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Computational models of plants have identified gaps in our understanding of biological systems, and have revealed ways to optimize cellular processes or organ-level architecture to increase productivity. Thus, computational models are learning tools that help direct experimentation and measurements. Models are simplifications of complex systems, and often simulate specific processes at single scales (e.g., temporal, spatial, organizational, etc.). Consequently, single-scale models are unable to capture the critical cross-scale interactions that result in emergent properties of the system. In this perspective article, we contend that to accurately predict how a plant will respond in an untested environment, it is necessary to integrate mathematical models across biological scales. Computationally mimicking the flow of biological information from the genome to the phenome is an important step in discovering new experimental strategies to improve crops. A key challenge is to connect models across biological, temporal, and computational (e.g. CPU vs GPU) scales, and then to visualize and interpret integrated model outputs. We address this challenge by describing the efforts of the international Crops in silico consortium.
This article was published in the following journal.
Name: The Plant journal : for cell and molecular biology
Peripheral Artery Disease (PAD) is an atherosclerotic disorder that leads to impaired lumen patency through intimal hyperplasia and the build-up of plaques, mainly localized in areas of disturbed flow...
Large scale biological responses are inherently uncertain, in part as a consequence of noisy systems that do not respond deterministically to perturbations and measurement errors inherent to technolog...
Here, we introduce models at three levels (molecular level, cellular and omics level, and organ and system level) that study drug mechanism and safety in preclinical drug discovery. The models differ ...
This special issue on "Multiscale phenomena and patterns in biological systems" is an homage to the seminal contributions of Hans Othmer. He has remained at the forefront of multiscale modelling and p...
Fundamental advances to increase the efficiency as well as stability of organic photovoltaics (OPVs) are achieved by designing ternary blends, which represents a clear trend toward multicomponent acti...
Computational simulation will be performed to represent motion of knees with a dislocating kneecap. Common surgical treatment methods will be simulated and anatomical parameters commonly a...
The purpose of this study is to (1) quantify cardiovascular anatomy and physiology using magnetic resonance imaging under both resting and exercise conditions in patients who have congenit...
The choice of treatment of patients with metastatic melanoma depends on the status of B-RAF of the tumor: in the absence of mutation, treatment with immunotherapy (currently anti-PD1) is p...
The investigators propose a single center prospective study that will assess two different strategies for measuring Fractional Flow Reserve (FFR) in patients undergoing clinically-indicate...
With 50% of post-operative biochemical failure, efficient predictive models are needed to guide post-operative management. Radiomic features are quantitative features extracted from medic...
Models connecting initiating events at the cellular and molecular level to population-wide impacts. Computational models may be at levels relating toxicology to adverse effects.
Human experimentation that is not intended to benefit the subjects on whom it is performed. Phase I drug studies (CLINICAL TRIALS, PHASE I AS TOPIC) and research involving healthy volunteers are examples of nontherapeutic human experimentation.
Human experimentation that is intended to benefit the subjects on whom it is performed.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Any dummy medication or treatment. Although placebos originally were medicinal preparations having no specific pharmacological activity against a targeted condition, the concept has been extended to include treatments or procedures, especially those administered to control groups in clinical trials in order to provide baseline measurements for the experimental protocol.
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...