Team:USTC Software/notebook 10

From 2010.igem.org

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{{Team:USTC_Software/Header}}
{{Team:USTC_Software/Header}}
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==ZHEN WANG==
+
===Zhen Wang===
Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Settle the DB format for good(hopefully).
Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Settle the DB format for good(hopefully).
Summary: As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development.
Summary: As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development.
Line 7: Line 7:
We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.
We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.
-
==Kun Jiang==
+
===Kun Jiang===
*ChenLiao finish his core demo, As our design. My ODE Solver Module can work with his core Module. But unfortunately, there is some bug in my source code. So I have work out the problem!
*ChenLiao finish his core demo, As our design. My ODE Solver Module can work with his core Module. But unfortunately, there is some bug in my source code. So I have work out the problem!
*I finally figure out the problem of my SBML ODE Solver programmer, I didn't make the right tolerance setting for Sundials cvodes function. I feel so good!
*I finally figure out the problem of my SBML ODE Solver programmer, I didn't make the right tolerance setting for Sundials cvodes function. I feel so good!
Line 14: Line 14:
*Start to porting the whole project to window, I am faced a serious problem. The 3rd part source code dbxml cannot be built successfully. I had to figure this out.
*Start to porting the whole project to window, I am faced a serious problem. The 3rd part source code dbxml cannot be built successfully. I had to figure this out.
-
==Luojun Wang==
+
===Luojun Wang===
Huh, I'm the first one writing wiki, yet my work this month is much more than that. Zhen has tons of documents for me to revise and I have to pick up some grammar, which is not that hard as to eliminate little mistakes from all of them.
Huh, I'm the first one writing wiki, yet my work this month is much more than that. Zhen has tons of documents for me to revise and I have to pick up some grammar, which is not that hard as to eliminate little mistakes from all of them.
And do you see our yellow shirts? It feels super cool to wear and the little monster is so cute, which intrigued the jealousy of the wet team. LOL~
And do you see our yellow shirts? It feels super cool to wear and the little monster is so cute, which intrigued the jealousy of the wet team. LOL~
Our work is going to an end. God bless our team!
Our work is going to an end. God bless our team!
 +
 +
'''10.2'''
 +
===Jue Wang===
 +
I ask for information and make flight reservations for 13 members (except Luo)
 +
 +
The itinerary
 +
*Heifei-Beijing
 +
Nov 3rd 10:55 CA1836
 +
 +
Gao Ge, Yao Xiaomo, An Duo, Zhu Ruijun, Zhang Yang, Zhang Ying, Wang zhen, Yang Jing, He Zhengda, Jiang Kun
 +
 +
Nov 3rd 17:55 CA1544
 +
 +
Wang Jue, Liao Chen, Liu Chang
 +
 +
'''10.7'''
 +
===Zhen Wang===
 +
Plan:
 +
Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document.
 +
Settle the DB format for good(hopefully).
 +
 +
Summary:
 +
As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development.
 +
 +
Most of our team members work intensively during the 7 days off, and the achievement of their work is rich. DB of both EFP-Lausanne and Synchronized Ecoli are basically finished. Tables and graphs on DB structure has been published. Our software core seems finally begin to function right. UI is under constructing. All the codes are now on github.
 +
 +
We schedule our trip and book plane tickets to Beijing, Chicago and Boston. Jue Wang is now in charge of money and team wear.
 +
 +
We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.
 +
 +
'''10.9'''
 +
 +
===Kun Jiang===
 +
ChenLiao finish his core demo,  As our design. My ODE Solver Module can work with his core Module. But unfortunately, there is some bug in my source code. So I have work out the problem!
 +
 +
'''10.11'''
 +
===Kun Jiang===
 +
I finally figure out the problem of my SBML ODE Solver programmer,  I didn't make the right tolerance setting for [https://computation.llnl.gov/casc/sundials/main.html Sundials] cvodes function. I feel so good!
 +
 +
'''10.12'''
 +
 +
===Kun Jiang===
 +
Because our teammate Xiaomo Yao. is to busy, so I take the job of design our wiki website, I am new to design a wiki, so there are so many ugly things!
 +
 +
'''10.13'''
 +
===Kun Jiang===
 +
We need a new ode solver data visual system, Should I develop one? May be there is a better chance, Hello [http://www.copasi.org/ COSPI]! Which is covered by [http://www.copasi.org/tiki-view_articles.php A Non−Commercial License]
 +
 +
'''10.17'''
 +
 +
===Kun Jiang===
 +
*Start to porting the whole project to windows operation system, I am faced a serious problem. The 3rd part source code dbxml cannot be built successfully. I had to figure this out.
 +
 +
'''10.18'''
 +
 +
===Kun Jiang===
 +
* Berkley dbxml can not built success in Mingw environment, so I decide to quit porting our project to windows operating system.
 +
 +
'''10.19'''
 +
 +
===Kun Jiang===
 +
*Start to cooperate with Xiaomo Yao to develop the GUI of our project.
 +
 +
'''10.20'''
 +
===Jue Wang===
 +
Receiving the thick shirts(17)
 +
* 15 blue
 +
* 2 pink (Liao & An)
 +
 +
Get in touch with the USTC Boston alumni association.(Gao Chi)
 +
 +
Arrange the meeting minutes of Oct 17th
 +
 +
'''10.21'''
 +
 +
===Kun Jiang===
 +
Design the schema file for MoDeL language with Zhen Wang. It is really a tough work need patient and concentration.
 +
 +
'''10.22'''
 +
 +
===Kun Jiang===
 +
*Modify and validate our MoDeL.xsd schema file. Lucky for I find a tool '''Altoval XMLSpay''' to help me to do this job, this software is good!
 +
 +
===Jue Wang===
 +
*Get further connection with the Boston alumni association, seen more familiar names I have admired before
 +
 +
'''10.23'''
 +
===Jue Wang===
 +
Receiving the team shirts(40)
 +
* 20 yellow (software)
 +
* 20 red (wet)
 +
 +
reserve the rehearsal classroom on main page schedule
 +
32－123 8:00-8:30 PM
 +
 +
'''10.24'''
 +
 +
===Jue Wang===
 +
correct some mistakes in the project introduction and get an over review of our model
 +
 +
'''10.25'''
 +
===Jue Wang===
 +
* receiving an email from a hard core schoolfellow of 9108 in the Harvard Medical School.
 +
 +
* temperature reduction test us all
 +
 +
'''10.26'''
 +
 +
=== Jue Wang ===
 +
 +
*have the daily notebook from March to October listed systematically in the monthly notebook.
 +
 +
* finish the part of acknowledgement and sponsorship

