On Quantitative Comparison of Chemical Reaction Network Models

Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations. Their dynamic behaviours are then analysed, often by using deterministic methods based on differential equations with a focus on the steady states. Here, we propose a method for comparing CRNs with respect to their behaviour in stochastic simulations. Our method is based on using the flux graphs that are delivered by stochastic simulations as abstract representations of their dynamic behaviour. This allows us to compare the behaviour of any two CRNs for any time interval, and define a notion of equivalence on them that overlaps with graph isomorphism at the lowest level of representation. The similarity between the compared CRNs can be quantified in terms of their distance. The results can then be used to refine the models or to replace a larger model with a smaller one that produces the same behaviour or vice versa.Comment: In Proceedings HCVS/PERR 2019, arXiv:1907.0352

A component-based collaboration infrastructure

Groupware applications allow geographically distributed users to collaborate on shared tasks. However, it is widely recognized that groupware applications are expensive to build due to coordination services and group dynamics, neither of which is present in single-user applications. Previous collaboration transparency systems reuse existing single-user applications as a whole for collaborative work, often at the price of inflexible coordination. Previous collaboration awareness systems, on the other hand, provide reusable coordination services and multi-user widgets, but often with two weaknesses: (1) the multi-user widgets provided are special-purpose and limited in number, while no guidelines are provided for developing multi-user interface components in general; and (2) they often fail to reach the desired level of flexibility in coordination by tightly binding shared data and coordination services. In this dissertation, we propose a component-based approach to developing group- ware applications that addresses the above two problems. To address the first prob- lem, we propose a shared component model for modeling data and graphic user inter- face(GUI) components of groupware applications. As a result, the myriad of existing single-user components can be re-purposed as shared GUI or data components. An adaptation tool is developed to assist the adaptation process. To address the second problem, we propose a coordination service framework which systematically model the interaction between user, data, and coordination protocols. Due to the clean separation of data and control and the capability to dynamically "glue" them together, the framework provides reusable services such as data distribution, persistence, and adaptable consistency control. The association between data and coordination services can be dynamically changed at runtime. An Evolvable and eXtensible Environment for Collaboration (EXEC) is built to evaluate the proposed approach. In our experiments, we demonstrate two benefits of our approach: (1) a group of common groupware features adapted from existing single- user components are plugged in to extend the functionalities of the environment itself; and (2)coordination services can be dynamically attached to and detached from these shared components at different granules to support evolving collaboration needs

A component-based collaboration infrastructure

Groupware applications allow geographically distributed users to collaborate on shared tasks. However, it is widely recognized that groupware applications are expensive to build due to coordination services and group dynamics, neither of which is present in single-user applications. Previous collaboration transparency systems reuse existing single-user applications as a whole for collaborative work, often at the price of inflexible coordination. Previous collaboration awareness systems, on the other hand, provide reusable coordination services and multi-user widgets, but often with two weaknesses: (1) the multi-user widgets provided are special-purpose and limited in number, while no guidelines are provided for developing multi-user interface components in general; and (2) they often fail to reach the desired level of flexibility in coordination by tightly binding shared data and coordination services. In this dissertation, we propose a component-based approach to developing group- ware applications that addresses the above two problems. To address the first prob- lem, we propose a shared component model for modeling data and graphic user inter- face(GUI) components of groupware applications. As a result, the myriad of existing single-user components can be re-purposed as shared GUI or data components. An adaptation tool is developed to assist the adaptation process. To address the second problem, we propose a coordination service framework which systematically model the interaction between user, data, and coordination protocols. Due to the clean separation of data and control and the capability to dynamically "glue" them together, the framework provides reusable services such as data distribution, persistence, and adaptable consistency control. The association between data and coordination services can be dynamically changed at runtime. An Evolvable and eXtensible Environment for Collaboration (EXEC) is built to evaluate the proposed approach. In our experiments, we demonstrate two benefits of our approach: (1) a group of common groupware features adapted from existing single- user components are plugged in to extend the functionalities of the environment itself; and (2)coordination services can be dynamically attached to and detached from these shared components at different granules to support evolving collaboration needs

Textual Assemblages and Transmission: Unified models for (Digital) Scholarly Editions and Text Digitisation

Scholarly editing and textual digitisation are typically seen as two distinct, though related, fields. Scholarly editing is replete with traditions and codified practices, while the digitisation of text-bearing material is a recent enterprise, governed more by practice than theory. From the perspective of scholarly editing, the mere digitisation of text is a world away from the intellectual engagement and rigour on which textual scholarship is founded. Recent developments have led to a more open-minded perspective. As scholarly editing has made increasing use of the digital medium, and textual digitisation begins to make use of scholarly editing tools and techniques, the more obvious distinctions dissolve. Such criteria as ‘critical engagement’ become insufficient grounds on which to base a clear distinction. However, this perspective is not without its risks either. It perpetuates the idea that a (digital) scholarly edition and a digitised text are interchangeable. This thesis argues that a real distinction can be drawn. It starts by considering scholarly editing and textual digitisation as textual transmissions. Starting from the ontological perspective of Deleuze and Guattari, it builds a framework capable for considering the processes behind scholarly editing and digitisation. In doing so, it uncovers a number of critical distinction. Scholarly editing creates a regime of representation that is self-consistent and self-validating. Textual digitisation does not. In the final chapters, this thesis uses the crowd-sourced Letters of 1916 project as a test-case for a new conceptualisation of a scholarly edition: one that is neither globally self-consistent nor self-validating, but which provides a conceptual model in which these absences might be mitigated against and the function of a scholarly edition fulfilled

Proceedings of the 19th Sound and Music Computing Conference

Proceedings of the 19th Sound and Music Computing Conference - June 5-12, 2022 - Saint-Étienne (France). https://smc22.grame.f