Team:USTC Software/Standard

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Revision as of 15:27, 21 October 2009

Kinetic Parameters Identification

First of all, we shall clarify that, being dedicated to dry lab experiments, we naturally doesn't have as many incarnated Bio-Parts as usual wet labs do.

In wet lab experiment, kinetic parameters are notorious for their difficulties to be obtained quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible part. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices.

Model 2 is a subsystem of Model 3.

Model 2 and Model 3 from 2009 USTC Wet Team

Here we put forward another feasible way to define dynamic parameters of biochemical reactions, and further characterization of single biobrick and combined bio-devices, in terms of chemical dynamics view.

Data Sheet and Related Construction.

A pool of standard reactions should be constructed according to following suggested rules.
1. Clear characterazation of reacting substances, grouped by reactants and products.
  1. substance's general physical properties, including molecular mass, phase diagram, infrared spectra, etc.
  2. substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc.
  3. '

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-{{USTCSW_Heading}}
-{|-
-|valign = "top"|
-{{USTCSW_SideBarL}}
-|valign = "top" align = "justify" border = "0" width = "600px" bordercolor = "#F3F3F3"|
-==The Angle==
-Devices by parts are constructed in a uniform way that is based on certain kind of biochemical reactions. The different responses to the same stimuli among these devices are due to the kinetic parameters which have close correlation with inherent chemical and physical property of parts particularly by directed evolution in project of USTC wet team.
-Here, we propose a new silico based standard for biobricks to facilitate the application in computer. We name it E-bricks in reciprocal to the concept of Biobrick. By applying our methods reversely to model devices on concerning static and dynamical properties, ODE model or frequency domain transfer function is established that is easy to drag and plug on a laptop like engineer did on CAD software.
-However, we are not only concerning on the simulation level but design issues: how to arrange existing device to construct a system that exhibit desired function.
-Thanks to the concept proposed by [endy_nbt], we try to establish a datasheet like the one in this paper. Considering the limit of current biobricks database, it is hard to construct sufficient and large database. While our USTC wet team is putting effort to following that standard, it’s lucky for us to obtain raw data that satisfies our model requirement. It is also be of great honor to assist our wet team.
 ==Kinetic Parameters Identification==
 First of all, we shall clarify that, being dedicated to dry lab experiments, we naturally doesn't have as many incarnated Bio-Parts as usual wet labs do.
-In wet lab experiment, kinetic parameters are notorious for their difficulties to obtain quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible parts. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices. [https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2]<partinfo>K176126 DeepComponents</partinfo> is a subsystem of [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3]<partinfo>K176066 DeepComponents</partinfo>.
+In wet lab experiment, kinetic parameters are notorious for their difficulties to be obtained quantitatively. To construct a well fabricated device, the kinetic parameters are crucial for an extensible part. When certain parts are placed in the network, certain biochemical reactions with holding kinetic parameters are introduced. To identify kinetic parameters of basic devices determines the extensibility of devices.
+[https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2]<partinfo>K176126 DeepComponents</partinfo> is a subsystem of [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3]<partinfo>K176066 DeepComponents</partinfo>.
 [[Image:wet2dry.png|center|500px|thumb|[https://2009.igem.org/Team:USTC/Modeling/Model-2 Model 2] and [https://2009.igem.org/Team:USTC/Modeling/Model-3 Model 3] from [https://2009.igem.org/Team:USTC/Modeling 2009 USTC Wet Team]]]
-==Robustness Analysis==
+Here we put forward another feasible way to define dynamic parameters of biochemical reactions, and further characterization of single biobrick and combined bio-devices, in terms of chemical dynamics view.
-In biological systems, kinetic parameters should be robust enough to resist uncertainties and noise. It is better to give a range of parameters in order to leave a design margin for users. Here, we propose [https://2009.igem.org/Team:USTC_Software/hoWAlgorithm#Global_Sensitivity_Analysis_.28GSA.29 robustness analysis algorithm] to determine the scope.
-After
-==Database Structure==
-==Our Proposal==
-|valign = "top"|
+Data Sheet and Related Construction.
-{{USTCSW_SideBarR}}
+# A pool of standard reactions should be constructed according to following suggested rules.
-|}
+## Clear characterazation of reacting substances, grouped by reactants and products.
-|}
+### substance's general physical properties, including molecular mass, phase diagram, infrared spectra, etc.
-{{USTCSW_Foot}}
+### substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc.
+### ''''''