Latest revision as of 11:59, 27 October 2010

Contents

Zhen Wang

Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Settle the DB format for good(hopefully). Summary: As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development. Most of our team members work intensively during the 7 days off, and the achievement of their work is rich. DB of both EFP-Lausanne and Synchronized Ecoli are basically finished. Tables and graphs on DB structure has been published. Our software core seems finally begin to function right. UI is under constructing. All the codes are now on github. We schedule our trip and book plane tickets to Beijing, Chicago and Boston. Jue Wang is now in charge of money and team wear. We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.

Kun Jiang

  • ChenLiao finish his core demo, As our design. My ODE Solver Module can work with his core Module. But unfortunately, there is some bug in my source code. So I have work out the problem!
  • I finally figure out the problem of my SBML ODE Solver programmer, I didn't make the right tolerance setting for Sundials cvodes function. I feel so good!
  • Because our teammate Xiaomo Yao. is to busy, so I take the job of design our wiki website, I am new to design a wiki, so there are so many ugly things!
  • We need a new ode solver data visual system, Should I develop one? May be there is a better chance, Hello COSPI! Which is covered by A No−Commercial License
  • Start to porting the whole project to window, I am faced a serious problem. The 3rd part source code dbxml cannot be built successfully. I had to figure this out.

Luojun Wang

Huh, I'm the first one writing wiki, yet my work this month is much more than that. Zhen has tons of documents for me to revise and I have to pick up some grammar, which is not that hard as to eliminate little mistakes from all of them. And do you see our yellow shirts? It feels super cool to wear and the little monster is so cute, which intrigued the jealousy of the wet team. LOL~ Our work is going to an end. God bless our team!

