User:Di Wu: Difference between revisions

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Di Wu. I graduated with an Honours degree in Comp Sci at Monash University, right now doing a second degree in Cell Biology major at Melbourne. I hope you will enjoy our [http://openwetware.org/wiki/IGEM:Melbourne/2008 iGEM project]!
Di Wu. I graduated with an Honours degree in Comp Sci at Monash University, right now doing a second degree in Cell Biology major at Melbourne. I hope you will enjoy our [http://openwetware.org/wiki/IGEM:Melbourne/2008 iGEM project]!
== Education ==
*Columbia University (M.S. in Computational Biology, Sep 2009 - Dec 2010)
*Melbourne University (B.S.)
*Columbia University (Stopped in the middle of M.S. Comp. Sci. because I really like biomedical sciences)
*Monash University (B.Comp.Sci Hon)


== Current Work ==
== Current Work ==
Line 28: Line 34:
Hi Friends,
Hi Friends,


This is Di, I know we are at the stage of brainstorming. I just thought about a feasible way of implementation on "bacteria counter", just to put it here in case I forgot, not intending to confuse or distract anyone. If not feeling like to read it now, you can always come back later. The "bacteria counter" not only can be used for "biological clock" but also could be used for related topics which we might come up later. Just as a proposed idea.
I know we are at the stage of brainstorming. I just thought about a feasible way of implementating a "bacteria counter", just to put it here in case I forgot, not intending to confuse or distract anyone. If not feeling like to read it now, just skip it or come back later. The "bacteria counter" not only can be used for "biological clock" but also could be used for related topics which we might come up later. Just as a proposed idea.


We could use the strategy of '''binary counting''' in biological systems. Before I start, I shall give a very brief idea (and that's all we need to know) on binary counting (I'm sure some people already knew this):
We could use the strategy of '''binary counting''' in biological counting systems. Before I start, I shall give a very brief idea (and that's all we need to know) on binary counting (I'm sure some people already knew this via mathematics, computer science, physics, engineering etc):




Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,
Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,


if we want to represent number 3 in binary numbers (bits), 3 = 1*<math>Insert formula here</math>2 + 1*1 = 1*2^1 + 1*2^0 = 11 (base 2)
if we want to represent number 3 in binary numbers (bits), <math>3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2) </math>


to represent number 4 in binary, 4 = 1*2^2 + 0*2^1 + 0*2^0 = 100 (base 2)
to represent number 4 in binary, <math>4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2)</math>


to represent number 5 in binary, 5 = 1*4 + 0*2^1 + 1*1 = 1*2^2 + 1*2^0 = 101 (base 2)
to represent number 5 in binary, <math>5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2)</math>


Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,
Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,


1011011 =
 
1*2^6 + 0*2^5 + 1*2^4 + 1*2^3 + 0*2^2 + 1*2^1 + 1*2^0  
{|
= 64 + 0 + 16 + 8 + 0 + 2 + 1 = 91
|-
!<math>2^6</math>
!<math>2^5</math>
!<math>2^4</math>
!<math>2^3</math>
!<math>2^2</math>
!<math>2^1</math>
!<math>2^0</math>
|-
|1
|0
|1
|1
|0
|1
|1
|} = <math>1\times2^6 + 0\times2^5 + 1\times2^4 + 1\times2^3 + 0\times2^2 + 1\times2^1 + 1\times2^0  
= 64 + 0 + 16 + 8 + 0 + 2 + 1 = 91~(base~10)</math>
   
   
 
===Implementing Binary expression on "bacteria counter"===
Ok, so how can we implement this in bacteria systems? Say we have 3 bacteria: B2 B1 B0, each with its own characteristic colour (or other traits) when its expression is turned on, e.g. B2=red
Ok, so how can we implement this in bacteria systems? Say we have 3 bacteria: B2 B1 B0, each with its own characteristic colour (or other traits) when its expression is turned on, e.g. B2=<font color = "red">red</font>
B1=green, B0=blue. Also, each B(n) needs the expression outcome of B(n-1) plus some another toggle control to express its own gene. Then we can read off the current number just by
B1=<font color = "green">green</font>, B0=<font color = "blue">blue</font>. Also, each B(n) needs the expression outcome only from B(n-1) plus a toggle control to express its own gene. Then we can read off the current number just by
reading the color combinations (or other characteristic traits). For example,
reading the color combinations (or other characteristic traits). For example,
{|
|-
!B2
!B1
!B0
!Binary
!Decimal(time)
|-
|clear 
|clear 
|clear 
|000
|0
|-
|clear
|clear
|<font color = "blue">blue</font>
|001
|1
|-
|clear
|<font color="green">green</font>
|clear
|010
|2
|-
|clear
|<font color="green">green</font>
| <font color="blue">blue</font>
|011
|3
|-
|<font color="red">red</font>
|clear
|clear
|100
|'''4'''
|-
|<font color="red">red</font>
|clear
|<font color="blue">blue</font>
|101
|5
|-
|<font color="red">red</font>
|<font color="green">green</font>
|clear
|110
|6
|-
|<font color="red">red</font>
|<font color="green">green</font>
|<font color="blue">blue</font>
|111
|'''7'''
|}


B2      B1      B0        Binary  Decimal
So for instance if our colour combination is <font color="red">red</font>, <font color="green">green</font>, <font color="blue">blue</font>, then we know our current time is '''7''', if colour combination is just <font color="red">red</font>, we know it's time '''4'''. Every expression of B(n) depends only on input from B(n-1) plus another toggle control. So the only bacteria determining counting speed is B0 (just like in a stop watch where the counting speed is entirely dependent on the last digit). Maybe we can race the real clock by adjusting the expression rates!
clear  clear  clear    0 0 0  0
clear  clear  blue      0 0 1  1
clear  green   clear    0 1 0  2
clear  green   blue     0 1 1  3
red    clear  clear    1 0 0  4
red    clear  blue     1 0 1  5
red     green  clear    1 1 0  6
red     green  blue      1 1 1  7


We can have as many bacteria as we want, thus as many combinations (numbers) as we want. We could just control the expression rate of B0 to control how fast our counter counts up,
As we know ALU (Arithmetic Logical Unit) is also based on binary number operation. This idea could be extended to be implemented on binary addition, substitution, multiplication.
and maybe we can race the real clock!


