Week 4 Individual Journal William P Fuchs: Difference between revisions

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==Notes==
The crash deleted some sections i.e. the scientific conclution
==Activity 2 (Parts 1 and 2)==
==Activity 2 (Parts 1 and 2)==


Line 6: Line 9:


===Methods===
===Methods===
#Upload the two files provided by the [[BIOL368/F16:Week 4|Assignment for Week 4]]page into the ''Biology Workbench'' tool. The complete file is too large so two files were created to accommodate the processing ability of ''Biology Workbench''. The clone amount for each subject was the amount of clones discovered at visit 1.
#To begin, create a multiple sequence alignment of 3 clones each for 4 subjects. Generate an unrooted tree for these values. Record which subjects and their respective clones in a table (see table 1 for reference).
#


===Data and Files===
===Data and Files===
[[Image:26237.CLUSTALW.1.gif|frame|center|CLUSTALW Multiple Sequence Alignment of Subjects 1,7,8,and 13]]
[[Image:Matrix 2 Values9262016.png|left]]
 
[[Image:26237.CLUSTALW.1.gif|frame|right|Part 1 CLUSTALW Multiple Sequence Alignment of Subjects 1,7,8,and 13]]
 
 
[[Image:Matrix Values9262016.png|center]]
 
====Data/Files References====
====Data/Files References====


[http://seqtool.sdsc.edu/CGI/BW.cgi#!|Biology Workbench ClustalW Tool]
[http://seqtool.sdsc.edu/CGI/BW.cgi#!|Biology Workbench ClustalW Tool and ClustalDist]


===Results===
===Results===
Line 21: Line 33:
==Defining the Research Project==
==Defining the Research Project==


===Question===
===Research Question===


Would a revaluation of the Markham et al. data points in the form of a correlation yield a stronger inclination of significance?
Would a revaluation of the Markham et al. data points in the form of a correlation yield a stronger inclination of significance in respect to diversity?


===Prediction===
===Prediction===
 
*If the targeted evaluation of the subjects with the larger amount data points is selected stronger comparison and statistical value will increase in respect to diversity.
===Subjects===
===Subjects===
*6,8,9,14
===Visits===
*Every available visit for the subjects in question
===Clones===
*64


====Reasoning for Selected Parameters====
* These constituents were selected because of the scale of our project. By selecting many clones will provide stronger grounds for statistical analysis as well as cover a larger scope experimentally.


===Visits===
==Acknowledgements==
I worked with [[User:Colin Wikholm|Colin Wikholm]] on this week's assignment and we collaborated in coming up with our project idea in class as well as cooperation with the group: [[User:Mia Huddleston|Mia Huddleston]] and [[User:Anindita Varshneya|Anindita Varshneya]] for a joint project regarding HIV. Also I had a 1 minute phone call with [[User: Matthew K. Oki|Matt Oki]] and asked some questions regarding table format.


While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source[[User:William P Fuchs|William P Fuchs]] 19:35, 26 September 2016 (EDT)


===Clones===
==References==
Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. [[http://www.pnas.org/content/95/21/12568.full.pdf|See PDF]].


SDSC Biology Workbench see link: [http://workbench.sdsc.edu/ here]
for ClustalW work and ClustDist tool.


------------
[[BIOL368/F16:Week 4|Assignment for Week 4]]:
Rubric/instructions for this assignment.


==Acknowledgements==
==References==


-----------------
{{Template:William P Fuchs}}
{{Template:William P Fuchs}}

Latest revision as of 13:12, 4 October 2016

Notes

The crash deleted some sections i.e. the scientific conclution

Activity 2 (Parts 1 and 2)

Purpose

To initiate an investigation on the 15 subjects's strains of HIV to see if they are derived from a common source in respect to diversity.

Methods

  1. Upload the two files provided by the Assignment for Week 4page into the Biology Workbench tool. The complete file is too large so two files were created to accommodate the processing ability of Biology Workbench. The clone amount for each subject was the amount of clones discovered at visit 1.
  2. To begin, create a multiple sequence alignment of 3 clones each for 4 subjects. Generate an unrooted tree for these values. Record which subjects and their respective clones in a table (see table 1 for reference).

Data and Files

Part 1 CLUSTALW Multiple Sequence Alignment of Subjects 1,7,8,and 13


Data/Files References

Workbench ClustalW Tool and ClustalDist

Results

Scientific Conclusion

Defining the Research Project

Research Question

Would a revaluation of the Markham et al. data points in the form of a correlation yield a stronger inclination of significance in respect to diversity?

Prediction

  • If the targeted evaluation of the subjects with the larger amount data points is selected stronger comparison and statistical value will increase in respect to diversity.

Subjects

  • 6,8,9,14

Visits

  • Every available visit for the subjects in question

Clones

  • 64

Reasoning for Selected Parameters

  • These constituents were selected because of the scale of our project. By selecting many clones will provide stronger grounds for statistical analysis as well as cover a larger scope experimentally.

Acknowledgements

I worked with Colin Wikholm on this week's assignment and we collaborated in coming up with our project idea in class as well as cooperation with the group: Mia Huddleston and Anindita Varshneya for a joint project regarding HIV. Also I had a 1 minute phone call with Matt Oki and asked some questions regarding table format.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another sourceWilliam P Fuchs 19:35, 26 September 2016 (EDT)

References

Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. [PDF].

SDSC Biology Workbench see link: here for ClustalW work and ClustDist tool.

Assignment for Week 4: Rubric/instructions for this assignment.


Individual Journals

Class Journals

Assignments

Useful Links

  1. Bio Class Page
  2. BIOL368/F16:People
  3. Will Fuchs
  4. Link to LMU: http://www.lmu.edu/
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