Description

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Code

This software, written in MatLab, implements a variancebased approach to sensitivity analysis of biochemical reaction systems based on a biophysically derived model for parameter fluctuations. It produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of highorder interaction effects.



This software, coded in MatLab, implements four techniques, derivative approximation, polynomial approximation, GaussHermite integration, and orthonormal Hermite approximation, for analytically approximating the variancebased sensitivity indices associated with a biochemical reaction system.



This software, coded in Matlab, implements a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. The method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations.



This software, coded in Matlab, implements a variancebased approach to sensitivity analysis of biochemical reaction systems that explicitly models experimental variability and effectively reduces the impact of this type of uncertainty on the results. The approach is based on a previously proposed approach to probabilistic sensitivity analysis and leads to a technique that can be effectively used to accomodate appreciable levels of experimental variability. The software uses a computational model of the epidermal growth factor receptor signaling pathway.



This software, coded in Matlab, implements a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. TCMC formulates the model calibration problem as a constrained optimization problems that takes thermodynamic constraints (and, if desired, additional nonthermodynamic constraints) into account. The provided software uses the Systems Biology Toolbox 2.1 that can be obtained by clicking here.



This software, coded in Matlab, implements a method for numerically integrating the master equation associated with the stochastic SIR model of epidemiology. The method is based on an informative stochastic process, known as the degreeofadvancement. Exploiting the stucture of the master equation governing this process results in a novel numerical algorithm for calculating the exact solution of the master equation, up to a desired precision, which is referred to as the implicit Euler method. The provided software uses the Expokit software package, whose details can be found by clicking here. 


This software, coded in Matlab, implements three examples of Markovian reaction networks used to illustrate key concepts of the theory of such networks. The examples include: opinion formation in social networks, transcription regulation in biochemical reaction networks, and avalanche formation in neural networks.



This software, coded in Matlab, implements four examples of an effective statistical methodology that addresses the problem of checking whether a particular analytical or computational scheme to the solution of the chemical master equation is valid. The proposed technique is based on drawing a moderate number of samples from the master equation and on using the wellknown KolmogorovSmirnov test statistic to reject the validity of a given approximation method or accept it with a certain level of confidence.



This software, coded in Matlab, implements a method proposed for investigating the role intrinsic fluctuations play in creating avalanches in leaky Markovian networks. Using this broad class of models, the method employs a potential energy landscape perspective, coupled with a macroscopic description based on statistical thermodynamics, to study the emergence of avalanching in many biological, physical and manmade interaction networks.



This software, coded in R, implements IntegraMir, a novel integrative computational method to infer certain types of deregulated miRNAmediated regulatory circuits at the transcriptional, posttranscriptional and signaling levels. To reliably predict miRNAtarget interactions from mRNA/miRNA expression data, the method collectively utilizes sequencebased miRNAtarget predictions obtained from several algorithms, known information about mRNA and miRNA targets of TFs available in existing databases, certain molecular structures identified to be statistically overrepresented in gene regulatory networks, available molecular subtyping information, and stateoftheart statistical techniques to appropriately constrain the underlying analysis.



This software, coded in Matlab, provides an insilico implementation of iPOLYMER by modelling the underlying reactions. The implementation is based on a realistic kinetic Monte Carlo simulation algorithm, which produces sufficiently accurate approximations of stochastic reaction/diffusion dynamics. The underlying model employs a stochastic biochemical reaction system, which contains three types of molecules, FKBP, FRB and rapamycin. These molecules interact according to four reversible reactions and are subject to random diffusion. The package also contains the two C++ executable files (by John Pfaltz) GR_RED and CYCLE_DIST, implemented in a Unix platform, which are used to identify chordless cycles in a graph. It also contains the text file PARAMETERS, which provides values for the physical lengths of the constituent molecules FKBP and FRB, their valencies, as well as the physical lenfth of the FKBPRapaFRB complex and the physical distance between consecutive binding sites on FKBP and FRB molecules.

H. Nakamura, A. A. Lee, A. S. Afshar, S. Watanabe, E. Rho, S. Razavi, A. Suarez, Y.C. Lin, M. Tanigawa, B. Huang, R. DeRose, D. Bobb,W. Hong, S. B. Gabelli, J. Goutsias, and T. Inoue,
Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions
Nature Materials
xx(xx): xxxxxx, 2017. 
