A novel strategy for dynamic modeling of genome-scale interaction networks.

MOTIVATION: The recent availability of omics data allows the construction of holistic maps of interactions between numerous role-playing biomolecules. However, these networks are often static, ignoring the dynamic behavior of biological processes. On the other hand, dynamic models are commonly constructed on small scales. Hence, the construction of large-scale dynamic models that can quantitatively predict the time-course cellular behaviors remains a big challenge. RESULTS: In this study, a pipeline is proposed for the automatic construction of large-scale dynamic models. The pipeline uses a list of biomolecules and their time-course trajectories in a given phenomenon as input. First, the interaction network of the biomolecules is constructed. To state the underlying molecular events of each interaction, it is translated into a map of biochemical reactions. Next, to define the kinetics of the reactions, an ordinary differential equation (ODE) is generated for each involved biomolecule. Finally, the parameters of the ODE system are estimated by a novel large-scale parameter approximation method. The high performance of the pipeline is demonstrated by modeling the response of a colorectal cancer cell line to different chemotherapy regimens. In conclusion, Systematic Protein Association Dynamic ANalyzer constructs genome-scale dynamic models, filling the gap between large-scale static and small-scale dynamic modeling strategies. This simulation approach allows for holistic quantitative predictions which are critical for the simulation of therapeutic interventions in precision medicine. AVAILABILITY AND IMPLEMENTATION: Detailed information about the constructed large-scale model of colorectal cancer is available in supplementary data. The SPADAN toolbox source code is also available on GitHub (https://github.com/PooyaBorzou/SPADAN). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Design of robust adaptive controller and feedback error learning for rehabilitation in Parkinson's disease: a simulation study.

Deep brain stimulation (DBS) is an efficient therapy to control movement disorders of Parkinson's tremor. Stimulation of one area of basal ganglia (BG) by DBS with no feedback is the prevalent opinion. Reduction of additional stimulatory signal delivered to the brain is the advantage of using feedback. This results in reduction of side effects caused by the excessive stimulation intensity. In fact, the stimulatory intensity of controllers is decreased proportional to reduction of hand tremor. The objective of this study is to design a new controller structure to decrease three indicators: (i) the hand tremor; (ii) the level of delivered stimulation in disease condition; and (iii) the ratio of the level of delivered stimulation in health condition to disease condition. For this purpose, the authors offer a new closed-loop control structure to stimulate two areas of BG simultaneously. One area (STN: subthalamic nucleus) is stimulated by an adaptive controller with feedback error learning. The other area (GPi: globus pallidus internal) is stimulated by a partial state feedback (PSF) controller. Considering the three indicators, the results show that, stimulating two areas simultaneously leads to better performance compared with stimulating one area only. It is shown that both PSF and adaptive controllers are robust regarding system parameter uncertainties. In addition, a method is proposed to update the parameters of the BG model in real time. As a result, the parameters of the controllers can be updated based on the new parameters of the BG model.