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| - | ==''AUGUST''==
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| - | ===Chen Liao===
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| - | *Liao Chen (8.1): Start writing core codes of our project.
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| - | ----
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| - | *Liao Chen (8.2~8.12): Construct MySpecies class whose objects are equivalent to real species in
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| - | biological system. Five modifications have been made until the final version.
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| - | ----
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| - | ;software : dbxml
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| - |
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| - | *Liao Chen (8.25, afternoon): leave for shanghai to get our passport visaed. We played Three Kingdom
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| - | Kills (TKK) on the train. The speed of the train is as slow as a turtle creeps.
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| - |
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| - | *Liao Chen (8.25, night): So many pretty, tall girls outside of Rolex faced to HuangPu river... what
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| - | a feel if...
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| - |
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| - | *Liao Chen (8.26): Face to face with visa officer. Three checked, 10 passed.
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| - |
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| - | ===Zhen Wang===
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| - | Aug 2 ~ Aug 15, 2010
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| - | At first we want to use MySQL to manage our database, later we find Berkeley DBXML is a better tool,
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| - | so I studied on how to use DBXML. Kun Jiang quickly write an interface using DBXML API and a small
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| - | PDF instruction, code genius!
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| - | Finish database format v3.0 – the 3rd version of database, now there are 4 lists, the global, the
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| - | module, the species, the reactions. Global list stores data that must be pre-defined. Specify
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| - | database format and give detailed examples on each list.
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| - | In order to realize the real species, we add substituent in module and chain in species(special
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| - | thanks to Hao Jiang).
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| - | Aug 16 ~ Aug 22, 2010
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| - | Read more documents on DBXML and XML.
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| - | Prepare materials for interview in Shanghai.
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| - | Liao upload the first version of iGAME core, Soimort upload the first version of iGAME web UI, this
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| - | is a big motivation to me, seems our game will be able to work finally.
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| - | Aug 23 ~ Aug 29, 2010
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| - | Prepare materials for interview in Shanghai.
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| - | All iGEM USTC TEAM members go to Shanghai for visa interview, I pass, but 3 of our member are
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| - | checked, best wishes for them!
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| - | Refine the database format, specify bioreactor in module list, compartment&condition in reaction
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| - | list, substituent changes in species list(special thanks to Hao Jiang).
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| - | We receive our passports with visas one by one.
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| - | Draw a couple of charts and diagrams to explain the construction of database, seems I am pretty good
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| - | at it.[pic]
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| - | Finish and upload database format PDF and database RAR v8.27, together with some photos taken at
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| - | Shanghai.
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| - | Realize work log is very important, so recall my work and write my notebook.
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| - |
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| - | ===Kun Jiang===
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| - | Aug 2 ~ Aug 22, 2010
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| - | Study the dbxml specification document for developing a more convenience database interface.
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| - | Aug 23 ~ Aug 29, 2010
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| - | Make preparation for visa interview in Shanghai.
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| - |
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| - | ===Luojun Wang===
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| - | Collaboration with Prof. Jiong Hong features the synthesis biology class with IGEM issues and our
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| - | program.
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| - | Lectures on ethnics and promotions for iGAME are given during the curriculum, which are partly
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| - | videotaped. : )
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| - | Surveys are also made for iGAME.
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| - | Statistics have been analysized in many different ways before CIRCOS software runs into my sight.
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| - | Methods of plotting chromesomes are used in the demonstration of the work, which is the most
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| - | innovative idea I have ever seen in any performance of survey.:D In the poll on favorite game type,
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| - | adventure game is on top, can we make a tutor game like ''Prince of Persia''?lol~
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| - | Interviewed by Yueyue Zhang, doctor of BIOS Centre of London School of Economics and Politics
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| - | Science. Opinions on human practice have been exchanged and much new information is obtained from
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| - | her.(Special thanks to her!)
