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	Study the dbxml specification document for developing a more convenience database interface.		Study the dbxml specification document for developing a more convenience database interface.

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Revision as of 12:04, 27 October 2010

Contents 1 Liao Chen 2 Zhen Wang 3 Kun Jiang 4 Luojun Wang 5 Shangyu Luo 6 Zhengda He 7 Shangyu Luo 8 Zhen Wang 9 Liao Chen 10 Liao Chen 11 Liao Chen 12 Liao Chen 13 Liao Chen 14 Liao Chen 15 Zhen Wang 16 Liao Chen 17 Kun Jiang 18 Luojun Wang 19 Shangyu Luo 20 Kun Jiang

Liao Chen

• Liao Chen (7.20): Discuss framework of core programme of simulation part of our project with Jiang

Hao. We decided to take consideration of the structure of complex, which solves problems we encountered when handling reactions with regard to complex molecules.

• Liao Chen (7.21): We decided to model the species (either complex or simple species) using two data

structures:

• 1. ChainList is used to describe chains of DNA, RNA or Protein molecules. Small molecules are also

of such structure with only one element on one chain.

• 1. Tree structure is used to describe binding state of elements of different chains. Children nodes

bind with each other and form their parent node. Thus, other than chains, a species has its binding state forest, which composed of many trees mentioned above.

• Liao Chen (7.22): We decided to store data of species and reactions in XML format.
• Liao Chen (7.23): To search reactions of species includes, we need powerful support of species and

reactions database. But first, we need a database manager to manage our XML data files, which must provide query operation of data we want.

• Liao Chen (7.24): We find it! Oracle Berkeley DB XML! It is a Native XML Database. It is capable of

storing and indexing collections of XML documents in both native and mapped forms for highly efficient querying, transformation, and retrieval.

• Liao Chen (7.25): A well designed database is quite important for our project. Start to design file

organization and format of database files.

• Liao Chen (7.26~7.30): Discussion with Jiang Hao about how to design database. We decide to make 4

file containers to hold different kind of contents:

• 1. global : contains unit definition, definition of standard conditions of cultivating bacterial, and

so on.

• 1. module : module of each species, including biobricks, virtual biobricks, cells, plasmids,

substituents and so on.

• 1. species : each species that occurs in reactions defined in reaction container is defined here.
  2. reactions : reactions of all species defined in species container are defined here.

Zhen Wang

Jul 19 ~ Jul 25, 2010 I Find myself have little knowledge about partregistry, so I read registry and summarize promoter, plasmid backbones, protein coding sequence, degradation reaction, plasmid, etc. The first edition of oscillator database pack and database documentation has been written by Liao, I only give some suggestions on naming our modules, and make little contribution on the whole thing.

Jul 26 ~ Aug 1, 2010 Talk together with Hao Jiang and Liao, write the second edition of oscillator database and database format. In order to deal with the real reactions and real species, we add virtual biobricks to our database, together with a bunch of new attributes. The database is constructed by 3 lists, the single compartment list, the species structure list, the reaction list, relationship of the 3 lists is shown in the following picture.[pic]

Kun Jiang

Study the CMake, a project manage tool for huge software project, and QT, a cross-platform application and UI framework. Try to develop a demo project.

Luojun Wang

Start of our human practice. Summer classes of synthesis biology begin and are lectured by Prof. Haiyan Liu and Jiong Hong, both of who are advisors of our team. After communicating with Prof. Haiyan Liu and Jiong Hong, I decide to do many things along with the curriculum. Surveys are written and done for the synthesis biology class. Lectures are also prepared for it. Much communication with other teams and people is done, which is quite educational and impressive.(it's fun, too!)

Shangyu Luo

Jul 19 ~ Jul 25, 2010 As the problem with simulation has finally been solved, I turn to acquire some knowledge about database which will be a huge and basic part of our project and then begin a long period cooperation with Zhen Wang. Obtain the classification of database: network database, hierarchical database, relational database

Jul 26 ~ Aug 1, 2010 have a general idea of database and have a discussion with Hao Jiang, Zhen Wang, Chen Liao frequently to deal with some difficulties in the construction of database, as well as some biological problem.

Zhengda He

The same as June .

7.14

Shangyu Luo

Jul 19 ~ Jul 25, 2010 As the problem with simulation has finally been solved, I turn to

acquire some knowledge about database which will be a huge and basic part of our project and

then begin a long period cooperation with Zhen Wang. Obtain the classification of database:

network database, hierarchical database, relational database

7.19

Zhen Wang

I Find myself have little knowledge about partregistry, so I read registry and summarize

promoter, plasmid backbones, protein coding sequence, degradation reaction, plasmid, etc. The

first edition of oscillator database pack and database documentation has been written by

Liao, I only give some suggestions on naming our modules, and make little contribution on the

whole thing.

7.20

Liao Chen

Discuss framework of core programme of simulation part of our project with Jiang Hao. We

decided to take consideration of the structure of complex, which solves problems we

encountered when handling reactions with regard to complex molecules.

7.21

Liao Chen

We decided to model the species (either complex or simple species) using two data structures:

ChainList is used to describe chains of DNA, RNA or Protein molecules. Small molecules are

also of such structure with only one element on one chain. Tree structure is used to describe binding state of elements of different chains. Children

nodes bind with each other and form their parent node. Thus, other than chains, a species has

its binding state forest, which composed of many trees mentioned above.

7.22

Liao Chen

We decided to store data of species and reactions in XML format.

7.23

Liao Chen

To search reactions of species includes, we need powerful support of species and reactions

database. But first, we need a database manager to manage our XML data files, which must

provide query operation of data we want.

7.24

Liao Chen

We find it! Oracle Berkeley DB XML! It is a Native XML Database. It is capable of storing and

indexing collections of XML documents in both native and mapped forms for highly efficient

querying, transformation, and retrieval.

7.25

Liao Chen

A well designed database is quite important for our project. Start to design file

organization and format of database files.

7.26

Zhen Wang

Talk together with Hao Jiang and Liao, write the second edition of oscillator database and

database format. In order to deal with the real reactions and real species, we add virtual

biobricks to our database, together with a bunch of new attributes. The database is

constructed by 3 lists, the single compartment list, the species structure list, the reaction

list, relationship of the 3 lists is shown in the following picture.[pic]

7.27

Liao Chen

Discussion with Jiang Hao about how to design database. We decide to make 4 file containers

to hold different kind of contents:

1 global : contains unit definition, definition of standard conditions of cultivating

bacterial, and so on. 2 module : module of each species, including biobricks, virtual biobricks, cells, plasmids,

substituents and so on. 3 species : each species that occurs in reactions defined in reaction container is defined

here. 4 reactions : reactions of all species defined in species container are defined here.

7.29

Kun Jiang

Study the CMake, a project manage tool for huge software project, and QT, a cross-platform

application and UI framework. Try to develop a demo project.

Luojun Wang

Start of our human practice. Summer classes of synthesis biology begin and are lectured by

Prof. Haiyan Liu and Jiong Hong, both of who are advisors of our team. After communicating

with Prof. Haiyan Liu and Jiong Hong, I decide to do many things along with the curriculum.

Surveys are written and done for the synthesis biology class. Lectures are also prepared for

it. Much communication with other teams and people is done, which is quite educational and

impressive.(it's fun, too!)

Shangyu Luo

Jul 26 ~ Aug 1, 2010 have a general idea of database and have a discussion with Hao Jiang,

Zhen Wang, Chen Liao frequently to deal with some difficulties in the construction of

database, as well as some biological problem.

7.31

Kun Jiang

Study the dbxml specification document for developing a more convenience database interface.