Team:USTC Software/Standard

From 2009.igem.org

Revision as of 17:06, 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.

Note: each quantitative archive below should have at least one record documented in SI units.

• 1. A pool of standard reactions should be constructed according to following suggested rules.
     1. (required) Clear characterazation of reacting substances, grouped by reactants and products.
        1. reactants' serial number, names and number of types
        2. products' serial number and names and number of types
     2. Finite division of reaction types (with unique serial numbers for each).
        1. (required) Reaction type (used for mathematical modeling, including Hill, Linear, etc.)
        2. (required) Parameters' names, values and number of types according to selected reaction type
        3. (optinal, default to be independent) Temperature dependence of parameters listed above, each described by an analytical function or quasi-continuous experimental data in deriative form
     3. (optional) Other reaction requirements
        1. physical conditions including reaction compartment, external magneitc field, lighting condition, etc.
        2. chemical conditional including PH, specific coexistence with other substances, etc.
     4. (optional) Notes for the reaction item

• 1. A pool of standard substances (applicable to any unit depictable by reaction types listed in the pool of reactions, including BioBricks, BioDevices, individual cell or even colony)
     1. (required) substance's serial number and name.
     2. (optional) substance's general physical properties, including molecular mass, magnetism, phase diagram, infrared spectra, etc.
     3. (optional) substance's general chemical properties, including chemical composition, hydrolysis constant, ionization constant, and the stability in conventional intermediate like air and distilled water, etc.
     4. (required) subtance's class (small molecule, DNA, mRNA, etc.), related reactions' serial numbers, status of the substance in that reaction (involved as reactant or product), etc.
     5. (required if type = "BioBrick" or "BioDevice") Standard requirement listed by partsregistry, including sequence length, coding sequence， etc.

• Parameter Definition

By constructing the two interwined database, we can easily retrieve chemical dynamics parameters, match reactions or substances, traverse possibly extended bio-network or reaction network. Above all, a

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