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From 2010.igem.org

BERKELY DBXML 2.5 introduction by LIAOCHEN

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JULY

• 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.
  2. 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.
  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.

AUGUST

• Liao Chen (8.1): Start writing core codes of our project.

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• 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.

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software 

dbxml