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Team:USTC-Software/notes.html
From 2012.igem.org
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.
Abstract:
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.
4. Chao Xu
Something about Eureqa.
Date: March 3, 2012
Time: 7:00pm-9:30pm
Attendants:
Kai Kang, Kaifeng Chen, Yunlong Zheng, Qi Hu, Kaishuai Yang, Litong Jiang, Wenjuan Zhang, Chao Xu
3 Litong Jiang:
Summary of 2010 iGEM Software Track
Relevant Literature Review
5 Chao Xu
Biobrick
6 Kai Kang
Two Reviews about Algorithmic and Modeling
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
GRN
Genetic circuits
Plasmid
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.
Plasmid
Extension connecting with other software. To gain this goal, interfaces of the database and output are must be considered.
Stress
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.
Date:2012.03.17
Time:From 7:00pm to 9:00pm
Participants:
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.
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
Judging:
Bronze\Silver\Gold metal
Special Awards: Clotho\SBOL\parts registry
To-do list:
Software
project promotion
wiki
human practice
Assignment:
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
Outline:
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
Agenda:
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.
NOTICE:
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
Agenda:
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:
Proposal is attached here:
Date: May 5
Place: 355
Attendees: Kang Kai, Chen Kaifeng, Yang Kaishuai, Hu Qi Zheng Yunlong, Jiang Litong
Agenda:
Kang Kai:
1. Overall plan for May
2. GUI discussion
3. Wiki discussion
4. Promotion
5. HP
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.
Group discussion:
1. What kind of wiki style.
2. Logo on T-shirt, including ACSII Art & shell-like style.
