Related papers: TinkerCell: Modular CAD Tool for Synthetic Biology
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or…
We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications…
The generative AI technology offers an increasing variety of tools for generating entirely synthetic images that are increasingly indistinguishable from real ones. Unlike methods that alter portions of an image, the creation of completely…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
The software development life cycle (SDLC) is a procedure used to develop a software system that meets both the customer s needs and real-world requirements. The first phase of the SDLC involves creating a conceptual model that represents…
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields.…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Analyzing medical data to find abnormalities is a time-consuming and costly task, particularly for rare abnormalities, requiring tremendous efforts from medical experts. Artificial intelligence has become a popular tool for the automatic…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…