This is just 1 of the topics we've thought, I'd love to listen to other topics from your brillian "brainstormers"!
This is just 1 out of the many thoughts we've put. We have the whole bucket of great ideas from other brilliant brainstormers!

Latest revision as of 19:03, 3 June 2010

Di Wu (an artistic interpretation)

About Me

Di Wu. I graduated with an Honours degree in Comp Sci at Monash University, right now doing a second degree in Cell Biology major at Melbourne. I hope you will enjoy our iGEM project!

Education

  • Columbia University (M.S. in Computational Biology, Sep 2009 - Dec 2010)
  • Melbourne University (B.S.)
  • Columbia University (Stopped in the middle of M.S. Comp. Sci. because I really like biomedical sciences)
  • Monash University (B.Comp.Sci Hon)

Current Work

I'm currently working at the St. Vincent's Institute of Medical Research as a UROP student. My focus is on Cancer Structural Biology, under the supervision of Professor Michael Parker. The main idea is to use crystallography to analyse structures of cancer causing/related proteins and find ways to inhibit them.

Oh, and I can't just walk away without telling you about my other interests, which is on insects! I'll put some photos and vidoes clips of my favourate insect pets. I bet you'll enjoy them.

Reserch Interests

  • Cancer, Cancer Stem Cell, cell cycle, signalling regulation
  • Biomedical informatics

Contact

ever_wudi@yahoo.com, diw@student.unimelb.edu.au


A Feasible implementation of Bacteria Counter

Hi Friends,

I know we are at the stage of brainstorming. I just thought about a feasible way of implementating a "bacteria counter", just to put it here in case I forgot, not intending to confuse or distract anyone. If not feeling like to read it now, just skip it or come back later. The "bacteria counter" not only can be used for "biological clock" but also could be used for related topics which we might come up later. Just as a proposed idea.

We could use the strategy of binary counting in biological counting systems. Before I start, I shall give a very brief idea (and that's all we need to know) on binary counting (I'm sure some people already knew this via mathematics, computer science, physics, engineering etc):


Binary counting (based on 2) is done in the same a way as decimal counting (based on 10, as we do everyday). For example,

if we want to represent number 3 in binary numbers (bits), [math]\displaystyle{ 3 = 1\times 2 + 1\times 1 = 1\times 2^1 + 1\times2^0 = 11~(base ~2) }[/math]

to represent number 4 in binary, [math]\displaystyle{ 4 = 1\times2^2 + 0\times2^1 + 0\times2^0 = 100~(base ~2) }[/math]

to represent number 5 in binary, [math]\displaystyle{ 5 = 1\times4 + 0\times2^1 + 1\times1 = 1\times2^2 + 1\times2^0 = 101~(base~ 2) }[/math]

Binary numbers can represent arbitarily large numbers just as digital numbers, e.g. if we have a binary number 1011011,


[math]\displaystyle{ 2^6 }[/math] [math]\displaystyle{ 2^5 }[/math] [math]\displaystyle{ 2^4 }[/math] [math]\displaystyle{ 2^3 }[/math] [math]\displaystyle{ 2^2 }[/math] [math]\displaystyle{ 2^1 }[/math] [math]\displaystyle{ 2^0 }[/math]
1 0 1 1 0 1 1

= [math]\displaystyle{ 1\times2^6 + 0\times2^5 + 1\times2^4 + 1\times2^3 + 0\times2^2 + 1\times2^1 + 1\times2^0 = 64 + 0 + 16 + 8 + 0 + 2 + 1 = 91~(base~10) }[/math]

Implementing Binary expression on "bacteria counter"

Ok, so how can we implement this in bacteria systems? Say we have 3 bacteria: B2 B1 B0, each with its own characteristic colour (or other traits) when its expression is turned on, e.g. B2=red B1=green, B0=blue. Also, each B(n) needs the expression outcome only from B(n-1) plus a toggle control to express its own gene. Then we can read off the current number just by reading the color combinations (or other characteristic traits). For example,

B2 B1 B0 Binary Decimal(time)
clear clear clear 000 0
clear clear blue 001 1
clear green clear 010 2
clear green blue 011 3
red clear clear 100 4
red clear blue 101 5
red green clear 110 6
red green blue 111 7

So for instance if our colour combination is red, green, blue, then we know our current time is 7, if colour combination is just red, we know it's time 4. Every expression of B(n) depends only on input from B(n-1) plus another toggle control. So the only bacteria determining counting speed is B0 (just like in a stop watch where the counting speed is entirely dependent on the last digit). Maybe we can race the real clock by adjusting the expression rates!

As we know ALU (Arithmetic Logical Unit) is also based on binary number operation. This idea could be extended to be implemented on binary addition, substitution, multiplication.

This is just 1 out of the many thoughts we've put. We have the whole bucket of great ideas from other brilliant brainstormers!

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