Related papers: TinkerCell: Modular CAD Tool for Synthetic Biology
Ecological systems can be seen as networks of interactions between individual, species, or habitat patches. A key feature of many ecological networks is their organization into modules, which are subsets of elements that are more connected…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
HYPERTILING is a high-performance Python library for the generation and visualization of regular hyperbolic lattices embedded in the Poincar\'e disk model. Using highly optimized, efficient algorithms, hyperbolic tilings with millions of…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
This paper discusses the implementation of a tactical network simulation tool. The tool is called Tactical Network Modeller (TNM). TNM uses some novel techniques to simplify the building of the network model using graph theory constrained…
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that…
Engineering simple, artificial models of living cells allows synthetic biologists to study cellular functions under well-controlled conditions. Reconstituting multicellular behaviors with synthetic cell-mimics is still a challenge because…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
Medical image processing demands specialized software that handles high-dimensional volumetric data, heterogeneous file formats, and domain-specific training procedures. Existing frameworks either provide low-level components that require…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
The modern deep learning field is a scale-centric one. Larger models have been shown to consistently perform better than smaller models of similar architecture. In many sub-domains of biomedical research, however, the model scaling is…
In this paper we present the latest version of the TCAD environment BICEP'S (Braunschweigs Integrated CAD-Environment for Product Planning and Process Simulation). By using a central process database, which allows the exchange of all…
In several applications, including in synthetic biology, one often has input/output data on a system composed of many modules, and although the modules' input/output functions and signals may be unknown, knowledge of the composition…
One of the major goals of nanobionics and bottom-up synthetic biology is the development of artificial cell organelles for the creation of cell-like structures operating similar to biological systems with a minimalistic set of building…
Early identification of a polyp in the lower gastrointestinal (GI) tract can lead to prevention of life-threatening colorectal cancer. Developing computer-aided diagnosis (CAD) systems to detect polyps can improve detection accuracy and…