User talk:Salman Ahmad

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Current revision (13:36, 18 April 2013) (view source)
(Week 12 Feedback: gave feedback on shared journal)
 
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== Week 12 Feedback ==
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* Thank you for submitting your assignment on time.
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* You included screenshots from your STEM results of profiles that were not significant.  Only the profiles that showed up in color in the first results screen were significant and should be considered.
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* You did not explicitly state which profile you chose, although it appears to be #23.
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* In answer to the question how many GO terms had a p value of < 0.05, you said 533, but it is really 116.  In answer to how many GO terms had a corrected p value of 0.05, you answered 116, but it is really 44.
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* The RegulationMatrix file that you uploaded had the wrong file extension, ".ppt" instead of ".xls".
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* In your narrative, you mention that you only want to add the transcription factors RAP1 and STE12, but in your file, SOK2, MSN2, and YAP5 are there as well.  Did you mean to add them?
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* In your discussion of the interpretation of the GO terms, you need to be specific about why the cell is up-/down-regulating these specific GO terms in response to cold.
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* Remember, you need to link back to the original assignment page from every individual journal page.
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''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 13:01, 18 April 2013 (EDT)''
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=== Week 12 Shared Journal Feedback ===
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* The STEM profiles were listed in order of significance.  The ones with the ''lowest'' p value were listed first.  The profiles that showed up in color were all significant, and the white ones were not.  The p value depends on the ratio of the number of genes in the profile versus the number of genes that would be expected in that profile due to chance.
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* For question 4 of the shared journal reflection, be careful in the way you state your answer. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes.
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''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 13:36, 18 April 2013 (EDT)''
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== Week 9 Spreadsheet Feedback ==
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* I've reviewed the spreadsheet you submitted for your week 9 assignment.  It all looks correct, except for the following:
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** On the "statistics" worksheet, you made a mistake on the formula for the Average Log Fold Change for t15.  The cell reference in the formula does not include all of the replicates for t15.  This will need to be fixed before doing the Week 12 assignment.
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** In formatting your "final" worksheet, you had four decimal places for the fold changes, not the two decimal places requested in the protocol.
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''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 01:35, 9 April 2013 (EDT)''
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== Week 1 Journal Feedback ==
== Week 1 Journal Feedback ==
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* Thank you for submitting your assignment on time.
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* There are a few of things that you need to fix on your individual user page and shared journal page.  Please make these changes by next week's journal deadline (midnight, February 8) to earn back the points you missed on this assignment.
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*# You need to put the complete street address for your box at LMU.
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*# On the Week 1 shared journal page, put the link to your user page underneath the header for your section.
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*# In addition to posting a question on Dr. Fitzpatrick's talk page, you need to post a question on [[User_talk:Kam D. Dahlquist | my talk page]].
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*# You have not filled out the summary field when you save changes to your pages.  You need to fill it out ''every time'' you make a change.
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*# You need to demonstrate that you can "comment out" something.  Your comment was just what was put there by the OpenWetWare script.
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*# Your link to a file needs a label.  What you did works, but it would be better to use the complete wiki syntax.  I.e., use <nowiki>[[Media:AhmadResume.doc | my resume]]</nowiki>, which looks like this:  [[Media:AhmadResume.doc | my resume]], instead of just [[Media:AhmadResume.doc]].
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*# While you have created a template, you have not actually ''invoked'' it on your page.  To invoke your template, use the wiki syntax <nowiki>{{Salman Ahmad}}</nowiki> on your page.  Furthermore, you need to use your template to your advantage.  It should contain links for each of the class assignment pages, your journal pages, and the class shared journal pages.  It is also helpful to put the class category on it as well.  Currently, the category is currently missing from your user page.  If you put it in your template and then invoke the template, you will never forget to put it in your journal page.
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* Please feel free to delete the message from OpenWetWare below.
