iGEM 2021 - Jianhua


In regards of cotribution to the latter teams, we contribute to iGEM community by adding several basic and composite parts. The submitted parts are listed below.

Parts Submitted

Basic Parts:

Part Name Type
BBa_K4081992 FKP
BBa_K4081996 Lac12
BBa_K4081998 FucT2
BBa_K4081995 TEF1 promoter
BBa_K4081994 GAP promoter
BBa_K4081990 ADH1 promoter
BBa_K4081888 CDT2

Composite Parts:

Part Name Type
BBa_K4081085 pGAP-FKP-tADH1
BBa_K4081238 pTEF1-Lac12-tADH1
BBa_K4081333 pADH1-FucT2-tADH1

In addition, we also planned a guide for modelling. During the competition, we found sufficient resources about constructing a wiki, whether from guides, online learning websites, or from past teams. However, we noticed the existance of the lack of modelling guide, while this is an essential part in the competition. It may be due to that wiki is neccessary for the competition, modelling is a more advance requirement. By our observavtion, many teams we contacted need to start modelling from the initial: learning the basics. Thus, we build this page as a modelling guide, to help those teams who want to optimize their solution using modelling, but have no experience. The guide is placed on another website (Link)
The page is also copied here.

1. What is mathematical modeling

1.1 What is a mathematical model

Mathematical model is a kind of mathematical structure described generally or approximately in mathematical language with reference to the characteristics or quantitative dependence of a certain thing system. This mathematical structure is a pure relational structure of a certain system described with the help of mathematical symbols. In a broad sense, mathematical models include various concepts, formulas and theories in mathematics.

1.2 Mathematical modeling

Mathematical modeling course is regarded as the process of transforming problem definition into mathematical model.

In short, for all the mathematical knowledge we have learned, to solve various problems encountered in life, we need to establish relevant models and use mathematics as a tool to solve various practical problems, which is the core of modeling.

1.3 The idea of mathematical modeling

The idea of mathematical modeling can be divided into the following methods:
Step 1, ask questions
(a) List the variables involved in the question, including the appropriate units.
(b) Be careful not to confuse variables with constants.
(c) List all the assumptions you make about variables, including equations and inequalities.
(d) Check the units to make sure your hypothesis makes sense, and (e) give the goal of the problem an exact mathematical expression.

Step 2 is to choose the modeling method
(a) Choose a general solution to your problem.
(b) Generally, success in this step requires experience, skill, and some familiarity with the relevant literature.
(c) In this book, we usually specify the modeling method to be used.(Note: in reality, we need to consult references or other reference books.)

Step 3, derive the formula of the model
(a) Reformulate the problem obtained in step 1 into the form required by the modeling method selected in step 2.
(b) You may need to change some of the variable names in step 1 to match the notation used in step 2.
(c) Make a note of any additional assumptions made to adapt the problem described in step 1 to the mathematical structure chosen in Step 2.

Step 4: Solve the model
(a) Apply the method selected in step 2 to the expression obtained in Step 3
(b) Pay attention to your mathematical derivations and check to see if there are any mistakes and if your answers make sense.
(c) With appropriate technology, computer algebra systems, graphics, numerical computation software, etc., can expand the range of problems you can solve and reduce calculation errors.

Step 5: Answer the questions
(a) Restate the results of step 4 in non-technical terms.

2. Method and code sharing

2.1 Monte Carlo method

2.1.1 Definition

Monte Carlo algorithm is a numerical calculation method based on the theories and methods of probability and statistics. It connects the solved problem with a certain probability model, and uses computer to realize statistical simulation or sampling to obtain the approximate solution of the problem. Therefore, it is also called random sampling method or statistical experiment method.

2.1.2 Scope of application

It can better solve the difficult and complex mathematical calculation problems such as multiple integral calculation, differential equation solution, integral equation solution, eigenvalue calculation and nonlinear equation group solution.

