Dev Notes USTC-Software

Dev Notes

Date: Feb.25

Time: 7:00pm-9:00pm

Attendants: Kai Kang, Kaifeng Chen, Yunlong Zheng, Qi Hu, Kaishuai Yang, Litong Jiang, Wenjuan Zhang, Chao xu.


1. Kai Kang

1) Program's feasibility.

2) How to gain advice and make others understood.

3) Global proposal.

4) A review of the project.

Meeting Feb 25 with Notes.pdf

Meeting Feb 25.pdf

2. Kaifeng Chen

Summary of 2011 iGEM Software Track.


3. Litong Jiang

Summary of 2010 iGEM Software Track.


4. Chao Xu

Something about Eureqa.

Date: March 3, 2012

Time: 7:00pm-9:30pm


Kai Kang, Kaifeng Chen, Yunlong Zheng, Qi Hu, Kaishuai Yang, Litong Jiang, Wenjuan Zhang, Chao Xu

1 Wenjuan Zhang:

Summary of 2009 iGEM Software Track

Relevant Literature Review


2 Kaifeng Chen:

Summary of 2011 iGEM Software Track

Relevant Literature Review


3 Litong Jiang:

Summary of 2010 iGEM Software Track

Relevant Literature Review

Summary info of IGEM2010.pdf

4 Yunlong Zheng:

PSO - Particle Swarm Optimization

PSO algorithm.rar

5 Chao Xu


6 Kai Kang

Two Reviews about Algorithmic and Modeling

SynBioSS DS Users Manual.pdf

group meeting3.3.pdf

Data: 2012.03.10

Time: 7:00 -- 9:40

Participants: Jack Kang, Francis Chen, Qi Hu, Litong Jiang, Chao Xu, Wenjuan Zhang, Kaishuai Yang

Major steps of our project

Time-course or steady states data to input

Generating ODEs

Concerned about chemical reaction

Reaction network


Genetic circuits


Further evolution

8 steps' challenges

Data input: the number of time courses within

Generating ODEs: complexity & computing expenses(as we know, a software, at least, should be time-saving, then we discuss about the noise in the data, and the solution to deal with it, gaining a perfect curve without noise, which can fully represent the system.

Writing down the chemical reaction

Chemical reaction network, and optimize it. GRN graph should not be concerned about in isolation, in fact we should considerate GRN graph and chemical reaction comprehensively

Genetic circuit contain more than we thought, it contains promoter for example. Genetic circuit is needed in the competition. Some genetic circuits cannot realize in actual world. Filter the database, achieving a more reliable database that could contain the parameter we could use in the algorithm.


Extension connecting with other software. To gain this goal, interfaces of the database and output are must be considered.


scoring function is needed in the report; Stability's definition; How to measure it.; How to quantify the stability.

comprehensively considering the chemical reaction and the gene circuit. If could,, we can infer some of the chemical substances from the chemical reaction, for example.


Time:From 7:00pm to 9:00pm


Members:Jack Kang, Francis Chen, Litong Jiang, Yunlong Zheng, Qi hu, Wenjuan Zhang, Chao Xu, Kaishuai Yang.

Instructors: Chen Liao, Zhen Wang.

Jack Kang:

1.Brief intro to 2004 PNAS paper.

2.Simplification of our project.

3.Registrations & funding.

Mar 17 Meeting.pdf

Francis Chen:

Specific details about the 2004 PNAS paper:

1.The reaction database.

2.Growth phase.

3.Selection phase.


During the meeting, our advisor Chen Liao gave us a short intro to the 2009 paper published in Science and a summary of the work we can do at present.

The 2009 paper: Distilling Free-Form Natrual Laws From Experiemental Data.pdf

Chen Liao's suggestions: Chen Liao's Suggestions.pdf

Data: 2012.03.24

Participants: Jack Kang, Francis Chen, Qi Hu, Litong Jiang, Chao Xu, Wenjuan Zhang, Kaishuai Yang

Time: 7:00 -- 8:40

Kai Kang:

Schedule of last year:

03.31: registration.