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| - |
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| - | ===Shangyu Luo===
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| - | Aug 2 ~ Aug 15, 2010 With Zhen Wang coming up with different generations of database, I make some discussion with him and help him to modify, specify and complement our database
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| - | Aug 16 ~ Aug 22, 2010 Start to learn how to utilize dbxml to aid us in the construction of our database. Be familiar with the environment and command of this software and scan the code to capture the basic features of it which will contribute to handling its APIs in our software
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| - | Try to learn how to add contents of our team’s wiki
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| - | Aug 23 ~ Aug 29, 2010 Use 2009 Minnesota igem team as a trial, I list out all the materials we need in our database but detect that there are some details we can not cover in our database. Try to tackle with this problem with Chen Liao.
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| - | What’s more, I apply for some financial aid or fund for my trip to MIT and fortunately I get it from my own department: School of Computer Science and Technology! Thanks to the support of my department, I can get a chance to America, to MIT, so I have to express my appreciation again! Though it is just founded before long and doesn’t have much finance at present, my school gives great supports to students and aids them to expand the horizon and improve their abilities in comprehensive fields. With a lot of young but full of research background teachers and professors, I think my school will have a bright future!
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| - |
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| - | === Zhengda He ===
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| - | Went to ShangHai to get my VISA . The journey was good . I'm not checked ~ so I feel kind of
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| - | lucky~~To help WangZhen create new database standard . At the same time , I was designing the Graphic
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| - | User Interface and game story . It was a busy month .
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| - |
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| - | ==''SEPTEMBER''==
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| - | ===Zhen Wang===
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| - | Aug 30 ~ Sep 5, 2010
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| - | Plan:
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| - | Think about what database modification tool a senior user would like to use.
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| - | Write full database that includes the whole oscillator.
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| - | Read more on XML.
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| - | Have fun working.
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| - | Summary:
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| - | Not having much fun working, with both sides’ tasks to be done.
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| - | Full database for oscillator is done 2010/9/2. I haven’t checked it in detail yet.
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| - | It is very likely we are going to change the db structure yet again, good thing though.
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| - | Learn from libsbml the sbml modification tool, our db modification should somehow like that. It
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| - | should focus on adding and constructing new model.
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| - | Discuss on UI&input with Liao, writing the new UI draft.
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| - | Sep 5 ~ Sep 12, 2010
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| - | Plan:
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| - | Discuss UI&input with Soimort.
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| - | Discuss ODE solver with Kun.
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| - | Teaching junior students how to write DB.
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| - | Have fun working.
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| - | Summary:
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| - | This is a crazy week for me! Together with Liao, we make huge modifications on the structure of for
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| - | at least 3 times! We change the xml structure for storing data, revise the attributes on each item,
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| - | and have heated debate on our standard of bio-modeling. At first the modification process seems
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| - | endless, but by the end of the week, we have come to agreement on most of the details. This gives me
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| - | a lot of hope, and this week has definitely been a big leap for our DB.
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| - | This time Liao finally realizes that we are actually making the next-generation standard of SBML,
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| - | haha. Settling a brand-new standard of bio-modeling has actually become the core of our work. As far
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| - | as I’m concerned, we have made 3 shifts on our goal, UI -> simulation -> bio-modeling standard, this
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| - | is poor goal-setting, we didn’t make a clear map of what we are doing at the very beginning.
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| - | I talk on DB and modeling with 2 junior students, they are all confident and eager to learn, I think
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| - | they can handle it properly very soon.
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| - | I just don’t have the time to talk with Soimort and Kun.
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| - | Sep 12 ~ Sep 19, 2010
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| - | Plan:
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| - | Write note on UI&input, discuss UI&input with Soimort.
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| - | Discuss ODE solver with Kun.
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| - | Settle the final edition of DB.
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| - | Writing DB of EPF-Lausanne with 2 junior students.
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| - | Have fun working.
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| - | Summary:
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| - | 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.
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| - | 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.
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| - | Liao’s first edition of document on DB standard is done, it’s now my turn to refine it and fix the bugs.
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| - | 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.
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| - | 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.
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| - | 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.
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| - | I do have fun working this week!
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| - | Sep 20 ~ Sep 26, 2010
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| - | Plan:
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| - | Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document.
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| - | Discuss UI with Soimort and push him to work faster, discuss synchronized E.coli with Zhaoyi Li.
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| - | Have fun working.
