Related papers: TinkerCell: Modular CAD Tool for Synthetic Biology
Chimeric Antigen Receptor (CAR) T-cell therapy is an immunotherapy that has recently become highly instrumental in the fight against life-threatening diseases. A variety of modeling and computational simulation efforts have addressed…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
We present a new approach for the design of a synthetic biological circuit whose behaviour is specified in terms of signal temporal logic (STL) formulae. We first show how to characterise with STL formulae the input/output behaviour of…
During the last decades, medical observations and multiscale data concerning tumor growth are mounting. At the same time, contemporary imaging techniques well established in clinical practice, provide a variety of information on real-time,…
Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of…
Designing synthetic routes for novel molecules is pivotal in various fields like medicine and chemistry. In this process, researchers need to explore a set of synthetic reactions to transform starting molecules into intermediates step by…
Background. Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and functional…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Advances in robotic automation, high-performance computing (HPC), and artificial intelligence (AI) encourage us to conceive of science factories: large, general-purpose computation- and AI-enabled self-driving laboratories (SDLs) with the…
A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to…
Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
In this paper we present SADDLE, a modular framework for automated design of cluster supercomputers and data centres. In contrast with commonly used approaches that operate on logic gate level (Verilog, VHDL) or board level (such as EDA…
Silicon has striking similarity with carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can…
With the rapidly increasing rate of microlensing planet detections, microlensing modeling software faces significant challenges in computation efficiency. Here, we develop the Twinkle code, an efficient and robust binary-lens modeling…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
Boundary Representation (B-Rep) is the widely adopted standard in Computer-Aided Design (CAD) and manufacturing. However, generative modeling of B-Reps remains a formidable challenge due to their inherent heterogeneity as geometric cell…
Background: Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides…