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Logic
From a truth table to abstract logic circuits
In BioBLESS, a truth table dialog box will be displayed for users to input
Boolean numbers 0/1. All you need to do is to click Boolean buttons and
then “Create”. The corresponding designed logic circuits with different
predicted performances will be automatically generated and displayed
in order. You can immediately and clearly see the configuration of a
designed logic circuit, which in most cases is supposed to be a compli-
cated multi-input circuit. Besides the function above, gates list will
provide many Boolean gates, and users can drag them freely to our
canvas to design logic circuits.
Gene Network
See the detailed structure of a designed gene circuit
A simple click on “Gene network” button will lead you to
another tab where the detailed structure of your designed
gene circuit is shown. When a gene circuit consists of many
Boolean gates, it is crucial to understand the internal sub-
stances and mechanisms. In this tab, you can see how
substances react with each other clearly, such as inhibition
and activation in or between Boolean gates.
SIMULATION
Get concentration-time simulation results
Given a designed gene circuit, such as a simple serial circuit composed of
an AND gate and an OR gate, you can use our default parameters and
change initial concentration of reactants to get simulation results. If you
want to get different results, you just need to change system parameters
such as the rate of reactions, namely, to fill constants into the dialog
boxes on our canvas. What’s more, simulation time slot is necessary as well to give
concentration-time figures of the inputs and outputs of a given gene circuit.
You are free to see the concentration-time evolution of every substance in
designed gene circuits individually.
ANALYSIS
Get robustness and sensitivity analysis
While offering various functions, BioBLESS also serves as an
analysis tool for designed gene circuits. Having designed a gene
circuit, you can click the “Analysis” button to reset parameters of
initial concentrations and reaction rates. Meanwhile, BioBLESS
will set simulation slots and carry the simulation task
automatically. According to the perturbation ratio you
input, such as 20% or 30%, the concentration-time
curves of inputs and outputs will be shown toge-
ther to shed light on the robustness of a designed
gene circuit. Moreover, data processing and
demonstration will help users to better
understand the robustness of
designed gene circuits.
DNA
Get the DNA sequence!
Users have the freedom to drag specific BioBricks on our canvas and
combine them into a functional gene circuit. Then the DNA sequence
and other information of the designed circuit are available for users
to check and download. Wet lab protocols are partly incorporated into
our DNA sequences which may make the design better and applicable in
laboratories.
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USTC-Software 2015
University of Science and Technology of China
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