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                            <img src="https://static.igem.org/mediawiki/2017/f/f5/Wojiushishishi.png" alt="INTELLIGENE" style="max-width: 800px;" />
                        <h2 class="lead">Sequential logic vs. combinational logic</h2>
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                        <h3>Introduction</h3>
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                                What will you do if you could <b>reprogram</b> cells and design there <b>life processes</b>?
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                            Combinational logic circuits implement Boolean functions, which always depend on input. Boolean functions are mappings of input to output. They are functions of input only. It means that if you feed in an input to a circuit, the output will always be the same for that circuit. If that value were not the same every single time, then the output must not completely depend on input. Something else must be affecting the output.
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                                A <b>periodic drug delivery</b> to precise drug release in sequential order, appropriate time?
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                                An<b> automatic cell factory</b> where all biosynthetic procedures in one fermentation tank?
                        <h3>Example-Buy coffee</h3>
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                            Let's consider a vending machine. We want to see if its output is solely dependent on the input.
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Imagine this vending machine only sells coffee, and that the price of a coffee is 75 cents. The machine can only take quarters. Once 75 cents are deposited, a coffee is dispensed without any button being pressed. (What a stupid machine!)
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One day, when you want to drink coffee, you see this machine, and you happen to be holding several quarters. You place the first quarter in the machine, and out comes...nothing! Undaunted, you put another quarter in, and out comes.... nothing! Frustrated, you decide to put in yet another quarter, and out comes a coffee! Delicious, savory and mellow Coke! You drink, and are content.
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                                Cells that can <b>survive</b> in harsh environements by doing a series of functions their surroundings going where <b>no cells have gone before</b>?
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Then, invigorated by caffeine, you begin to think "Is this machine a function?"  
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You gave the same input, three times in a row, but it did not produce the same output.
 
  
A mathematical function maps inputs to outputs. Thus, once you know what the input maps to, that should be it. In this case, the input (a quarter) mapped to nothing. So, clearly, this does not behave like a function.
 
 
What's happening? Clearly, the machine is storing some information. In particular, it's records how much money you have entered so far. The output is determined not only by the input, but also by this stored information.
 
 
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         <!-- Welcome
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            ============================================= -->
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                        <h3>Sequential logicS</h3>
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                <h2><span>Why </span>sequential logic?</h2>
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                    <p class="sub-lead">Cells are responsive to a myriad signals under most conditions and adjust their own internal mechanisms order to survive. This adjustment depends not only on processing a combination of current environmental signal inputs , but also on determining the cell’s current state, which is a result of a series of past inputs.  In digital circuit theory, this operating mode is known as <b>sequential logic</b>. Nowadays, a wide variety of tasks can be performed by synthetically engineered genetic circuits, mostly constructed using combinational logic. Contrast to sequential logic, it's output is a function of the present input only. It is difficult to perform functions in a specific order, which has limited the widespread implementation of such systems. The ability of sequential logic circuits to store modest amounts of information within living systems and to act upon them would enable new approaches to the study and control of biological processes . A cell can be designed to do work that is more complex if it has more states. In other words, we can reach a new dimensionality in designing synthetic life – <b>time</b>.
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Key things to notice:
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 Like combinational logic circuits, a sequential logic circuit has inputs and outputs.
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 Unlike combinational logic circuits, a sequential logic circuit is related to time.
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 Also, there is a box inside the circuit called State. This box contains flip flops. Assume it has k flip flops. The flip flops basically store a k-bit number representing the current state. The state can be updated.
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 The output is computed based on the inputs and the state coming out of the state box.
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The information needed to update to the state (called the next state) comes from the current state (the current value of q) and the input, which is fed through combinational logic, and fed back into the state box, telling the state box how to update itself.
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                <h2><span>What </span>we did</h2>
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                    <p class="sub-lead">This year, the Peking iGEM team is attempting to develop a frame of biological sequential circuits that are programmable. The envisioned circuit is capable of both storing states in DNA and automatically running a series of instructions in a specific order. More specifically, the sequential logic that consists of a <b>clock</b> , <b>flip flop</b> and <b>control unit</b> in bacteria. The clock is an oscillator with a repeated signal cycle that is utilized like a metronome to trigger actions of sequential logic circuits. <b>Flip-flop</b> is a memory device that can remember a state. Paired with a clock signal, it can realize state transition. The <b>control unit</b> is a functional part which can convert a signal from flip-flop into complex functions. With such a design, historical events are recorded and influence current cell behavior.</p>
            <section class="">
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<p class="sub-lead">This work tries to point the way toward building large computational sys-tems from modular biological parts—basic sequential computing devices in living cells—and ultimately, programming complex biological functions. Computers have thus become "alive". A unicellular organism itself cannot pack much computational power, but considered as a modular building block, its potential is impressive.
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                        <h3>Summary</h3>
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The main difference between sequential circuits and combinational circuits is that sequential circuits compute their output based on input and state, and that the state is updated. Combinational logic circuits implement Boolean functions, so they are functions only of their inputs, and are not based on clocks.
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Latest revision as of 01:13, 17 November 2017

iGEM EPFL 2016

INTELLIGENE

What will you do if you could reprogram cells and design there life processes?

A periodic drug delivery to precise drug release in sequential order, appropriate time?

An automatic cell factory where all biosynthetic procedures in one fermentation tank?

Cells that can survive in harsh environements by doing a series of functions their surroundings going where no cells have gone before?

Why sequential logic?


Cells are responsive to a myriad signals under most conditions and adjust their own internal mechanisms order to survive. This adjustment depends not only on processing a combination of current environmental signal inputs , but also on determining the cell’s current state, which is a result of a series of past inputs. In digital circuit theory, this operating mode is known as sequential logic. Nowadays, a wide variety of tasks can be performed by synthetically engineered genetic circuits, mostly constructed using combinational logic. Contrast to sequential logic, it's output is a function of the present input only. It is difficult to perform functions in a specific order, which has limited the widespread implementation of such systems. The ability of sequential logic circuits to store modest amounts of information within living systems and to act upon them would enable new approaches to the study and control of biological processes . A cell can be designed to do work that is more complex if it has more states. In other words, we can reach a new dimensionality in designing synthetic life – time.

What we did


This year, the Peking iGEM team is attempting to develop a frame of biological sequential circuits that are programmable. The envisioned circuit is capable of both storing states in DNA and automatically running a series of instructions in a specific order. More specifically, the sequential logic that consists of a clock , flip flop and control unit in bacteria. The clock is an oscillator with a repeated signal cycle that is utilized like a metronome to trigger actions of sequential logic circuits. Flip-flop is a memory device that can remember a state. Paired with a clock signal, it can realize state transition. The control unit is a functional part which can convert a signal from flip-flop into complex functions. With such a design, historical events are recorded and influence current cell behavior.

This work tries to point the way toward building large computational sys-tems from modular biological parts—basic sequential computing devices in living cells—and ultimately, programming complex biological functions. Computers have thus become "alive". A unicellular organism itself cannot pack much computational power, but considered as a modular building block, its potential is impressive.