Team:ZJU-China/Model
Overview
In the process of advancing iGEM projects, there will be a lot of situations which enable iGEMers to use mathematical knowledge and programming skills to verify some conclusions or predict some experimental results. In our project, we just use such idea to solve the problems encountered in the experiment several times. At the same time, we studied the meaning of modeling, hoping that through our modeling work, we can provide some ideas on the direction selection and self-cognition of modeling to future iGEM teams to a certain extent.
After summarizing, we believe that modeling plays a major role in at least three aspects in an iGEM project:
1. Before the start of the experiment, judge the rationality of the experimental design according to the given limitation factors.
2. After the experiment was completed, give corresponding explanation to illustrate the correctness of the results.
3. Because of various accidents, not all experiments can be successfully completed in a certain period of time. Therefore, modeling can play a role in explaining that the system itself is effective.
Our modeling work is closely related to the real needs of our team members. Based on the three principles, we designed four models in total. For the hybridization chain reaction (HCR), we have used several ODE equations to predict the dynamic characteristics of this biochemistry system. In addition, we have integrated the image processing tools and statistical methods to give sufficient and reasonable explanations and proofs for the special phenomena generated in HCR. For hardware design, we have applied the knowledge of fluid dynamics to provide highly instructive advice on the possibilities of the design when it is difficult to experiment in advance.
In order to promote the reusability and evolutionary concepts of iGEM modeling work, in our model description, we also added the “Independent Model Design” module, organizing and summarizing some previous teams’ and scholars’ work about the PCR/RPA reaction process. Based on this, we also put forward our optimization schemes.
Model Map
In order to visually show the connection between our modeling module and other modules in our team, we designed the Model Map as shown below. When reading it, if you want to quickly jump to the model you are interested in, you can click on the corresponding model block. Of course, clicking on the button "modelling" on the top of this web page will also be OK.
The correspondences between the following modules and models are: HCR Chemical Model → HCR ODE Model, HCR Statistical Characteristic → HCR Statistical Model, Hardware Design → Fluid Dynamics Model, Model Optimization → RPA/PCR Model.
Reference
[1] Ausubel, F.M. et al. (1988) Current Protocols in Molecular Biology, John Wiley and Sons, New York.
[2] Erase-a-Base® System Technical Manual #TM006, Promega Corporation.
[3] Henikoff, S. (1987) Unidirectional digestion with exonuclease III in DNA sequence analysis. Meth. Enzymol. 155, 156–65.
[4] Ke Bingshen.(2002) Kinetic Mathematical Model of PCR Amplification Experiment[J]. Genetics. 55-59.
[5] He Chengcai. (2002). Flow law of eccentric annular laminar flow. Oil and gas storage and transportation (11).
[6] Cortes, C. and Vapnik, V., 1995, Support-vector network. Machine Learning, 20, 273–297.
[7] Piepenburg, O. , Williams, C. H. , Stemple, D. L. , & Armes, N. A. . (2006). Dna detection using recombination proteins. PLoS Biology, 4(7), 1115-1121.