10.2

Jue Wang

I ask for information and make flight reservations for 13 members (except Luo)

The itinerary

  • Heifei-Beijing

Nov 3rd 10:55 CA1836

Gao Ge, Yao Xiaomo, An Duo, Zhu Ruijun, Zhang Yang, Zhang Ying, Wang zhen, Yang Jing, He Zhengda, Jiang Kun

Nov 3rd 17:55 CA1544

Wang Jue, Liao Chen, Liu Chang

10.7

Zhen Wang

Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Settle the DB format for good(hopefully).

Summary: As our simulation program becomes more and more mature, we encounter more problems in consistency of our database. We all want to make major changes and make it right this time, but sadly we don’t have the time. So we make minor changes, add patches to fix the bugs, but we have to let go of the unconsistency in substituent, compartment and other places. Now the DB looks not beautiful or elegant, but usable. This is good enough since our first goal now is to make our software work, and a DB that can properly describe simple reaction networks should be enough. We plan to leave major changes to further development.

Most of our team members work intensively during the 7 days off, and the achievement of their work is rich. DB of both EFP-Lausanne and Synchronized Ecoli are basically finished. Tables and graphs on DB structure has been published. Our software core seems finally begin to function right. UI is under constructing. All the codes are now on github.

We schedule our trip and book plane tickets to Beijing, Chicago and Boston. Jue Wang is now in charge of money and team wear.

We dined together on Oct 1, but without a relaxed mind, it was not fun for me. What actually thrills me up is to explore my potential and to find how much can be done in the 7 days. I do have fun working beyond my limit.

10.9

Kun Jiang

ChenLiao finish his core demo, As our design. My ODE Solver Module can work with his core Module. But unfortunately, there is some bug in my source code. So I have work out the problem!

10.11

Kun Jiang

I finally figure out the problem of my SBML ODE Solver programmer, I didn't make the right tolerance setting for Sundials cvodes function. I feel so good!

10.12

Kun Jiang

Because our teammate Xiaomo Yao. is to busy, so I take the job of design our wiki website, I am new to design a wiki, so there are so many ugly things!

10.13

Kun Jiang

We need a new ode solver data visual system, Should I develop one? May be there is a better chance, Hello [http://www.copasi.org/ COSPI]! Which is covered by [http://www.copasi.org/tiki-view_articles.php A Non−Commercial License]

10.17

Kun Jiang

  • Start to porting the whole project to windows operation system, I am faced a serious problem. The 3rd part source code dbxml cannot be built successfully. I had to figure this out.

10.18

Kun Jiang

  • Berkley dbxml can not built success in Mingw environment, so I decide to quit porting our project to windows operating system.

10.19

Kun Jiang

  • Start to cooperate with Xiaomo Yao to develop the GUI of our project.

10.20

Jue Wang

Receiving the thick shirts(17)

  • 15 blue
  • 2 pink (Liao & An)

Get in touch with the USTC Boston alumni association.(Gao Chi)

Arrange the meeting minutes of Oct 17th

10.21

Kun Jiang

Design the schema file for MoDeL language with Zhen Wang. It is really a tough work need patient and concentration.

10.22

Kun Jiang

  • Modify and validate our MoDeL.xsd schema file. Lucky for I find a tool Altoval XMLSpay to help me to do this job, this software is good!

Jue Wang

  • Get further connection with the Boston alumni association, seen more familiar names I have admired before

10.23

Jue Wang

Receiving the team shirts(40)

  • 20 yellow (software)
  • 20 red (wet)

reserve the rehearsal classroom on main page schedule 32－123 8:00-8:30 PM

10.24

Jue Wang

correct some mistakes in the project introduction and get an over review of our model

10.25

Jue Wang

  • receiving an email from a hard core schoolfellow of 9108 in the Harvard Medical School.
  • temperature reduction test us all

10.26

Jue Wang

  • have the daily notebook from March to October listed systematically in the monthly notebook.
  • finish the part of acknowledgement and sponsorship
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