A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research

Reduced-order models based on level-set methods are widely used tools to qualitatively capture and track the nonlinear dynamics of an interface. The aim of this paper is to develop a physics-informed, data-driven, statistically rigorous learning algorithm for state and parameter estimation with level-set methods. A Bayesian approach based on data assimilation is introduced. Data assimilation is enabled by the ensemble Kalman filter and smoother, which are used in their probabilistic formulations. The level-set data assimilation framework is verified in onedimensional and two-dimensional test cases, where state estimation, parameter estimation and uncertainty quantification are performed. The statistical performance of the proposed ensemble Kalman filter and smoother is quantified by twin experiments. In the twin experiments, the combined state and parameter estimation fully recovers the reference solution, which validates the proposed algorithm. The level-set data assimilation framework is then applied to the prediction of the nonlinear dynamics of a forced premixed flame, which exhibits the formation of sharp cusps and intricate topological changes, such as pinch-off events. The proposed physics-informed statistical learning algorithm opens up new possibilities for making reduced-order models of interfaces quantitatively predictive, any time that reference data is available.

We propose an on-the-fly statistical learning method to take a qualitative reduced-order model of the dynamics of a premixed flame and make it quantitatively accurate. This physics-informed data-driven method is based on the statistically optimal combination of (i) a reduced-order model of the dynamics of a premixed flame with a level-set method, (ii) high-quality data, which can be provided by experiments and/or high-fidelity simulations, and (iii) assimilation of the data into the reduced-order model to improve the prediction of the dynamics of the premixed flame. The reduced-order model learns the state and the parameters of the premixed flame on the fly with the ensemble Kalman filter, which is a Bayesian filter used, for example, in weather forecasting. The proposed method and algorithm are applied to two test cases with relevance to reacting flows and instabilities. First, the capabilities of the framework are demonstrated in a twin experiment, where the assimilated data are produced from the same model as that used in prediction. Second, the assimilated data are extracted from a high-fidelity reacting-flow direct numerical simulation (DNS), which provides the reference solution. The results are analyzed by using Bayesian statistics, which robustly provide the level of confidence in the calculations from the reduced-order model. The versatile method we propose enables the optimal calibration of computationally inexpensive reduced-order models in real-time when experimental data become available, for example, from gas-turbine sensors.

We combine a thermoacoustic experiment with a thermoacoustic reduced order model using Bayesian inference to accurately learn the parameters of the model, rendering it predictive. The experiment is a vertical Rijke tube containing an electric heater. The heater drives a base flow via natural convection, and thermoacoustic oscillations via velocity-driven heat release fluctuations. The decay rates and frequencies of these oscillations are measured every few seconds by acoustically forcing the system via a loudspeaker placed at the bottom of the tube. More than 320,000 temperature measurements are used to compute state and parameters of the base flow model using the Ensemble Kalman Filter. A wave-based network model is then used to describe the acoustics inside the tube. We balance momentum and energy at the boundary between two adjacent elements, and model the viscous and thermal dissipation mechanisms in the boundary layer and at the heater and thermocouple locations. Finally, we tune the parameters of two different thermoacoustic models on an experimental dataset that comprises more than 40,000 experiments. This study shows that, with thorough Bayesian inference, a qualitative model can become quantitatively accurate, without overfitting, as long as it contains the most influential physical phenomena.

No abstract

We propose an on-the-fly statistical learning method to take a qualitative reduced-order model of the dynamics of a premixed flame and make it quantitatively accurate. This physics-informed data-driven method is based on the statistically optimal combination of (i) a reduced-order model of the dynamics of a pre-mixed flame with a level-set method, (ii) high-quality data, which can be provided by experiments and/or high-fidelity simulations, and (iii) assimilation of the data into the reduced-order model to improve the prediction of the dynamics of the premixed flame. The reduced-order model learns the state and the parameters of the premixed flame on the fly with the ensemble Kalman filter, which is a Bayesian filter used, for example, in weather forecasting. The proposed method and algorithm are applied to two test cases with relevance to reacting flows and instabilities. First, the capabilities of the framework are demonstrated in a twin experiment, where the assimilated data is produced from the same model as that used in prediction. Second, the assimilated data is extracted from a high-fidelity reacting-flow direct numerical simulation (DNS), which provides the reference solution. The results are analyzed by using Bayesian statistics, which robustly provide the level of confidence in the calculations from the reduced-order model. The versatile method we propose enables the optimal calibration of computationally inexpensive reduced-order models in real time when experimental data becomes available, for example, from gas-turbine sensors.

No abstract

We combine a thermoacoustic experiment with a thermoacoustic reduced order model using Bayesian inference to accurately learn the parameters of the model, rendering it predictive. The experiment is a vertical Rijke tube containing an electric heater. The heater drives a base flow via natural convection, and thermoacoustic oscillations via velocity-driven heat release fluctuations. The decay rates and frequencies of these oscillations are measured every few seconds by acoustically forcing the system via a loudspeaker placed at the bottom of the tube. More than 320,000 temperature measurements are used to compute state and parameters of the base flow model using the Ensemble Kalman Filter. A wave-based network model is then used to describe the acoustics inside the tube. We balance momentum and energy at the boundary between two adjacent elements, and model the viscous and thermal dissipation mechanisms in the boundary layer and at the heater and thermocouple locations. Finally, we tune the parameters of two different thermoacoustic models on an experimental dataset that comprises more than 40,000 experiments. This study shows that, with thorough Bayesian inference, a qualitative model can become quantitatively accurate, without overfitting, as long as it contains the most influencial physical phenomena.