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&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 02:20, 31 January 2013 (EST)
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Hello, Salman Ahmad! This is a welcome message from OpenWetWare. By the way, we've announced you on the [[Main Page|home page]]! You can leave messages to any OWW member by editing their User_talk pages like this one.  And don't forget to personalize your [[User:Salman Ahmad|User Page]] so that we can get to know you better!  We've included some tips below to get you started.
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You asked: "Hello Dr. Fitzpatrick: Students are learning higher levels of math earlier in their lives than before, how do you think that will affect the applications of math in the future? Salman Ahmad 21:23, 22 January 2013 (EST)"
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== Basic Wiki Instructions ==
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My answer:  That's a really good question.  I don't think universities in general (or LMU in particular) have caught up educational programs to the way students are being taught pre-collegeCollege calculus classes (depending on the professor) can be very different from high school ones, tho. I'd hope that it will help "across the board" with people being able to approach a lot of things more quantitativelySo many applications today involve large data sets in which the data points have many attributes (we often call this high dimensional data)I think the need may drive the math, rather than the other way around. We may see the type of math taught changing from calculus based stuff to linear algebra (vectors and matrices), statistical, and computational.
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*'''Don't be afraid to edit!'''  As with all pages on the wiki, all versions are saved so its easy to undoIf you have any questions feel free to [[Special:Contact|send us an email]].
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# Start off by clicking the 'edit' button to the right of this section, or at the top of the page.
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# Now you should see the text of this section as text within an editor boxThere are several buttons in the editor box, but don't worry about those for nowJust type something in the box, scroll down to the bottom, and hit the 'Preview' button.
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# You should see the web-page and text box views, but now with your edits!  Don't forget to save your changes by clicking 'Save Page'!
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# Editing pages is as easy as that.  There are of course many ways to format your text.  The easiest way to learn is to find an OWW page with the formatting you like, click on the edit button again, and see for yourself how it was created in the text box.  Here's an extensive list of [http://en.wikipedia.org/wiki/Wikipedia:Tutorial_%28Formatting%29 formating examples]. '''Or look at this OpenWetWare [[OpenWetWare:Welcome|introductory tutorial]]'''. 
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# When you are done, remove these instructions by clicking the edit button for this section again, erase everything you see in the text box and click 'Save Page'. (And remember you can always retrieve these by clicking on the 'history' tab at the top of this page.)
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Note that these instructions apply to ''any'' page on OWW. Feel free to contribute to OWW by editing pages to add content, update them, or even correct mistakes. OWW relies on an active community to manage our growing resource of open access information, and we need your help!
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'''[[User:Ben G. Fitzpatrick|Ben G. Fitzpatrick]] 14:00, 3 February 2013 (EST)'''
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== Personal/Lab Info ==  
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== Week 2 Journal Feedback ==
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We have gone ahead and filled in some information you provided us in your membership application on your [[User:Salman Ahmad|User Page]].  Please take a moment to embellish this and tell the community a little more about you.  Put links to your lab pages, your projects and your interests.  If you run out of ideas, take a look at some of the other User pages.  For example, check out [[User:Julius_B._Lucks]], [[User:Jason_R._Kelly]] and [[User:Reshma_P._Shetty]]. 
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You'll also notice that we have put an 'image' placeholder at the top of your [[User:Salman Ahmad|User Page]]We encourage you to upload an image of yourself to give OWW a more personal feel.  To upload an image, click on the [[Special:Upload|Upload file]] link on the left-hand side (toolbar)Choose a file from your computer, and remember the file nameAfter you have uploaded the image, you should see it loaded on its own page. Go back to your [[User:Salman Ahmad|User Page]], click on edit, and replace 'OWWEmblem.png' with the name of your file that you have uploaded in the second line of this page.
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* Thanks for submitting your work on time.
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* Your discussion is a bit thinYou need to include a little more detail on the simulations you performed.
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* Graphs would be very helpful in backing up your discussionSee Elizabeth's page for a good example of a file containing some well-annotated simulations, or Ashley's for graphs embedded in the discussionPaul's screencaps, while a bit difficult to view due to size, may also help you.
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* How might you model waste with the differential equations?
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'''[[User:Ben G. Fitzpatrick|Ben G. Fitzpatrick]] 14:00, 4 February 2013 (EST)'''
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Current revision

