Talk:Tokyo Tech

how about arranging this page
like this? --[[User:Hiro|Hiroki]] 22:33, 16 October 2007 (EDT)

[[Image:homepage design.jpg]]


Previous homepage design--[[User:Hiro|Hiroki]] 12:25, 17 October 2007 (EDT)
[[Image:tokyo_alliance_header.JPG]]


{| cellspacing="5"


|width="300px" valign="top" | 
<h1> Project</h1>

'''Concept'''
* [[Tokyo/Concept |Concept]]
* [[Tokyo/Model |Model ]]
* [[Tokyo/Genetic Cricuit |Genetic Cricuit]]
* [[Tokyo/Brainstorming|Brainstorming]]
* [[Tokyo/Schedule|Schedule]]
* [[Tokyo/Reference|Reference]]

|width="300px" valign="top" |

<h1>Works</h1>

'''Parts'''
* [[Tokyo/Plasmids |Plasmids ]]
* [[Tokyo/A_side |A_side ]]
* [[Tokyo/B_side |B_side ]]
* [[Tokyo/New parts |New parts ]]

''' Wet'''
* [[Tokyo/Construct |Construct ]]
* [[Tokyo/Experiments |Experiments ]]

''' Dry'''
* [[Tokyo/Modeling |Modeling ]]
* [[Tokyo/Analysis |Analysis ]]



|width="250px"  valign="top" | 
<h1>Information</h1>

'''Team'''
* [[Tokyo/About our team |About our team]]

'''Members'''
* [[Tokyo/Satoru Akama |Satoru Akama ]]
* [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki ]]
* [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]]
* [[Tokyo/Hajime Nakatani|Hajime Nakatani]]

'''Advisors''' 
* [[Tokyo/Syotarou Ayukawa |Syotarou Ayukawa ]]:Last year's member
* [[Tokyo/Akio Kobayashi|Akio Kobayashi]]:Last year's member

'''Instructors'''
* [http://www.sb.dis.titech.ac.jp/ Daisuke Kiga]
* [http://www.es.dis.titech.ac.jp/ Masayuki Yamamura]
* [http://nicosia.is.s.u-tokyo.ac.jp/~hagiya/ Masami Hagiya]
* [http://www.sb.dis.titech.ac.jp/ Masahiko Uchiyama]

'''Links'''
* [[Tokyo/Links|Links]]

[[Image:cycle.jpg]]
<br>
<br>
<br>
<!--[[Image:homepage1.JPG]]-->
[[Image:Title.JPG|700px]]
__NOTOC__
{| cellspacing="5"



|width="550px" valign="top" | 
<h1> ''' 1. [[Tokyo/Project |Abstruct]]''' </h1>
===[[Tokyo/Model|Concept & Model]]===
A bacterial society designed in this project follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.
<br>
To realize this model, the behaviors of the model '''- bistability of each individual and the system's stability under the coexsistence of the two types - '''have been confirmed ''in silico'' and ''in virto''.
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
<br>[[Image:our goal.JPG|350px]]

===[[Tokyo/Requirements |Requirements]]===
Bistability
<br>Coexistence by cell-cell communication.
 <!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->


|width="400px" valign="top" |

<h1>'''2. [[Tokyo/Works |Works]]'''</h1>
<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
<!--[[Image:homepage4.jpg]]-->

===2-a. [[Tokyo/Genetic circuit|Genetic circuits]] ===

===2-b. [[Tokyo/Approach |Combinational Wet & Dry Approaches]]===

===0. <span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
{| cellspacing="5"
|width="350px" valign="top" |

[[Tokyo/Hybrid promoter|The newly deviced hybrid promoter regulated by two inputs.]] 
<!--New part development:Hybrid promoterPBとして、2つの入力を受けるプロモータを開発する必要があった
<br>図　概念図、配列とグラフ図
-->
|width="150px" valign="top" |
[[Image:Hybridgraph.JPG|200px|]]
|}

