do UML, possibilita a comunicação destas equipas entre si, utilizando para isso uma linguagem comum a todos. Através das várias características da notação (diagramas, estereótipos, entre outras), é possível transmitir as ideias de forma clara e inequívoca. O objectivo desta Tese passa por analisar todos estes aspectos teóricos e práticos, para que seja possível apresentar conclusões sobre a notação e a sua utilidade na modelação de sistema de sistemas.In recent years, the existence of system of systems is considered usual, as something that we can rely on. One example of this type of systems is the car, made from various secondary systems, which as a whole, allow us to create an unique system, capable of moving us from point A to point B. However, the making of such systems involves a great number of teams, each one with their own resources, methodologies and knowledges, leading to a rather difficult inter-communication. The SysML notation, derived from UML, allows the communication between the different teams, using a common language. With the help of several characteristics of the language (such as diagrams, stereotypes, among others), the clear and undoubtful transmission of ideas and knowledges is made possible. The objective of this Thesis is to analyze all theorical and practical aspects of the notation, so that is possible to conclude about its utility in the modeling of system of systems