scholarly journals SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

Processes ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1830
Author(s):  
Takahiro G. Yamada ◽  
Kaito Ii ◽  
Matthias König ◽  
Martina Feierabend ◽  
Andreas Dräger ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Steady State ◽  
Systems Biology ◽  
Source Code ◽  
Data Availability ◽  
Easy Access ◽  
Free Access ◽  
Web Based ◽  
Steady State Analysis ◽  
State Analysis

In systems biology, biological phenomena are often modeled by Ordinary Differential Equations (ODEs) and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulation, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the Systems Biology Simulation Core Library (SBSCL), and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code freely available. At the end of this article, the Data Availability Statement gives the internet links to the two websites to find the source code and run the program online.

scholarly journals SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

2021 ◽  
Author(s):  
Takahiro G. Yamada ◽  
Kaito Ii ◽  
Matthias König ◽  
Martina Feierabend ◽  
Andreas Dräger ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Steady State ◽  
Systems Biology ◽  
Easy Access ◽  
Free Access ◽  
Web Based ◽  
Steady State Analysis ◽  
Ode Models ◽  
Biological Phenomena ◽  
State Analysis

In systems biology, biological phenomena are often modeled by ODE and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulations, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the SBSCL, and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code available from https://github.com/TakahiroYamada/SBMLWebApp. The program runs online at http://simulate-biology.org.

Analysis of Single Buffer Random Polling System With State-Dependent Input Process and Server/Station Breakdowns

2018 ◽  
Vol 9 (1) ◽  
pp. 22-50 ◽  
Author(s):  
Thomas Y.S. Lee
Keyword(s):  
Steady State ◽  
Linear Model ◽  
Repair Process ◽  
Polling System ◽  
Steady State Analysis ◽  
Relaxation System ◽  
Polling Model ◽  
State Dependent ◽  
Non Linear ◽  
State Analysis

Models and analytical techniques are developed to evaluate the performance of two variations of single buffers (conventional and buffer relaxation system) multiple queues system. In the conventional system, each queue can have at most one customer at any time and newly arriving customers find the buffer full are lost. In the buffer relaxation system, the queue being served may have two customers, while each of the other queues may have at most one customer. Thomas Y.S. Lee developed a state-dependent non-linear model of uncertainty for analyzing a random polling system with server breakdown/repair, multi-phase service, correlated input processes, and single buffers. The state-dependent non-linear model of uncertainty introduced in this paper allows us to incorporate correlated arrival processes where the customer arrival rate depends on the location of the server and/or the server's mode of operation into the polling model. The author allows the possibility that the server is unreliable. Specifically, when the server visits a queue, Lee assumes that the system is subject to two types of failures: queue-dependent, and general. General failures are observed upon server arrival at a queue. But there are two possibilities that a queue-dependent breakdown (if occurs) can be observed; (i) is observed immediately when it occurs and (ii) is observed only at the end of the current service. In both cases, a repair process is initiated immediately after the queue-dependent breakdown is observed. The author's model allows the possibility of the server breakdowns/repair process to be non-stationary in the number of breakdowns/repairs to reflect that breakdowns/repairs or customer processing may be progressively easier or harder, or that they follow a more general learning curve. Thomas Y.S. Lee will show that his model encompasses a variety of examples. He was able to perform both transient and steady state analysis. The steady state analysis allows us to compute several performance measures including the average customer waiting time, loss probability, throughput and mean cycle time.

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