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| - | Summary:
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| - | 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!
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| - | 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…
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| - | Here’s what I can remember.
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| - | 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.
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| - | 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.
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| - | 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…
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| - | 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.
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| - |
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| - | ===Kun Jiang===
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| - | Sep 5 ~ Sep 12, 2010
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| - | Build two tool softwares to help Zhen Wang to edit our database input files.
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| - | Sep 12 ~ Sep 30, 2010
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| - | Modify the soslib v1.6.0 source code to base on libsbml v4.0.1, Which enable soslib support sbml
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| - | version2 level 4 to meet our database format requirements.
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| - | Summary:
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| - | (we will see~)
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| - |
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| - | ===Luojun Wang===
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| - | Idea of starting a community has been discussed with the wet team and will be realized soon.
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| - | Concerned with IPR issue, I consult the IPRs Centre of USTC for safety of iGAME.
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| - | Start of wiki scripts.
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| - | Summary:
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| - | Finally, I decide to give a name to the human practice project, "the C project". "C" stands for
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| - | "curriculum","communication" and "community", it is also ''cool'', huh?
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| - |
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| - | ===Shangyu Luo===
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| - | 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.
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| - |
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| - | === Zhengda He ===
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| - | Starting completing our database , writing the story for the game . Collected appropriate
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| - | 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 .
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| - | ==OCTOBER==
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| - |
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| - | ===ZHEN WANG===
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| - | Sep 27 ~ Oct 7, 2010
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| - | Plan:
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| - | Finish EPF-Lausanne database, finish E.coli oscillator database, update DB document.
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| - | Settle the DB format for good(hopefully).
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| - | Summary:
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| - | 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.
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| - | 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.
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| - |
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| - | We schedule our trip and book plane tickets to Beijing, Chicago and Boston. Jue Wang is now in charge of money and team wear.
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| - | 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.
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| - |
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| - | == Lab Notebook ==
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| | <html> | | <html> |
| | <style type="text/css"> | | <style type="text/css"> |
| Line 227: |
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| | </style> | | </style> |
| | </html> | | </html> |
| | + | ==Monthly Notebook== |
| | + | {| style="background-color:white; " align="center" border="1" |
| | + | |-valign="top" |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_3 March] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_4 April] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_5 May] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_6 June] |
| | + | |-valign="top" |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_7 July] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_8 August] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_9 September] |
| | + | |width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_10 October] |
| | + | |} |
| | | | |
| - | Meetings are set every Saturday since Feb.15th, then three
| + | ==Daily Notebook== |
| - | more discussions (Mon, Wes, Fri) are added when we start to
| + | |
| - | determine our project since Mar 21th.
| + | |
| - | | + | |
| - | *2010.4.10 – 2010.5.14 reports of the former iGEM works
| + | |
| - | | + | |
| - | *2010.5.21 – 2010.6.11 broach of candidate projects
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| - | ** cell density control
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| - | ** Reporter and imaging
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| - | ** DNA writing and reading in the cell
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| - | ** Biodegradation of plastics
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| - | | + | |
| - | *2010.6.12 – 2010.6.30 further research by small groups on
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| - | the candidate projects
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| - | | + | |
| - | * sketch map of our final project host-cell free reaction
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| - | chamber was set up
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| - | | + | |
| - | All the reports information, slides and audio records of our
| + | |
| - | meetings are arranged here.
| + | |
| - | | + | |
| | {| style="background-color:#ffffff;" align="center" border="1"" | | {| style="background-color:#ffffff;" align="center" border="1"" |
| | |-valign="top" | | |-valign="top" |
| - | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
| |
| - | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2009 |month=12 }}
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| - | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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| - | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=01 }}
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| - | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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| - | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=02 }}
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| | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=03 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=03 }} |
| - | |-valign="top"
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| | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=04 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=04 }} |
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| | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=06 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=06 }} |
| | + | |-valign="top" |
| | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=07 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=07 }} |
| - | |-valign="top"
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| | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings | | |{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings |
| | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=08 }} | | |title=Team:USTC_SOFTWARE/Notebook/Meetings |year=2010 |month=08 }} |
"
