Team:USTC Software/notebook

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'''BERKELY DBXML 2.5 introduction by LIAOCHEN'''
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{{Team:USTC_Software/Header}}
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----
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<html>
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<style type="text/css">
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table.calendar          { margin: 0; padding: 10px; }
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table.calendar td      { margin: 0; padding: 2px; vertical-align: top; }
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table.month .heading td { padding:2px; background-color:#66b3ff; color:#ffffff;
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text-align:center; font-size:120%; font-weight:bold; }
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table.month .dow td    { color:#000000; text-align:center; font-size:110%; }
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table.month td.today    { background-color:#66b3ff; }
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table.month td {
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border: none;
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margin: 0;
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padding: 1pt 1.5pt;
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font-weight: bold;
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font-size: 100%;
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text-align: right;
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background-color: white;
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}
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#bodyContent table.month a {
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background:none; padding:0 }
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.day-active { color:#0000aa }
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.day-empty  { color:#aaa }
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==JULY==
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</style>
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*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.
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</html>
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*Liao Chen (7.21): We decided to model the species (either complex or simple species) using two data structures:
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==Monthly Notebook==
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*# 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.
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{| style="background-color:white; " align="center" border="1"
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*# 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.
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|-valign="top"
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*Liao Chen (7.22): We decided to store data of species and reactions in XML format.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_3 March]
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*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.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_4 April]
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*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.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_5 May]
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*Liao Chen (7.25): A well designed database is quite important for our project. Start to design file organization and format of database files.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_6 June]
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*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:
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|-valign="top"
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*#global : contains unit definition, definition of standard conditions of cultivating bacterial, and so on.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_7 July]
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*#module : module of each species, including biobricks, virtual biobricks, cells, plasmids, substituents and so on.  
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_8 August]
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*#species : each species that occurs in reactions defined in reaction container is defined here.
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_9 September]
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*#reactions : reactions of all species defined in species container are defined here.  
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|width=200px; align="center" |[https://2010.igem.org/Team:USTC_Software/notebook_10 October]
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|}
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==AUGUST==
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==Daily Notebook==
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Liao Chen (8.1): Start writing core codes of our project.
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{| style="background-color:#ffffff;" align="center" border="1""
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Liao Chen (8.2~8.7): Construct MySpecies class whose objects are equivalent to real species in biological system.
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|{{ #calendar: query=preload=Team:USTC_SOFTWARE/Template/Meetings
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|}

Latest revision as of 20:58, 25 October 2010

Monthly Notebook

March April May June
July August September October

Daily Notebook

March
MTWTFSS
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30 31
April
MTWTFSS
      1 2 3 4
5 6 7 8 9 10 11
12 13 14 15 16 17 18
19 20 21 22 23 24 25
26 27 28 29 30
May
MTWTFSS
          1 2
3 4 5 6 7 8 9
10 11 12 13 14 15 16
17 18 19 20 21 22 23
24 25 26 27 28 29 30
31
June
MTWTFSS
  1 2 3 4 5 6
7 8 9 10 11 12 13
14 15 16 17 18 19 20
21 22 23 24 25 26 27
28 29 30
July
MTWTFSS
      1 2 3 4
5 6 7 8 9 10 11
12 13 14 15 16 17 18
19 20 21 22 23 24 25
26 27 28 29 30 31
August
MTWTFSS
            1
2 3 4 5 6 7 8
9 10 11 12 13 14 15
16 17 18 19 20 21 22
23 24 25 26 27 28 29
30 31
September
MTWTFSS
    1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28 29 30
October
MTWTFSS
        1 2 3
4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30 31
Retrieved from "http://2010.igem.org/Team:USTC_Software/notebook"