Contents

Week 12 Feedback

  • Thank you for submitting your assignment on time.
  • You included screenshots from your STEM results of profiles that were not significant. Only the profiles that showed up in color in the first results screen were significant and should be considered.
  • You did not explicitly state which profile you chose, although it appears to be #23.
  • In answer to the question how many GO terms had a p value of < 0.05, you said 533, but it is really 116. In answer to how many GO terms had a corrected p value of 0.05, you answered 116, but it is really 44.
  • The RegulationMatrix file that you uploaded had the wrong file extension, ".ppt" instead of ".xls".
  • In your narrative, you mention that you only want to add the transcription factors RAP1 and STE12, but in your file, SOK2, MSN2, and YAP5 are there as well. Did you mean to add them?
  • In your discussion of the interpretation of the GO terms, you need to be specific about why the cell is up-/down-regulating these specific GO terms in response to cold.
  • Remember, you need to link back to the original assignment page from every individual journal page.

Kam D. Dahlquist 13:01, 18 April 2013 (EDT)

Week 12 Shared Journal Feedback

  • The STEM profiles were listed in order of significance. The ones with the lowest p value were listed first. The profiles that showed up in color were all significant, and the white ones were not. The p value depends on the ratio of the number of genes in the profile versus the number of genes that would be expected in that profile due to chance.
  • For question 4 of the shared journal reflection, be careful in the way you state your answer. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes.

Kam D. Dahlquist 13:36, 18 April 2013 (EDT)

Week 9 Spreadsheet Feedback

  • I've reviewed the spreadsheet you submitted for your week 9 assignment. It all looks correct, except for the following:
    • On the "statistics" worksheet, you made a mistake on the formula for the Average Log Fold Change for t15. The cell reference in the formula does not include all of the replicates for t15. This will need to be fixed before doing the Week 12 assignment.
    • In formatting your "final" worksheet, you had four decimal places for the fold changes, not the two decimal places requested in the protocol.

Kam D. Dahlquist 01:35, 9 April 2013 (EDT)

Week 1 Journal Feedback

  • Thank you for submitting your assignment on time.
  • There are a few of things that you need to fix on your individual user page and shared journal page. Please make these changes by next week's journal deadline (midnight, February 8) to earn back the points you missed on this assignment.
    1. You need to put the complete street address for your box at LMU.
    2. On the Week 1 shared journal page, put the link to your user page underneath the header for your section.
    3. In addition to posting a question on Dr. Fitzpatrick's talk page, you need to post a question on my talk page.
    4. You have not filled out the summary field when you save changes to your pages. You need to fill it out every time you make a change.
    5. You need to demonstrate that you can "comment out" something. Your comment was just what was put there by the OpenWetWare script.
    6. Your link to a file needs a label. What you did works, but it would be better to use the complete wiki syntax. I.e., use [[Media:AhmadResume.doc | my resume]], which looks like this: my resume, instead of just Media:AhmadResume.doc.
    7. While you have created a template, you have not actually invoked it on your page. To invoke your template, use the wiki syntax {{Salman Ahmad}} on your page. Furthermore, you need to use your template to your advantage. It should contain links for each of the class assignment pages, your journal pages, and the class shared journal pages. It is also helpful to put the class category on it as well. Currently, the category is currently missing from your user page. If you put it in your template and then invoke the template, you will never forget to put it in your journal page.
  • Please feel free to delete the message from OpenWetWare below.

Kam D. Dahlquist 02:20, 31 January 2013 (EST)


You asked: "Hello Dr. Fitzpatrick: Students are learning higher levels of math earlier in their lives than before, how do you think that will affect the applications of math in the future? Salman Ahmad 21:23, 22 January 2013 (EST)"

My answer: That's a really good question. I don't think universities in general (or LMU in particular) have caught up educational programs to the way students are being taught pre-college. College calculus classes (depending on the professor) can be very different from high school ones, tho. I'd hope that it will help "across the board" with people being able to approach a lot of things more quantitatively. So many applications today involve large data sets in which the data points have many attributes (we often call this high dimensional data). I think the need may drive the math, rather than the other way around. We may see the type of math taught changing from calculus based stuff to linear algebra (vectors and matrices), statistical, and computational.

Ben G. Fitzpatrick 14:00, 3 February 2013 (EST)

Week 2 Journal Feedback

  • Thanks for submitting your work on time.
  • Your discussion is a bit thin. You need to include a little more detail on the simulations you performed.
  • Graphs would be very helpful in backing up your discussion. See Elizabeth's page for a good example of a file containing some well-annotated simulations, or Ashley's for graphs embedded in the discussion. Paul's screencaps, while a bit difficult to view due to size, may also help you.
  • How might you model waste with the differential equations?

Ben G. Fitzpatrick 14:00, 4 February 2013 (EST)


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