Team:Melbourne/Overview

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Latest revision as of 14:16, 29 October 2008

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We want to build a biological clock that can count up when it is "ticked" by input light pulse signals. As the signal "ticks" the clock, the clock changes color and observer can use the color or combination of colors to tell what "time" it is.

There are two types of clocks proposed by our team.

The first type is a Binary Clock. In the Binary Clock, there are identical units (in fact not totally identical but almost) which are connected in series to make the entire clock. We call each unit a bit-unit. Each bit-unit can be turned on and off by its input signal and give its output as the input signal for the next bit in the series. So for example Bit1 can have 2 states ON or OFF, Bit1's output is the input for Bit2 to turn Bit2 ON and OFF. So with 2 bit-units, there are totally for states and these 4 states happen in a sequential order 00 -> 01 -> 02 -> 03, because Bit2's input is Bit1's output. If we extend to 3 bit-units, the number of possible states will grow exponentially to 8.

Each bit-unit is said to be modular because, apart from input receptor and output molecule, the internal machinery are identical.

We also proposed a Linear Clock. The linear model is similar to and simpler than the Binary model. The difference is that each bit-unit is turned ON only once and once it is turned OFF by the next bit-unit, it will stay OFF forever. So you can imagine this system as a string of light globes, the light jumps from one globe to the next and people can read the time by just looking at which globe is on. This model is also highly modular and the internal machinery is considerably less complex than the binary system.

The ultimate goal of these systems is to construct a biological production pipeline of which the systems can keep track on what stage it is and decide what reagents to release for the next step.

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+We want to build a biological clock that can count up when it is "ticked" by input light pulse signals. As the signal "ticks" the clock, the clock changes color and observer can use the '''color''' or '''combination of colors''' to tell what "time" it is.
+<br><br>
+There are two types of clocks proposed by our team.
+<br><br>
+The first type is a '''[https://static.igem.org/mediawiki/2008/5/5c/BinaryClock.pdf Binary Clock]'''. In the Binary Clock, there are identical units (in fact not totally identical but almost) which are connected in series to make the entire clock. We call each unit a '''bit-unit'''. Each bit-unit can be turned on and off by its input signal and give its output as the input signal for the next bit in the series. So for example Bit1 can have 2 states ON or OFF, Bit1's output is the input for Bit2 to turn Bit2 ON and OFF. So with 2 bit-units, there are totally for states and these 4 states happen in a sequential order 00 -> 01 -> 02 -> 03, because Bit2's input is Bit1's output. If we extend to 3 bit-units, the number of possible states will grow ''exponentially'' to 8.
-The [[IGEM:Melbourne/2008/BioClock/Binary counting|original binary idea]]. The ultimate goal of this idea is to construct a biological production line of which the system can keep track on what metabolites are present and what are being produced. The reason for favouring a binary model is that the multiplicity of the binary version is double than a linear one. However, through many attempts of constructing a biologically practical and feasible pathway for the binary version, it was realised that parts within each counting bit had to be unique, therefore posed a great limitation on the feasibility of the version. As thus, we turned our attention on developing a linear model of which the parts are interchangable with the binary model, so when a solution is found, we can resume the development of the binary model.
+Each bit-unit is said to be '''modular''' because, apart from input receptor and output molecule, the '''[[Team:Melbourne/BinModel | internal machinery]]''' are identical.
-This wiki details the development procedures of both the binary and linear models. It includes the designed pathways which integrate several team members' ideas; mathematical modellings and laboratory works that were done on developing the physical model of the bioclock.
+We also proposed a '''[[Team:Melbourne/LinModel | Linear Clock]]'''. The linear model is similar to and simpler than the Binary model. The difference is that each bit-unit is turned ON only once and once it is turned OFF by the next bit-unit, it will stay OFF forever. So you can imagine this system as a string of light globes, the light jumps from one globe to the next and people can read the time by just looking at which globe is on. This model is also '''[[Team:Melbourne/LinModel#Extension | highly modular]]''' and the internal machinery is considerably less complex than the binary system.
+The ultimate goal of these systems is to construct a biological production pipeline of which the systems can keep track on what stage it is and decide what reagents to release for the next step.
+<!-- Wiki site maintained by Di Wu>