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Team:Peking/Notebook/ZZYin
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| + | Using computional methods to search for proper topology whose input and output have a linear correlationship. Additionally They conduct modeling to explain and simulate the operation mechanism of MerR family TFs on their cognate promoters. | ||
| - | < | + | <html> |
| - | < | + | <img src="https://static.igem.org/mediawiki/2010/9/91/PKU_Adobe_Reader_Logo.jpg" width=20> |
| - | + | <a href="https://static.igem.org/mediawiki/2010/2/28/Notebook-zzy.pdf"><font color=#FFFFFF>download her notes</font></a> | |
| - | + | </html> | |
| - | + | =='''Contents'''== | |
| - | <a href="https:// | + | * <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#June| June, 2010]]</span> |
| - | < | + | |
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| - | + | ||
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| - | </ | + | |
| - | < | + | * <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#July| July, 2010]]</span> |
| - | + | ||
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| - | + | ||
| - | + | ||
| - | </ | + | * <span style="font-size:4mm;">[[Team:Peking/Notebook/JZZYin#August| August, 2010]]</span> |
| + | |||
| + | * <span style="font-size:4mm;">[[Team:Peking/Notebook/ZZYin#September| September, 2010]]</span> | ||
| + | |||
| + | * <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=== | ||
| + | *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 notes again and again. | ||
| + | |||
| + | ===10.25-10.27=== | ||
| + | |||
| + | *Upload wiki materials. | ||
| + | |||
| + | ===10.27-11.4=== | ||
| + | |||
| + | *Prepare for the presentation. | ||
| + | <html> | ||
</div> | </div> | ||
| + | |||
| + | |||
<div id="project description bottom"> | <div id="project description bottom"> | ||
Latest revision as of 02:15, 28 October 2010
NOTEBOOK HOME
CountDown
Vistors From...
Zhenzhen Yin's Notes
Using computional methods to search for proper topology whose input and output have a linear correlationship. Additionally They conduct modeling to explain and simulate the operation mechanism of MerR family TFs on their cognate promoters.
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
- 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 notes again and again.
10.25-10.27
- Upload wiki materials.
10.27-11.4
- Prepare for the presentation.
