Team:USTC Software/notebook 8

From 2010.igem.org

Contents

Chen Liao

  • Liao Chen (8.1): Start writing core codes of our project.
  • Liao Chen (8.2~8.12): Construct MySpecies class whose objects are equivalent to real species in

biological system. Five modifications have been made until the final version.

software 
dbxml
  • Liao Chen (8.25, afternoon): leave for shanghai to get our passport visaed. We played Three Kingdom

Kills (TKK) on the train. The speed of the train is as slow as a turtle creeps.

  • Liao Chen (8.25, night): So many pretty, tall girls outside of Rolex faced to HuangPu river... what

a feel if...

  • Liao Chen (8.26): Face to face with visa officer. Three checked, 10 passed.

Zhen Wang

Aug 2 ~ Aug 15, 2010 At first we want to use MySQL to manage our database, later we find Berkeley DBXML is a better tool, so I studied on how to use DBXML. Kun Jiang quickly write an interface using DBXML API and a small PDF instruction, code genius! Finish database format v3.0 – the 3rd version of database, now there are 4 lists, the global, the module, the species, the reactions. Global list stores data that must be pre-defined. Specify database format and give detailed examples on each list. In order to realize the real species, we add substituent in module and chain in species(special thanks to Hao Jiang).

Aug 16 ~ Aug 22, 2010 Read more documents on DBXML and XML. Prepare materials for interview in Shanghai. Liao upload the first version of iGAME core, Soimort upload the first version of iGAME web UI, this is a big motivation to me, seems our game will be able to work finally.

Aug 23 ~ Aug 29, 2010 Prepare materials for interview in Shanghai. All iGEM USTC TEAM members go to Shanghai for visa interview, I pass, but 3 of our member are checked, best wishes for them! Refine the database format, specify bioreactor in module list, compartment&condition in reaction list, substituent changes in species list(special thanks to Hao Jiang). We receive our passports with visas one by one. Draw a couple of charts and diagrams to explain the construction of database, seems I am pretty good at it.[pic] Finish and upload database format PDF and database RAR v8.27, together with some photos taken at Shanghai. Realize work log is very important, so recall my work and write my notebook.

Kun Jiang

Aug 2 ~ Aug 22, 2010 Study the dbxml specification document for developing a more convenience database interface.

Aug 23 ~ Aug 29, 2010 Make preparation for visa interview in Shanghai.

Luojun Wang

Collaboration with Prof. Jiong Hong features the synthesis biology class with IGEM issues and our program. Lectures on ethnics and promotions for iGAME are given during the curriculum, which are partly videotaped. : ) Surveys are also made for iGAME. Statistics have been analysized in many different ways before CIRCOS software runs into my sight. Methods of plotting chromesomes are used in the demonstration of the work, which is the most innovative idea I have ever seen in any performance of survey.:D In the poll on favorite game type, adventure game is on top, can we make a tutor game like Prince of Persia?lol~ Interviewed by Yueyue Zhang, doctor of BIOS Centre of London School of Economics and Politics Science. Opinions on human practice have been exchanged and much new information is obtained from her.(Special thanks to her!)

Shangyu Luo

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

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 Try to learn how to add contents of our team’s wiki

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. 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!

Zhengda He

Went to ShangHai to get my VISA . The journey was good . I'm not checked ~ so I feel kind of lucky~~To help WangZhen create new database standard . At the same time , I was designing the Graphic User Interface and game story . It was a busy month .

8.1

Chen Liao

Start writing core codes of our project.

Zhen Wang

At first we want to use MySQL to manage our database, later we find Berkeley DBXML is a

better tool, so I studied on how to use DBXML. Kun Jiang quickly write an interface using

DBXML API and a small PDF instruction, code genius! Finish database format v3.0 – the 3rd

version of database, now there are 4 lists, the global, the module, the species, the

reactions. Global list stores data that must be pre-defined. Specify database format and give

detailed examples on each list. In order to realize the real species, we add substituent in

module and chain in species(special thanks to Hao Jiang).

8.2

Shangyu Luo

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

8.3

Chen Liao

Liao Chen (8.2~8.12): Construct MySpecies class whose objects are equivalent to real species

in biological system. Five modifications have been made until the final version.

software dbxml

8.12

Luojun Wang

Collaboration with Prof. Jiong Hong features the synthesis biology class with IGEM issues and

our program. Lectures on ethnics and promotions for iGAME are given during the curriculum, which are

partly videotaped. : ) Surveys are also made for iGAME. Statistics have been analysized in many different ways before CIRCOS software runs into my

sight. Methods of plotting chromesomes are used in the demonstration of the work, which is the most innovative idea I have ever seen in any performance of survey.:D In the poll on favorite game

type, adventure game is on top, can we make a tutor game like Prince of Persia?lol~ Interviewed by Yueyue Zhang, doctor of BIOS Centre of London School of Economics and Politics Science. Opinions on human practice have been exchanged and much new information is obtained

from her.(Special thanks to her!)

8.16

Zhen Wang

  • Read more documents on DBXML and XML.
  • Prepare materials for interview in Shanghai.
  • Liao upload the first version of iGAME core, Soimort upload the first version of iGAME web

UI, this is a big motivation to me, seems our game will be able to work finally.

Shangyu Luo

  • 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

  • Try to learn how to add contents of our team’s wiki

8.23

Shangyu Luo

  • 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.

  • 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!

8.25

Chen Liao

  • leave for shanghai to get our passport visaed. We played Three Kingdom Kills (TKK) on the

train. The speed of the train is as slow as a turtle creeps.

  • So many pretty, tall girls outside of Rolex faced to HuangPu river... what a feel if...

8.26

Chen Liao

Face to face with visa officer. Three checked, 10 passed.


Zhen Wang

All iGEM USTC TEAM members go to Shanghai for visa interview, I pass, but 3 of our member are

checked, best wishes for them!

All Team Memebers

Visa Interview. Everything is OK!

8.28

Zhen Wang

Refine the database format, specify bioreactor in module list, compartment&condition in

reaction list, substituent changes in species list(special thanks to Hao Jiang).

8.30

Zhen Wang

  • We receive our passports with visas one by one.
  • Draw a couple of charts and diagrams to explain the construction of database, seems I am

pretty good at it.[pic]

  • Finish and upload database format PDF and database RAR v8.27, together with some photos

taken at Shanghai.

  • Realize work log is very important, so recall my work and write my notebook.

8.31

Zhengda He

  • Went to ShangHai to get my VISA . The journey was good . I'm not checked ~ so I feel kind of

lucky~~

  • To help WangZhen create new database standard . At the same time , I was designing the

Graphic User Interface and game story . It was a busy month .