Team:Peking/Notebook/ZZYin

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*Revise the PPT and the lecture nodes again and again.
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*Revise the PPT and the lecture notes again and again.
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Latest revision as of 02:15, 28 October 2010




   Zhenzhen Yin's Notes
                                                                                                                                                goto her page
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.

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

  • 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.