Noncoder : a web interface for exon array-based detection of long non-coding RNAs

Due to recent technical developments, a high number of long non-coding RNAs (lncRNAs) have been discovered in mammals. Although it has been shown that lncRNAs are regulated differently among tissues and disease statuses, functions of these transcripts are still unknown in most cases. GeneChip Exon 1.0 ST Arrays (exon arrays) from Affymetrix, Inc. have been used widely to profile genome-wide expression changes and alternative splicing of protein-coding genes. Here, we demonstrate that re-annotation of exon array probes can be used to profile expressions of tens of thousands of lncRNAs. With this annotation, a detailed inspection of lncRNAs and their isoforms is possible. To allow for a general usage to the research community, we developed a user-friendly web interface called 'noncoder'. By uploading CEL files from exon arrays and with a few mouse clicks and parameter settings, exon array data will be normalized and analysed to identify differentially expressed lncRNAs. Noncoder provides the detailed annotation information of lncRNAs and is equipped with unique features to allow for an efficient search for interesting lncRNAs to be studied further. The web interface is available at http://noncoder.mpi-bn.mpg.de

Fast generation of stability charts for time-delay systems using continuation of characteristic roots

Many dynamic processes involve time delays, thus their dynamics are governed by delay differential equations (DDEs). Studying the stability of dynamic systems is critical, but analyzing the stability of time-delay systems is challenging because DDEs are infinite-dimensional. We propose a new approach to quickly generate stability charts for DDEs using continuation of characteristic roots (CCR). In our CCR method, the roots of the characteristic equation of a DDE are written as implicit functions of the parameters of interest, and the continuation equations are derived in the form of ordinary differential equations (ODEs). Numerical continuation is then employed to determine the characteristic roots at all points in a parametric space; the stability of the original DDE can then be easily determined. A key advantage of the proposed method is that a system of linearly independent ODEs is solved rather than the typical strategy of solving a large eigenvalue problem at each grid point in the domain. Thus, the CCR method significantly reduces the computational effort required to determine the stability of DDEs. As we demonstrate with several examples, the CCR method generates highly accurate stability charts, and does so up to 10 times faster than the Galerkin approximation method.Comment: 12 pages, 6 figure

Recommendations and illustrations for the evaluation of photonic random number generators

The never-ending quest to improve the security of digital information combined with recent improvements in hardware technology has caused the field of random number generation to undergo a fundamental shift from relying solely on pseudo-random algorithms to employing optical entropy sources. Despite these significant advances on the hardware side, commonly used statistical measures and evaluation practices remain ill-suited to understand or quantify the optical entropy that underlies physical random number generation. We review the state of the art in the evaluation of optical random number generation and recommend a new paradigm: quantifying entropy generation and understanding the physical limits of the optical sources of randomness. In order to do this, we advocate for the separation of the physical entropy source from deterministic post-processing in the evaluation of random number generators and for the explicit consideration of the impact of the measurement and digitization process on the rate of entropy production. We present the Cohen-Procaccia estimate of the entropy rate $h(\epsilon,\tau)$ as one way to do this. In order to provide an illustration of our recommendations, we apply the Cohen-Procaccia estimate as well as the entropy estimates from the new NIST draft standards for physical random number generators to evaluate and compare three common optical entropy sources: single photon time-of-arrival detection, chaotic lasers, and amplified spontaneous emission

Parameter estimation of an electrochemistry-based lithium-ion battery model

The final publication is available at Elsevier via http://doi.org/10.1016/j.jpowsour.2015.04.154" © 2015. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Parameters for an electrochemistry-based Lithium-ion battery model are estimated using the homotopy optimization approach. A high-fidelity model of the battery is presented based on chemical and electrical phenomena. Equations expressing the conservation of species and charge for the solid and electrolyte phases are combined with the kinetics of the electrodes to obtain a system of differential-algebraic equations (DAEs) governing the dynamic behavior of the battery. The presence of algebraic constraints in the governing dynamic equations makes the optimization problem challenging: a simulation is performed in each iteration of the optimization procedure to evaluate the objective function, and the initial conditions must be updated to satisfy the constraints as the parameter values change. The ε-embedding method is employed to convert the original DAEs into a singularly perturbed system of ordinary differential equations, which are then used to simulate the system efficiently. The proposed numerical procedure demonstrates excellent performance in the estimation of parameters for the Lithium-ion battery model, compared to direct methods that are either unstable or incapable of converging. The obtained results and estimated parameters demonstrate the efficacy of the proposed simulation approach and homotopy optimization procedure.The financial support of the NSERC/Toyota/Maplesoft Industrial Re-search Chair program is gratefully acknowledged

Development of an Integrated Control Strategy Consisting of an Advanced Torque Vectoring Controller and a Genetic Fuzzy Active Steering Controller

