Team:Peking/Notebook/ZZYin

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Using computional methods to search for proper topology whose input and output have an linear correlationship. Additionally They conduct modeling to explain and simulate the operation mechanism of MerR family TFs on their cognate promoters.
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<p><font color=#FFFFFF>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href="http://2010.igem.org/Team:Peking/Bioabsorbenthome"><font size=4><b><font color=#FFFFFF>----contents----</font></font></b></a>
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href="http://2010.igem.org/wiki/images/2/28/Notebook-zzy.pdf"><font color=#FFFFFF>download her notes</font></a>
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<font size=3><font color=#FFFFFF>*Personal Notes</font></font>
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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=='''Contents'''==
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<a href="http://2010.igem.org/Team:Peking/Protocols"><font size=3><font color=#FFFFFF>*Protocols</font></font></a>
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* <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#June| June, 2010]]</span>
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<font size=3><font color=#FFFFFF>*Others</font></font>
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* <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#July| July, 2010]]</span>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<a href=""><font size=5><b><font color=#74DF00>SUBTITLE</font></font></b></a>
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* <span style="font-size:4mm;">[[Team:Peking/Notebook/JZZYin#August| August, 2010]]</span>
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* <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#September| September, 2010]]</span>
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* <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#October| October, 2010]]</span>
 +
 
 +
==June==
 +
 
 +
===6.19-6.22===
 +
 
 +
Paper reading, learning about Stochastic Models and network types such as bifan networks
 +
 
 +
==July==
 +
 
 +
===7.5-7.7===
 +
 
 +
Paper Reading: Negative feedback that improves information transmission in yeast signaling &one master thesis of Long Yan, Peking University.
 +
 
 +
Learn about wiki language.
 +
 
 +
===7.9-7.11===
 +
 
 +
*Construct the wiki website.
 +
 
 +
===7.12===
 +
 
 +
*Meet with Qi Ouyang and Xiaomeng Zhang
 +
 
 +
Discuss about Reverse Engineering Method and decide to adopt it for designing our project.
 +
 
 +
Decide to search for input-output linear function for making up the shortages of current biosensors.
 +
 
 +
*Discuss with Yuheng Lu and Haoqian Zhang
 +
 
 +
Decide to use the tri-node network and the essence of each TF Node is still to be discussed.
 +
 
 +
===7.13===
 +
===7.14===
 +
*Discuss with Yuheng Lu
 +
 
 +
Decide to use TF as the essence of each TF node.
 +
 
 +
Start to derive the ODEs.
 +
 
 +
Try to search for the right form of equations to describe the combinational regulation of TFs.
 +
 
 +
Paper reading: On schemes of combinatorial transcription logic
 +
 
 +
Try to find the answer to the problem discussed today.
 +
 
 +
===7.14-7.19===
 +
 
 +
*Continue paper reading and search for some other materials and papers about combinational regulation.
 +
 
 +
===7.20-7.24===
 +
 
 +
*Derive the ODEs to describe the tri-node network.
 +
 
 +
===7.25-7.30===
 +
 
 +
*Fix the LINUX system on my laptop and start to familiar with coding under LINUX, study about vim operator, gcc and gdb.
 +
 
 +
===7.31===
 +
 
 +
*Meet with Xiaomeng Zhang
 +
 
 +
Discuss the equations derived to see whether it can describe our network precisely.
 +
 
 +
Discuss how to derive the equations describing the binding of Hg to MerR dimer.
 +
 
 +
Discuss whether the hypotheses of our equations fit for the real condition.
 +
 
 +
Discuss with Yuheng Lu
 +
 
 +
Develop our equations and discuss about the paper.
 +
 
 +
Find out that the calculation may be too much for our computer that has 16 CPUs in the laboratory so decide to take a more simple form to only consider the combinational regulation instead of also considering the interactions between TFs and RNAP.
 +
 
 +
==August==
 +
 
 +
===8.1===
 +
 
 +
*Derive one set of equations and discuss with Yuheng Lu to revise the equation.
 +
 
 +
===8.2===
 +
 
 +
*After derivation, get the ODEs meet all of our requirements, and so the equations are obtained.
 +
 
 +
*Examine again the ODEs to see whether there’s any problem with them.
 +
 
 +
===8.3===
 +
 
 +
*Meet with Xiaomeng Zhang
 +
 
 +
Examine again our ODEs
 +
 
 +
Start to code the object function and read the makefile codes.
 +
 
 +
===8.4-8.9===
 +
 
 +
*Code the object function and other related function codes.
 +
 
 +
===8.10-8.15===
 +
 
 +
Put the codes together with Yuheng Lu’s.
 +
 
 +
Examine the codes.
 +
 
 +
===8.16===
 +
===8.17===
 +
*Meet with Xiaomeng Zhang
 +
 
 +
Examine our codes.
 +
 
 +
Discuss running the program on laboratory’s computer in details.
 +
 
 +
===8.17-8.19===
 +
 
 +
Examine the codes again and again with gdb because there’re some bugs when running on the computer.
 +
 
 +
===8.21===
 +
 
 +
Try to run the program and find some bugs still present.
 +
 
 +
Revise and examine the codes.
 +
 
 +
===8.22===
 +
 
 +
Run again and examine a small part of the results, find them fit the expectation.
 +
 