===1. <span style="color:#0066ff;">Dry </span>:　 [[Tokyo/Formulation |Formulation]]===
<!--リプレッサーＡ，Ｂ，シグナル分子Ｓの時間変化を式として表し、安定性解析を行った結果、Hill係数が大切であることがわかった
<br>図　3つの式
-->

===2. <span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===

For the parameters of Hill coefficients by AHL and IPTG assays
 <!--新しいパーツであるハイブリッドプロモータに関して、大腸菌を用いた実験から、2つの入力それぞれに対するHill係数を求めた。
<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
-->
[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]

===3. <span style="color:#0066ff;">Dry </span>: 　[[Tokyo/Simulation |Simulation]]===

===4. <span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using ''E. coli''.

===5. Future works===

Continue this combinational approaches to sophisticate our model.
[[See more.]]


<!--
<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>

<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
<br>[[Tokyo/Bistability analisis|Bistability analysis]]
<br>[[Tokyo/Others |Others ]]
-->

<h1> '''3. About our team'''</h1>
<!--[[Image:team photo.jpg]] -->
'''Students'''
<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]

'''Advisors: Last year's member ''' 
<br>[[Tokyo/Shotaro Ayukawa |Shotaro Ayukawa ]] | [[Tokyo/Akio Kobayashi|Akio Kobayashi ]]

'''Instructors'''
<br>[http://www.sb.dis.titech.ac.jp/ Daisuke Kiga] | [http://www.es.dis.titech.ac.jp/ Masayuki Yamamura] | [http://nicosia.is.s.u-tokyo.ac.jp/~hagiya/ Masami Hagiya] | [http://www.sb.dis.titech.ac.jp/ Masahiko Uchiyama]

'''Links'''
[[Tokyo/sunaba |sunaba ]]

----
----
<!--[[Image:homepage1.JPG]]-->
[[Image:tokyotech3.JPG|700px]]
__NOTOC__
{| cellspacing="5"



|width="550px" valign="top" | 
<h1> ''' 1,Abstruct''' </h1>
===[[Tokyo/Model|Concept & Model]]===
====We made a bacterial society that follows Pareto's principle as an [[Tokyo/Concept|Ant society]] does.====
<br>[[Image:TOP.JPG|250px]]

===[[Tokyo/Requirements |Requirements]]===
====Our requirements to construct this model are two things, bistability and coexistence by cell-cell communication.====
 <!--<br>[[Image:Bistability.JPG|200px]][[Image:Coexistence.JPG|250px]]-->

===[[Tokyo/Genetic circuit|Genetic circuit]]===
====We designed the genetic circuit to satisfy its requirements and developed necessary [[Tokyo/new parts |new parts]]. ====
<br>[[Image:Tokyo_genetic circuit_s.jpg|100px]]

====　　　　　　　　　　　　　　　Our constructed parts are [[Tokyo/construction|Here]]!!! ====

===[[Tokyo/simulation|Our GOAL]]===
====We indicated [[Tokyo/simulation|our goal]] of the project by the simulation!! The simulation proved that our genetic circuit have existence of solution.====
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]
<br>[[Image:our goal.JPG|350px]]
|width="400px" valign="top" |

<h1>'''2,Works'''</h1>
<!--<h1> ''' [[Tokyo/Experiments |Experiments]]''' </h1>-->
<!--[[Image:homepage4.jpg]]-->

===[[Tokyo/Approach |Approach]]===
====Combination of Wet & Dry trials====
We have alternated/combined Wet and Dry experiments to achieve our goal

===0.<span style="color:#ff33cc;">Wet </span>:　[[Tokyo/Hybrid promoter|Hybrid promoter]]===
{| cellspacing="5"
|width="350px" valign="top" |

====We need to develop the promoter that can receive two input, AHL & reperssor. We tried to create and [[Tokyo/Hybrid promoter|succeeded]]!! ====
<!--New part development:Hybrid promoterPBとして、2つの入力を受けるプロモータを開発する必要があった
<br>図　概念図、配列とグラフ図
-->
|width="150px" valign="top" |
[[Image:Hybridgraph.JPG|200px|]]
|}

