Related papers: Process Bigraphs and the Architecture of Compositi…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The role of scalable high-performance workflows and flexible workflow management systems that can support multiple simulations will continue to increase in importance. For example, with the end of Dennard scaling, there is a need to…
Hierarchical Gaussian Process (H-GP) models divide problems into different subtasks, allowing for different models to address each part, making them well-suited for problems with inherent hierarchical structure. However, typical H-GP models…
In modern cloud-based architectures, containers play a central role: they provide powerful isolation mechanisms such that developers can focus on the logic and dependencies of applications while system administrators can focus on deployment…
Parallel dataflow systems have become a standard technology for large-scale data analytics. Complex data analysis programs in areas such as machine learning and graph analytics often involve control flow, i.e., iterations and branching.…
Motivation: Estimating model parameters from experimental observations is one of the key challenges in systems biology and can be computationally very expensive. While the Julia programming language was recently developed as a high-level…
Bigraph reactive systems offer a powerful and flexible mathematical framework for modelling both spatial and non-spatial relationships between agents, with practical applications in domains such as smart technologies, networks, sensor…
This paper tries to reduce the effort of learning, deploying, and integrating several frameworks for the development of e-Science applications that combine simulations with High-Performance Data Analytics (HPDA). We propose a way to extend…
Biopharmaceutical manufacturing is a rapidly growing industry with impact in virtually all branches of medicines. Biomanufacturing processes require close monitoring and control, in the presence of complex bioprocess dynamics with many…
The notion of complex systems is common to many domains, from Biology to Economy, Computer Science, Physics, etc. Often, these systems are made of sets of entities moving in an evolving environment. One of their major characteristics is the…
Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step…
Causal models capture cause-effect relations both qualitatively - via the graphical causal structure - and quantitatively - via the model parameters. They offer a powerful framework for analyzing and constructing processes. Here, we…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
Bigraphical Reactive Systems (BRSs) are a graph-rewriting formalism describing systems evolving in two dimensions: spatially, e.g. a person in a room, and non-spatially, e.g. mobile phones communicating regardless of location. Despite use…
This volume contains the proceedings of the Second International Workshop Hybrid Systems and Biology (HSB 2013) held in Taormina (Italy), on September 2th, 2013. The workshop is affiliated to the 12th European Conference on Artificial Life…
Understanding cellular trajectories via time-resolved single-cell transcriptomics is vital for studying development, regeneration, and disease. A key challenge is inferring continuous trajectories from discrete snapshots. Biological…
From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…