2.1.3 Characteristics

Monte Carlo algorithm can be used in many occasions, but it only seeks the approximate solution. The larger the simulation sample, the closer it is to the real value. The increase of the number of single samples will lead to a significant increase in the amount of calculation. For some simple problems, Monte Carlo is a stupid method, but for many problems, it is often an effective, sometimes even the only feasible method.

2.1.4 Examples

y = x^2, y = 12 - x and x axis form a curved triangle with X axis in the first quadrant. Design a random experiment to find the approximate value of the figure.

2.1.5 Code

x = 0:0.25:12;
y1 = x.^2;
y2 = 12 - x;
plot(x, y1, x, y2)
% Generate legend
legend('y1=x^2', 'y2=12-x');
title(' Monte Carlo method ');
% The range of x-axis and y-axis in the figure. The range of y-axis is in front of the brackets and the range of
x-axis is behind the brackets
axis([0 15 0 15]);
text(3, 9, ' intersection ');
% Grid line
grid on

2.2 Data fitting

2.2.1 Definition

Given a limited number of data points, the approximate function can be obtained, but given the data points, it is only required to minimize the total deviation at these points in a sense, so as to better reflect the overall change trend of the data.

2.2.2 Common methods

The least square method is generally used.
The realization of fitting is divided into Matlab and excel. The realization of MATLAB is polyfit function, mainly polynomial fitting.

2.2.3 Examples

The data are as follows:

No. x y z
1 426.6279 0.066 2.897867
2 465.325 0.123 1.621569
3 504.0792 0.102 2.429227
4 419.1864 0.057 3.50554
5 464.2019 0.103 1.153921
6 383.0993 0.057 2.297169
7 416.3144 0.049 3.058917
8 464.2762 0.088 1.369858
9 453.0949 0.09 3.028741
10 376.9057 0.049 4.047241
11 409.0494 0.045 4.838143
12 449.4363 0.079 4.120973
13 372.1432 0.041 3.604795
14 389.0911 0.085 2.048922
15 446.7059 0.057 3.372603
16 347.5848 0.03 4.643016
17 379.3764 0.041 4.74171
18 453.6719 0.082 1.841441
19 388.1694 0.051 2.293532
20 444.9446 0.076 3.541803
21 437.4085 0.056 3.984765
22 408.9602 0.078 2.291967
23 393.7606 0.059 2.910391
24 443.1192 0.063 3.080523
25 514.1963 0.153 1.314749
26 377.8119 0.041 3.967584
27 421.5248 0.063 3.005718
28 421.5248 0.063 3.005718
29 421.5248 0.063 3.005718
30 421.5248 0.063 3.005718
31 421.5248 0.063 3.005718
32 421.5248 0.063 3.005718
33 421.5248 0.063 3.005718
34 421.5248 0.063 3.005718
35 421.5248 0.063 3.005718
36 421.5248 0.063 3.005718
37 416.1229 0.111 1.281646
38 369.019 0.04 2.861201
39 362.2008 0.03 3.060995
40 417.1425 0.038 3.69532 Method 1: use matlab to write code

%Read the form
A = xlsread('E:\form\1.xls', 'Sheet1', 'A1:AN2');
B = A;
[I, J] = size(B);

%Data fit
%x is the first line of the matrix and y is the second line of the matrix
x = A(1,:);
y = A(2,:);
%Polyfit is a fitting function in matlab, and the first argument is the horizontal coordinates of the data
%The second argument is the ordinate of the data, and the third argument is the highest order of polynomials
%The return value p contains n+1 polynomial coefficient
p = polyfit(x, y, 2);
%Here's the code for the diagram
x1 = 300:10:600;
%Polyval is the evaluation function in matlab, and the function value y1 corresponding to x1 is sought
y1 = polyval(p,x1);
%figure(gcf); Method 2: Use MATLAB's graphical fit package

Import data into the workspace and open the graphical fit package for matlab with the cftool command

Select the x,y variables

Select how to fit and the maximum number of items

Gets the result of the fit

Using the Graphic Fit tool is not only quick and easy, but also uses a variety of fit methods to find the best fit curve.