===1.<span style="color:#0066ff;">Dry </span>:　 [[Tokyo/Formulation |Formulation]]===
We wrote the Formulation
<!--リプレッサーＡ，Ｂ，シグナル分子Ｓの時間変化を式として表し、安定性解析を行った結果、Hill係数が大切であることがわかった
<br>図　3つの式
-->

===2.<span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===

====We decided the parameter of hill coefficients by the assay of AHL & IPTG====
 <!--新しいパーツであるハイブリッドプロモータに関して、大腸菌を用いた実験から、2つの入力それぞれに対するHill係数を求めた。
<br>図大腸菌の絵、FLAの絵、フィッティングのグラフ
-->
[[Image:hill AHL.JPG|190px]]|[[Image:hill IPTG.JPG|190px]]

===3.<span style="color:#0066ff;">Dry </span>: 　[[Tokyo/Simulation |Simulation]]===

wet実験で求められたパラメータを用いて、集団が怠け者の細胞のみとなった場合に、一度不安定化して、続いて働き者と怠け者になれることをStocastic Simulationで確認した。このシステムの挙動に必要な他のパラメータ範囲が判明した。
Based on stochastic simulation using parameters obtained from our wet experiments, we have confirmed that the whole system becomes unstable when there are only idlers left, and then, they become either of workers and idlers. Also we have determined other parameters necessary for the desired behavior of this system. 
 <!--最終日に動画と差し替え？？-->
<br>
<br>[[Image:Tokyo_simulation_s2.jpg|350px]]

===4.<span style="color:#ff33cc;">Wet </span>: 　[[Tokyo/Assay |Assay]]===
 <!--====We determined the feasibility test of this ====-->
Simulationを満たすための他のパラメータが現在のプラスミドで可能であるかを、大腸菌を用いた実験で確認した。
<br>
1. By the wet experiments using ''E. coli'', we testified whether our current plasmids could satisfy the other required conditions (for the desired behavior of the system) estimated by the simulation.
<br>
2. We tested whether our plasmids gave the other parameters to satisfy the simulation by the experiments using ''E. coli''.

===5.Future works===

Based on the results from the wet experiments in the step 4, the next dry approach - analysis and simulation - should be performed, which will in turn be testified and confirmed by wet experiments.
Continueing these processes, if time permits, would further sophisticate our model.


<!--
<h1> '''3,[[Tokyo/Achievements |Achievements ]]'''</h1>

<br>[[Tokyo/Hybrid promoter |Hybrid promoter ]]
<br>[[Tokyo/Bistability analisis|Bistability analysis]]
<br>[[Tokyo/Others |Others ]]
-->

<h1> '''3,[[Tokyo/About our team |About our team ]][[Image:TeamLogo.jpg]]'''</h1>
<!--[[Image:team photo.jpg]] -->


'''Students'''
<br>[[Tokyo/Satoru Akama |Satoru Akama ]] | [[Tokyo/Kenichiro Iwasaki |Kenichiro Iwasaki]] | [[Tokyo/Hiroki Kawahara |Hiroki Kawahara ]] | [[Tokyo/Hajime Nakatani|Hajime Nakatani]]

'''Advisors: Last year's member ''' 
<br>[[Tokyo/Shotaro Ayukawa |Shotaro Ayukawa ]] | [[Tokyo/Akio Kobayashi|Akio Kobayashi ]]

'''Instructors'''
<br>[http://www.sb.dis.titech.ac.jp/ Daisuke Kiga] | [http://www.es.dis.titech.ac.jp/ Masayuki Yamamura] | [http://nicosia.is.s.u-tokyo.ac.jp/~hagiya/ Masami Hagiya] | [http://www.sb.dis.titech.ac.jp/ Masahiko Uchiyama]

'''Links'''
[[Tokyo/sunaba |sunaba ]]
<br>[[Tokyo/sunaba2 |sunaba2 ]]4分割表紙バージョン
<br>[[Tokyo/alternative|alternative]]こんな表紙はいかが？
<br>[[Tokyo/alternative2|alternative2]]