Team:USTC Software/notebook 9

From 2010.igem.org

Summary: Not having much fun working, with both sides’ tasks to be done. Full database for oscillator is done 2010/9/2. I haven’t checked it in detail yet. It is very likely we are going to change the db structure yet again, good thing though. Learn from libsbml the sbml modification tool, our db modification should somehow like that. It should focus on adding and constructing new model. Discuss on UI&input with Liao, writing the new UI draft.

Sep 5 ~ Sep 12, 2010 Plan: Discuss UI&input with Soimort. Discuss ODE solver with Kun. Teaching junior students how to write DB. Have fun working.

Summary: This is a crazy week for me! Together with Liao, we make huge modifications on the structure of for at least 3 times! We change the xml structure for storing data, revise the attributes on each item, and have heated debate on our standard of bio-modeling. At first the modification process seems endless, but by the end of the week, we have come to agreement on most of the details. This gives me a lot of hope, and this week has definitely been a big leap for our DB. This time Liao finally realizes that we are actually making the next-generation standard of SBML, haha. Settling a brand-new standard of bio-modeling has actually become the core of our work. As far as I’m concerned, we have made 3 shifts on our goal, UI -> simulation -> bio-modeling standard, this is poor goal-setting, we didn’t make a clear map of what we are doing at the very beginning. I talk on DB and modeling with 2 junior students, they are all confident and eager to learn, I think they can handle it properly very soon. I just don’t have the time to talk with Soimort and Kun.

Sep 12 ~ Sep 19, 2010 Plan: Write note on UI&input, discuss UI&input with Soimort. Discuss ODE solver with Kun. Settle the final edition of DB. Writing DB of EPF-Lausanne with 2 junior students. Have fun working.

Summary: Write a detailed note on UI&Input and discuss it with Soimort. I believe it is not easy for him to understand the whole design of UI&Input and its connection with the database, I should spend more time to explain the details for him. Kun says he has finished the L2V4 update of ODE solver, he is now working on the boolean value judging module which will be used in Liao’s code. Liao’s first edition of document on DB standard is done, it’s now my turn to refine it and fix the bugs. Zhengda He has written part of the DB of EPF-Lausanne 2009 under my guidance, we can see the whole DB by next week, hopefully. Another junior student Zhaoyi Li is working on synchronized E.coli oscillator, a biological breakthrough published on Nature 2009. Last but not least, this is a busy week for scheduling trip, paying fee and talking to sponsor. Handling these things cost me lots of time, we should have a secretary for this, luckily we find one, she is Jue Wang. My boss doesn’t push me so hard on finishing his assignment, and I’m grateful for that, he must know that I don’t have much time. I do have fun working this week!

Sep 20 ~ Sep 26, 2010 Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Discuss UI with Soimort and push him to work faster, discuss synchronized E.coli with Zhaoyi Li. Have fun working.

Summary: Today is Oct 7, and I have just start writing work summary of the last week in Sep. During last 2 weeks we celebrated Mid-Autumn Festival and had 7 day off for National Day, while others are enjoying themselves traveling, we iGEM team members didn’t take a day off. We have to seize every minute to make our software work! I guess I’m just too busy to write my work log, and right now I am trying my best to recall what exactly I did in the last week of Sep…

Here’s what I can remember.

Zhaoyi Li looked into the nature article on synchronized ecoli clock and gave a brief lecture, then he started to analyze all the reaction and species in the model, and prepare to write the DB of it. Zhengda He’s parents came to see him, so he disappeared for 3 days or so. He has finished part of EPF-Lausanne DB but not all, so Yubo Qi kicked in to investigate the proper parameters for reaction. Unfortunately, it’s almost a hopeless task, no reliable source with specified parameters can be found, so we gave up at last.

I finished another detail draft on input UI design, and Soimort is constructing our UI according to it. I tried to discuss more with Soimort and push him harder, but can’t find the right way…

My girlfriend came and we spent 3 days together. It was 3 halves of days actually, since there are tasks I cannot put aside. However, she was so thoughtful and supportive, and didn’t complain about my absence. We had our sweet moments together. Her visiting means a lot to me, and fuels me up with energy to work on.

