Team:SYSU-Software/model
From 2013.igem.org
Overview
Mathematical modeling is the soul of our magical software “Computer Aided Synbio Tools”, C.A.S.T. In our models, we take into account the intrinsic dynamics of different circuits or systems hierarchically by deterministic, stochastic and time delay models. Here are the highlights of our models and algorithms:
*We place great emphasis on various kinds of promoters, operons, coding parts, RBSs, terminators and apply different kinds of ODEs to describe their diverse behaviors in living cells;
*What our modeling tries to achieve is to creatively build a bridge between parts and modules in the Registry and widespread experimental data in the papers so that researchers can have a brand new perspective of how these parts are related to each other;
*Standardized output PoPS and RIPS is generated from raw experimental parameters, which represents our goal of establishing sets of standardized data;
*We create a new algorithm FoldChangeDecoder to calculate the fold-change in different cascades, widely used synthetic circuits, to make researchers have a more direct understanding of the regulatory networks;
* As the current focus of synthetic biology is readily combining modules into complex synthetic pathways[1], statistical and probability distribution models are also applied to estimate extrinsic variability among synthetic systems.