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Team:USTC Software/notebook 10
From 2010.igem.org
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{{Team:USTC_Software/Header}} | {{Team:USTC_Software/Header}} | ||
| - | == | + | ===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~ | ||
| Line 34: | Line 34: | ||
'''10.7''' | '''10.7''' | ||
| - | === | + | ===Zhen Wang=== |
Plan: | Plan: | ||
Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. | Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. | ||
| Line 49: | Line 49: | ||
'''10.9''' | '''10.9''' | ||
| + | |||
===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! | ||
| Line 58: | Line 59: | ||
'''10.12''' | '''10.12''' | ||
| - | ==Kun Jiang== | + | ===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! | 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! | ||
| Line 67: | Line 68: | ||
'''10.17''' | '''10.17''' | ||
| - | ==Kun Jiang== | + | ===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. | *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''' | '''10.18''' | ||
| - | ==Kun Jiang== | + | ===Kun Jiang=== |
* Berkley dbxml can not built success in Mingw environment, so I decide to quit porting our project to windows operating system. | * Berkley dbxml can not built success in Mingw environment, so I decide to quit porting our project to windows operating system. | ||
'''10.19''' | '''10.19''' | ||
| - | ==Kun Jiang== | + | ===Kun Jiang=== |
*Start to cooperate with Xiaomo Yao to develop the GUI of our project. | *Start to cooperate with Xiaomo Yao to develop the GUI of our project. | ||
| Line 92: | Line 93: | ||
'''10.21''' | '''10.21''' | ||
| - | ==Kun Jiang== | + | ===Kun Jiang=== |
Design the schema file for MoDeL language with Zhen Wang. It is really a tough work need patient and concentration. | Design the schema file for MoDeL language with Zhen Wang. It is really a tough work need patient and concentration. | ||
'''10.22''' | '''10.22''' | ||
| - | ==Kun Jiang== | + | ===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! | *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== | + | ===Jue Wang=== |
*Get further connection with the Boston alumni association, seen more familiar names I have admired before | *Get further connection with the Boston alumni association, seen more familiar names I have admired before | ||
| - | + | '''10.23''' | |
===Jue Wang=== | ===Jue Wang=== | ||
Receiving the team shirts(40) | Receiving the team shirts(40) | ||
| Line 112: | Line 113: | ||
32－123 8:00-8:30 PM | 32－123 8:00-8:30 PM | ||
| - | + | '''10.24''' | |
| - | ==Jue Wang== | + | |
| + | ===Jue Wang=== | ||
correct some mistakes in the project introduction and get an over review of our model | correct some mistakes in the project introduction and get an over review of our model | ||
| - | + | '''10.25''' | |
===Jue Wang=== | ===Jue Wang=== | ||
* receiving an email from a hard core schoolfellow of 9108 in the Harvard Medical School. | * receiving an email from a hard core schoolfellow of 9108 in the Harvard Medical School. | ||
| Line 122: | Line 124: | ||
* temperature reduction test us all | * temperature reduction test us all | ||
| - | + | '''10.26''' | |
| - | == Jue Wang == | + | === Jue Wang === |
*have the daily notebook from March to October listed systematically in the monthly notebook. | *have the daily notebook from March to October listed systematically in the monthly notebook. | ||
* finish the part of acknowledgement and sponsorship | * 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