Kun Jiang

Sep 5 ~ Sep 12, 2010 Build two tool softwares to help Zhen Wang to edit our database input files.

Sep 12 ~ Sep 30, 2010 Modify the soslib v1.6.0 source code to base on libsbml v4.0.1, Which enable soslib support sbml version2 level 4 to meet our database format requirements.

Summary: (we will see~)

Luojun Wang

Idea of starting a community has been discussed with the wet team and will be realized soon. Concerned with IPR issue, I consult the IPRs Centre of USTC for safety of iGAME. Start of wiki scripts.

Summary: Finally, I decide to give a name to the human practice project, "the C project". "C" stands for "curriculum","communication" and "community", it is also cool, huh?

Shangyu Luo

I am in Hong Kong now! Thanks to school of computer again! I obtain a chance to live and study in Hong Kong for one semester! Though there is much to do and I have to get familiar with the environment in Hong Kong, I try my best to find time for our project. I skim most of igem teams in latest three years and list some teams whose work can show the advantages and innovations of our database. Their works are about some biological reactions related to light, temperature, PH, etc. Read a paper of Nature about synchronized Ecoli clock, try to master the idea of it and list the reactions in it. It will be added into our database.

Zhengda He

Starting completing our database , writing the story for the game . Collected appropriate project for us to design it into a game . Designing Wiki was the same-time work for me . And I also pay attention in the creative idea of our Logo and uniform . The jamboree is coming , so I must concentrate on what I'm doing . And I will have it done beautifully .

9.1

Zhen Wang

Plan: Think about what database modification tool a senior user would like to use. Write full

database that includes the whole oscillator. Read more on XML. Have fun working.

Summary: Not having much fun working, with both sides’ tasks to be done. Full database for

oscillator is done 2010/9/2. I haven’t checked it in detail yet. It is very likely we are

going to change the db structure yet again, good thing though. Learn from libsbml the sbml

modification tool, our db modification should somehow like that. It should focus on adding

and constructing new model. Discuss on UI&input with Liao, writing the new UI draft.

9.5

Kun Jiang

2010 Build two tool softwares to help Zhen Wang to edit our database input files.

9.6

Zhen Wang

Plan: Discuss UI&input with Soimort. Discuss ODE solver with Kun. Teaching junior students

how to write DB. Have fun working.

Summary: This is a crazy week for me! Together with Liao, we make huge modifications on the

structure of for at least 3 times! We change the xml structure for storing data, revise the

attributes on each item, and have heated debate on our standard of bio-modeling. At first the

modification process seems endless, but by the end of the week, we have come to agreement on

most of the details. This gives me a lot of hope, and this week has definitely been a big

leap for our DB. This time Liao finally realizes that we are actually making the next-

generation standard of SBML, haha. Settling a brand-new standard of bio-modeling has actually

become the core of our work. As far as I’m concerned, we have made 3 shifts on our goal, UI

-> simulation -> bio-modeling standard, this is poor goal-setting, we didn’t make a clear

map of what we are doing at the very beginning. I talk on DB and modeling with 2 junior

students, they are all confident and eager to learn, I think they can handle it properly very

soon. I just don’t have the time to talk with Soimort and Kun.

9.12

Kun Jiang

Modify the soslib v1.6.0 source code to base on libsbml v4.0.1, Which enable soslib support

sbml version2 level 4 to meet our database format requirements.

9.13

Zhen Wang

Plan: Write note on UI&input, discuss UI&input with Soimort. Discuss ODE solver with Kun.

Settle the final edition of DB. Writing DB of EPF-Lausanne with 2 junior students. Have fun

working.

Summary: Write a detailed note on UI&Input and discuss it with Soimort. I believe it is not

easy for him to understand the whole design of UI&Input and its connection with the database,

I should spend more time to explain the details for him. Kun says he has finished the L2V4

update of ODE solver, he is now working on the boolean value judging module which will be

used in Liao’s code. Liao’s first edition of document on DB standard is done, it’s now my

turn to refine it and fix the bugs. Zhengda He has written part of the DB of EPF-Lausanne

2009 under my guidance, we can see the whole DB by next week, hopefully. Another junior

student Zhaoyi Li is working on synchronized E.coli oscillator, a biological breakthrough

published on Nature 2009. Last but not least, this is a busy week for scheduling trip, paying

fee and talking to sponsor. Handling these things cost me lots of time, we should have a

secretary for this, luckily we find one, she is Jue Wang. My boss doesn’t push me so hard on

finishing his assignment, and I’m grateful for that, he must know that I don’t have much

time. I do have fun working this week!