07.15: project discribtion\safty proposal

09.02: region fee\track\project abstract\team roster\safty question

10.05: project documentation\biobrick due\judging form\wiki

Middle of Oct.: region jamboree

Early Nov.: Global jamboree


Bronze\Silver\Gold metal

Special Awards: Clotho\SBOL\parts registry

To-do list:


project promotion


human practice


Jack Kang, Francis Chen:software programming\GUI

Yunlong Zheng: (undecided)

Qi Hu: Wiki\promotion

Litong Jiang: Wiki\human practice

Kaishuai Yang: Wiki

Wenjuan Zhang: Clotho\human practice

Chao Xu: Video\SBOL

Date: 2012/4/7

Attendees: Jack Kang, Francis Chen, Yunlong Zheng, Qi Hu, Kaishuai Yang, Litong Jiang, Chao Xu.

Absent: Wenjuan Zhang

Time: 19:15-21:00


1. Jack Kang: Software

1.1 Division of Labor

1.2 Schedule

1.3 Basics of current software in development

1.3.1 Classes

1.3.2 Implementations

2. Francis Chen: GUI

2.1 QMainWindow, QDiolog, QWedgit

2.2 QWedgit Example

2.3 QDiolog Example

2.4 QMainWindow Example

3. Kaishuai Yang:

3.1 Wiki

3.2 Video Demo

Date: April 21

Time: 19:15 - 20:30

Attendees: Jack Kang, Francis Chen, Yunlong Zheng, Chao Xu, Qi Hu, Kaishuai Yang, Wenjuan Zhang, Litong Jiang


1. Clotho

2. Human Practice

3. Wiki

4. Promotion

5. GUI design discussions

Litong Jiang&Yunlong Zheng:

Some ideas about promotion to people with different ages(especially children in kindergarden.

Qi Hu:

Some well-done websites and suggestions about our wiki.

Wenjuan Zhang:

principles and philosophy of clotho.

Francis Chen:

Some ideas about GUI.

Chao Xu:

Some good video work from internet.

Work to do for the next meeting:

Litong Jiang & Yunlong Zheng: 10 proposals about the promotion to kindergarden children.

Francis Chen: some excellent GUI design.


date for the next meeting: 2012.04.29 a.m.

Date:April 29th

Lasting time:9:00---11:00

Participants: Jack Kang(On Video),Francis Chen, Chao Xu, Litong Jiang, Qi Hu, Kiashuai Yang, Wenjuan Zhang


1. List of possible proposals about promotion

2. GUI

3. What we can do now

Francis Chen:

GUI design

Litong Jiang:

Some practical proposals about Human Practice

PPT is attached here:

Group Meeting.pdf

Proposal is attached here:

Promotion Proposals.pdf

Date: May 5

Place: 355

Attendees: Kang Kai, Chen Kaifeng, Yang Kaishuai, Hu Qi Zheng Yunlong, Jiang Litong


Kang Kai:

1. Overall plan for May

2. GUI discussion

3. Wiki discussion

4. Promotion

5. HP

May 5 Meeting.pdf

Litong Jiang

details about one specific proposal

Yunlong Zheng

Ideas about promotion in kindergarden

Date: 2012.05.12

Lasting Time: 7:00-9:10

Participants: Jack Kang, Francis Chen, Qi Hu, Kaishuai Yang, Yunlong Zheng, Chao Xu

Main Topics : Logo Design, Wiki Design

Jack Kang:

Some ideas about team logo and T-shirt.

Kaishuai Yang:

Some wiki styles.

Francis Chen:

GUI Design.

PPT is attached here: GUI.pdf

Group discussion:

1. What kind of wiki style.

2. Logo on T-shirt, including ACSII Art & shell-like style.