Replicated with permission by SAE Copyright © 2017 SAE International. Further distribution of this material is not permitted without prior permission from SAE.The optimum driving dynamics can be achieved only when the tire forces on all four wheels and in all three coordinate directions are monitored and controlled precisely. This advanced level of control is possible only when a vehicle is equipped with several active chassis control systems that are networked together in an integrated fashion. To investigate such capabilities, an electric vehicle model has been developed with four direct-drive in-wheel motors and an active steering system. Using this vehicle model, an advanced slip control system, an advanced torque vectoring controller, and a genetic fuzzy active steering controller have been developed previously. This paper investigates whether the integration of these stability control systems enhances the performance of the vehicle in terms of handling, stability, path-following, and longitudinal dynamics. An integrated approach is introduced that distributes the required control effort between the in-wheel motors and the active steering system. Several test maneuvers are simulated to demonstrate the performance and effectiveness of the integrated control approach, and the results are compared to those obtained using each controller individually. Finally, the integrated controller is implemented in a hardware- and operator-in-the-loop driving simulator to further evaluate its effectiveness.Funding for this work was provided by the Natural Sciences and Engineering Research Council of Canada and agrant from AUTO21, a Canadian Network of Centres of Excellenc

Development of a Fuzzy Slip Control System for Electric Vehicles with In-wheel Motors

Replicated with permission by SAE Copyright © 2017 SAE International. Further distribution of this material is not permitted without prior permission from SAE.A two-passenger all-wheel drive urban electric vehicle (AUTO21EV) with four direct-drive in-wheel motors and an active steering system has been designed and developed at the University of Waterloo. A novel fuzzy slip control system is developed for this vehicle using the advantage of four in-wheel motors. A conventional slip control system uses the hydraulic brake system in order to control the tire slip ratio, which is the difference between the wheel center velocity and the velocity of the tire contact patch along the wheel plane, thereby influencing the longitudinal dynamics of a vehicle. The advantage of the proposed fuzzy slip controller is that it acts as an ABS system by preventing the tires from locking up when braking, as a TCS by preventing the tires from spinning out when accelerating. More importantly, the proposed slip controller is also capable of replacing the entire hydraulic brake system of the vehicle by automatically distributing the braking force between the wheels using the available braking torque of the in-wheel motors. In this regard, the proposed fuzzy slip controller guarantees the highest traction or braking force on each wheel on every road condition by individually controlling the slip ratio of each tire with a much faster response time. The performance of the proposed fuzzy slip controller is confirmed by driving the AUTO21EV through several test maneuvers using a driver model in the simulation environment. As the final step, the fuzzy slip controller is implemented in a hardware- and operator-in-the-loop driving simulator and its performance and effectiveness is confirmed.Funding for this work was provided by the Natural Sciences and Engineering Research Council of Canada(NSERC) and a grant from AUTO21, a Canadian Network of Centres of Excellence

Development of an Advanced Torque Vectoring Control System for an Electric Vehicle with In-Wheel Motors using Soft Computing Techniques

Replicated with permission by SAE Copyright © 2017 SAE International. Further distribution of this material is not permitted without prior permission from SAE.A two-passenger, all-wheel-drive urban electric vehicle (AUTO21EV) with four direct-drive in-wheel motors has been designed and developed at the University of Waterloo. A 14-degree-of-freedom model of this vehicle has been used to develop a genetic fuzzy yaw moment controller. The genetic fuzzy yaw moment controller determines the corrective yaw moment that is required to stabilize the vehicle, and applies a virtual yaw moment around the vertical axis of the vehicle. In this work, an advanced torque vectoring controller is developed, the objective of which is to generate the required corrective yaw moment through the torque intervention of the individual in-wheel motors, stabilizing the vehicle during both normal and emergency driving maneuvers. Novel algorithms are developed for the left-to-right torque vectoring control on each axle and for the front-to-rear torque vectoring distribution action. Several maneuvers are simulated to demonstrate the performance and effectiveness of the proposed advanced torque vectoring controller, and the results are compared to those obtained using the ideal genetic fuzzy yaw moment controller. The advanced torque vectoring controller is also implemented in a hardware- and operator-in-the-loop driving simulator to further evaluate its performance.Funding for this work was provided by the Natural Sciences and Engineering Research Council of Canada and agrant from AUTO21, a Canadian Network of Centres of Excellenc

Development of an Advanced Fuzzy Active Steering Controller and a Novel Method to Tune the Fuzzy Controller

Replicated with permission by SAE Copyright © 2017 SAE International. Further distribution of this material is not permitted without prior permission from SAE.A two-passenger, all-wheel-drive urban electric vehicle (AUTO21EV) with four direct-drive in-wheel motors has been designed and developed at the University of Waterloo. An advanced genetic-fuzzy active steering controller is developed based on this vehicle platform. The rule base of the fuzzy controller is developed from expert knowledge, and a multi-criteria genetic algorithm is used to optimize the parameters of the fuzzy active steering controller. To evaluate the performance of this controller, a computational model of the AUTO21EV is driven through several standard test maneuvers using an advanced path-following driver model. As the final step in the evaluation process, the genetic-fuzzy active steering controller is implemented in a hardware- and operator-in-the-loop driving simulator to confirm its performance and effectiveness.Funding for this work was provided by the Natural Sciences and Engineering Research Council of Canada and agrant from AUTO21, a Canadian Network of Centres of Excellenc