9.15

Luojun Wang

Idea of starting a community has been discussed with the wet team and will be realized soon. Concerned with IPR issue, I consult the IPRs Centre of USTC for safety of iGAME. Start of wiki scripts.

Summary: Finally, I decide to give a name to the human practice project, "the C project". "C" stands

for "curriculum","communication" and "community", it is also cool, huh?

9.20

Zhen Wang

Plan: Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document. Discuss UI with Soimort and push him to work faster, discuss synchronized E.coli with Zhaoyi

Li. Have fun working.

Summary: Today is Oct 7, and I have just start writing work summary of the last week in Sep. During

last 2 weeks we celebrated Mid-Autumn Festival and had 7 day off for National Day, while

others are enjoying themselves traveling, we iGEM team members didn’t take a day off. We

have to seize every minute to make our software work! I guess I’m just too busy to write my work log, and right now I am trying my best to recall

what exactly I did in the last week of Sep…

Here's what I can remember.

Zhaoyi Li looked into the nature article on synchronized ecoli clock and gave a brief

lecture, then he started to analyze all the reaction and species in the model, and prepare to

write the DB of it. Zhengda He’s parents came to see him, so he disappeared for 3 days or so. He has finished

part of EPF-Lausanne DB but not all, so Yubo Qi kicked in to investigate the proper

parameters for reaction. Unfortunately, it’s almost a hopeless task, no reliable source with

specified parameters can be found, so we gave up at last.

I finished another detail draft on input UI design, and Soimort is constructing our UI

according to it. I tried to discuss more with Soimort and push him harder, but can’t find

the right way…

My girlfriend came and we spent 3 days together. It was 3 halves of days actually, since

there are tasks I cannot put aside. However, she was so thoughtful and supportive, and didn’

t complain about my absence. We had our sweet moments together. Her visiting means a lot to

me, and fuels me up with energy to work on.

9.22

Shangyu Luo

I am in Hong Kong now! Thanks to school of computer again! I obtain a chance to live and

study in Hong Kong for one semester! Though there is much to do and I have to get familiar

with the environment in Hong Kong, I try my best to find time for our project. I skim most of

igem teams in latest three years and list some teams whose work can show the advantages and

innovations of our database. Their works are about some biological reactions related to

light, temperature, PH, etc. Read a paper of Nature about synchronized Ecoli clock, try to

master the idea of it and list the reactions in it. It will be added into our database.

Zhengda He

Starting completing our database , writing the story for the game . Collected appropriate project for us to design it into a game . Designing Wiki was the same-time work for me . And

I also pay attention in the creative idea of our Logo and uniform . The jamboree is coming ,

so I must concentrate on what I'm doing . And I will have it done beautifully .

9.30

Kun Jiang

igame in github!

To help cooperation in our teams. I decide to use a

version control software to help to

manage our source code. Because our team members come from different department and we don't

live together, especially me, I live ten kilometers far away from USTC. So a distributed

Version control System is needed. Git is the chosen one!

We create a repository igame in [http://github.com

github], and our team member can get the source by using [http://en.wikipedia.org/wiki/Git_

(software) git] with git URL git@github.com:jkdirac/igame.git.

Jue Wang

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

The itinerary

Beijing-Boston

1. AA186 WE03NOV PEKORD 0655 0625

2. AA444 WE03NOV ORDBOS 1005 1310

Boston-Beijing

3. AA1561 TU09NOV BOSORD 1545 1730

4. AA187 TU09NOV ORDPEK 2000 2330+1

Team:USTC Software/notebook 9

From 2010.igem.org

Contents

Zhen Wang

Kun Jiang

Luojun Wang

Shangyu Luo

Zhengda He

Zhen Wang

Kun Jiang

Zhen Wang

Kun Jiang

Zhen Wang

Luojun Wang

Zhen Wang

Shangyu Luo

Zhengda He

Kun Jiang

Jue Wang