Team:USTC Software/Database

From 2009.igem.org

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__NOTOC__
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<font size = "3">'''Links'''</font>
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----
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{{USTCSW_Heading}}
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{|-
{|-
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|<font color = "white">Col1</font>
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|align = "left"|
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*[[Team:USTC|USTC Team Wiki]]
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==Basic Description==
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*[http://biotech.ustc.edu.cn/forum/forumdisplay.php?fid=26 External Team Forum]
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*[http://igem.ustc.edu.cn/ External Team Wiki]
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The '''Database''' part is designated to build up the bridge combining the abstract parameters yielded by the '''System Identification''' process and the concrete needs from users via '''SBML'''. Therefore, corresponding to its transitive role here, the inputs and outputs of this part is similarity characterized.
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*[http://spreadsheets.google.com/pub?key=plR27rERjfUK_lAs01fg5YA Summary of iGEM Teams]
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*[http://en.ustc.edu.cn/about.php About USTC]
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==The Functions==
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1.Filter all matching reactions from the database via matching suitable parameters of all terms of the ODE array, provided by preceding '''GA''' and '''PSO''' part;<br />
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2.Yield a complete list of substances contained in these reactions;<br />
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3.Sort reactions by reaction type, reactant/product’s type or number;<br />
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4.Make it possible for users to expand the database in directed form.<br />
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==Abstract and approximation==
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1.All bio-chemical reactions on the genetic level are characterized in a finite set of reaction types, specifically as listed in [[Media:keneticlaw.png]] here;<br />
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2.Each term of the ODE can be mapped to part of a prototype of reactions (including all info from reactants and partial info from products);<br />
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3.Space-independent and Compartment-independent.<br />
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==Data Structure and Organization==
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<pre>
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struct reactor{
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int rnum;//number of reactants
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char **ract;//names of reactants
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};
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struct product{
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int pnum;//number of products
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char **prdt;//names of products
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};
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struct reaction{
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int num;//reaction number
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struct reactor RACT;//info of reactants
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struct product PRDT;//info of products
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int type;//reaction type as listed in keneticlaw.pdf
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double *para;//all parameters
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char note[MAXLEN];//self-defined notes
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};
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</pre>
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==Visualization==
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[[Image:database_ustcsw.png|center|800px|The organization of data structure and storage form.]]<br />
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==Instructions==
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{
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1.Input the tolerance of deviation of stored reactions from idea identified parameters in percentage (temporarily confined to 0% to 1000%);<br />
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2.How many results counting down from the top of the list do you want to see? Input an integer no bigger than 10;<br />
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3.Or you may tell the substances’ name you want to include just in string form less than 50 bytes.<br />
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<br />
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<br />
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[[Image:ITinCP_database_ustcsw.png|left|frame|300px|Independent test in console application]]
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==Outputs==
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'''dbt0.dat, dbt1.dat …, dbt9.dat''': all reactions contained in best ten models <br />
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'''sub0.dat, sub1.dat …, sub9.dat''': all related substances respectively related in the ten sets of reaction<br />
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==Defects==
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1.Not ready for repeated searches at one traverse of the original database;<br />
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2.Better performs if parameters could be interchanged though RAM/ROM;<br />
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3.Limited forms of reaction types;<br />
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4.If ordered itself, the database will be capable to offer higher searching efficiency;<br />
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|<font color = "white">Col1</font>
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Latest revision as of 17:20, 19 October 2009

Links

  • USTC Team Wiki
  • [http://biotech.ustc.edu.cn/forum/forumdisplay.php?fid=26 External Team Forum]
  • [http://igem.ustc.edu.cn/ External Team Wiki]
  • [http://spreadsheets.google.com/pub?key=plR27rERjfUK_lAs01fg5YA Summary of iGEM Teams]
  • [http://en.ustc.edu.cn/about.php About USTC]
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