 +
===8.23-8.25===
 +
 
 +
Wait for the program running on the computer.
 +
 
 +
===8.26-9.3===
 +
 
 +
Get our results and start to analyze it with Matlab and Excel and SPSS.
 +
 
 +
==September==
 +
 
 +
===9.4===
 +
===9.5===
 +
*Meet with Qi Ouyang
 +
 
 +
Get the guidance to revise our object function for significance in field use
 +
 
 +
Revise the object function and run again the program on computer.
 +
 
 +
===9.5-9.7===
 +
 
 +
Wait for the program running on the computer.
 +
 
 +
===9.8-9.12===
 +
 
 +
Get the results and analyze them.
 +
 
 +
===9.19-9.21===
 +
 
 +
Write wiki modeling part.
 +
 
 +
===9.22===
 +
 
 +
*Meet with Qi Ouyang
 +
 
 +
Get some advice about how to revise the wiki modeling part.
 +
 
 +
==October==
 +
 
 +
===9.26-10.10===
 +
 
 +
Revise wiki and draw the figures with Matlab and origin and PowerPoint that used in wiki.
 +
 
 +
Further analyze the second results.
 +
 
 +
===10.14===
 +
 
 +
Work on some drawings need in the biosensor wiki part.
 +
 
 +
===10.16===
 +
 
 +
Work on the Modelling Part Presentation’s PPT
 +
 
 +
===10.17===
 +
 
 +
Meet with members and Discuss about the PPT.
 +
 
 +
===10.18-10.19===
 +
 
 +
Prepare and present the PPT for the first time.
 +
 
 +
===10.20-10.24===
 +
 
 +
Revise the PPT and the lecture nodes again and again.
 +
 
 +
 
 +
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<div id="project description bottom">
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Revision as of 12:29, 26 October 2010




   Zhenzhen Yin's Notes
                                                                                                                                                goto her page
Using computional methods to search for proper topology whose input and output have an linear correlationship. Additionally They conduct modeling to explain and simulate the operation mechanism of MerR family TFs on their cognate promoters.

download her notes

Contents

June

6.19-6.22

Paper reading, learning about Stochastic Models and network types such as bifan networks

July

7.5-7.7

Paper Reading: Negative feedback that improves information transmission in yeast signaling &one master thesis of Long Yan, Peking University.

Learn about wiki language.

7.9-7.11

  • Construct the wiki website.

7.12

  • Meet with Qi Ouyang and Xiaomeng Zhang

Discuss about Reverse Engineering Method and decide to adopt it for designing our project.

Decide to search for input-output linear function for making up the shortages of current biosensors.

  • Discuss with Yuheng Lu and Haoqian Zhang

Decide to use the tri-node network and the essence of each TF Node is still to be discussed.

7.13

7.14

  • Discuss with Yuheng Lu

Decide to use TF as the essence of each TF node.

Start to derive the ODEs.

Try to search for the right form of equations to describe the combinational regulation of TFs.

Paper reading: On schemes of combinatorial transcription logic

Try to find the answer to the problem discussed today.

7.14-7.19

  • Continue paper reading and search for some other materials and papers about combinational regulation.

7.20-7.24

  • Derive the ODEs to describe the tri-node network.

7.25-7.30

  • Fix the LINUX system on my laptop and start to familiar with coding under LINUX, study about vim operator, gcc and gdb.

7.31

  • Meet with Xiaomeng Zhang

Discuss the equations derived to see whether it can describe our network precisely.

Discuss how to derive the equations describing the binding of Hg to MerR dimer.

Discuss whether the hypotheses of our equations fit for the real condition.

Discuss with Yuheng Lu

Develop our equations and discuss about the paper.

Find out that the calculation may be too much for our computer that has 16 CPUs in the laboratory so decide to take a more simple form to only consider the combinational regulation instead of also considering the interactions between TFs and RNAP.

August

8.1

  • Derive one set of equations and discuss with Yuheng Lu to revise the equation.

8.2

  • After derivation, get the ODEs meet all of our requirements, and so the equations are obtained.
  • Examine again the ODEs to see whether there’s any problem with them.

8.3

  • Meet with Xiaomeng Zhang

Examine again our ODEs

Start to code the object function and read the makefile codes.

8.4-8.9

  • Code the object function and other related function codes.

8.10-8.15

Put the codes together with Yuheng Lu’s.

Examine the codes.

8.16

8.17

  • Meet with Xiaomeng Zhang

Examine our codes.

Discuss running the program on laboratory’s computer in details.

8.17-8.19

Examine the codes again and again with gdb because there’re some bugs when running on the computer.

8.21

Try to run the program and find some bugs still present.

Revise and examine the codes.

8.22

Run again and examine a small part of the results, find them fit the expectation.

8.23-8.25

Wait for the program running on the computer.

8.26-9.3

Get our results and start to analyze it with Matlab and Excel and SPSS.

September

9.4

9.5

  • Meet with Qi Ouyang

Get the guidance to revise our object function for significance in field use

Revise the object function and run again the program on computer.

9.5-9.7

Wait for the program running on the computer.

9.8-9.12

Get the results and analyze them.

9.19-9.21

Write wiki modeling part.

9.22

  • Meet with Qi Ouyang

Get some advice about how to revise the wiki modeling part.

October

9.26-10.10

Revise wiki and draw the figures with Matlab and origin and PowerPoint that used in wiki.

Further analyze the second results.

10.14

Work on some drawings need in the biosensor wiki part.

10.16

Work on the Modelling Part Presentation’s PPT

10.17

Meet with members and Discuss about the PPT.

10.18-10.19

Prepare and present the PPT for the first time.

10.20-10.24

Revise the PPT and the lecture nodes again and again.