computational modeling

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of …

A brief history of COMBINE

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and to reproduce scientific results. Over the past …

Toward Community Standards and Software for Whole-Cell Modeling

Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell …

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

COMBINE (Computational Modeling in Biology Network) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE's aim is to act as a coordinator, facilitator, and …

An Improvement in Partial Order Reduction Using Behavioral Analysis

Efficacy of partial order reduction in reducing state space relies on adequate extraction of the independence relation among possible behaviors. However, traditional approaches by statically analyzing system model structures are often not able to …

Utilizing stochastic model checking to analyze genetic circuits

When designing and analyzing genetic circuits, researchers are often interested in the probability of the system reaching a given state within a certain amount of time. Usually, this involves simulating the system to produce some time series data and …