User talk:Helena M. Olivieri - Revision history

Kam D. Dahlquist: /* Further Feedback Week 12 Individual Journal */ discrepancy between profile and go and TF results

2013-04-19T19:57:39Z

Further Feedback Week 12 Individual Journal: discrepancy between profile and go and TF results

←Older revision		Revision as of 19:57, 19 April 2013
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	* I received your files. I looked at the GO list file for profile 45 and it has 164 GO terms (not 165) that are p < 0.05; it has 104 GO terms (not 35) that have a corrected p < 0.05.		* I received your files. I looked at the GO list file for profile 45 and it has 164 GO terms (not 165) that are p < 0.05; it has 104 GO terms (not 35) that have a corrected p < 0.05.
		+	* The GO terms that you list the definitions for do not seem to be the top terms for profile 45, which profile did you use?
		+	* Also, the top transcription factors do not seem to be from profile 45 either, which profile did you use?

	''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:55, 19 April 2013 (EDT)''		''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:55, 19 April 2013 (EDT)''

Kam D. Dahlquist: /* Week 12 Journal Feedback */ further feedback on GO terms with p values

2013-04-19T19:55:40Z

Week 12 Journal Feedback: further feedback on GO terms with p values

←Older revision		Revision as of 19:55, 19 April 2013
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	''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:30, 19 April 2013 (EDT)''		''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:30, 19 April 2013 (EDT)''
		+
		+	=== Further Feedback Week 12 Individual Journal ===
		+
		+	* I received your files. I looked at the GO list file for profile 45 and it has 164 GO terms (not 165) that are p < 0.05; it has 104 GO terms (not 35) that have a corrected p < 0.05.
		+
		+	''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:55, 19 April 2013 (EDT)''

	== Week 9 Spreadsheet Feedback ==		== Week 9 Spreadsheet Feedback ==

Kam D. Dahlquist: /* Week 12 Journal Feedback */ shared journal feedback

2013-04-19T19:30:52Z

Week 12 Journal Feedback: shared journal feedback

←Older revision		Revision as of 19:30, 19 April 2013
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	* Profile 45 is a profile of genes whose expression is up-regulated at the cold shock time points and then down-regulated at the recovery time points. ''All'' the genes in that profile fit that pattern. Since the GO terms are associated with the genes in that profile, then you can think of them as similarly up-regulated during cold shock and down-regulated during recovery. In other words, each of the GO terms that are associated with that profile contains genes that are up-regulated during cold shock and then down-regulated during recovery.		* Profile 45 is a profile of genes whose expression is up-regulated at the cold shock time points and then down-regulated at the recovery time points. ''All'' the genes in that profile fit that pattern. Since the GO terms are associated with the genes in that profile, then you can think of them as similarly up-regulated during cold shock and down-regulated during recovery. In other words, each of the GO terms that are associated with that profile contains genes that are up-regulated during cold shock and then down-regulated during recovery.
	* Remember that each individual journal page needs to link back to your User page, link to the original assignment page, and needs to have the category BIOL398-03/S13.		* Remember that each individual journal page needs to link back to your User page, link to the original assignment page, and needs to have the category BIOL398-03/S13.
		+
		+	=== Week 12 Shared Journal Feedback ===
		+
		+	* For question 4 of the shared journal reflection, be careful in the way you state your answer. The individual gene's p value just tells us that we would see that big of a change in gene expression due to chance, that percentage of the time. 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. Also, the Gene Ontology terms and transcription factors are two separate considerations. GO terms are associated with a group of genes who all play a part in that process the term describes. There ''are'' some terms related to transcription and transcription factors, but most GO terms are related to other parts of a cell's physiology. YEASTRACT tells us about which transcription factors regulate a group of genes.
		+
		+	''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 15:30, 19 April 2013 (EDT)''

	== Week 9 Spreadsheet Feedback ==		== Week 9 Spreadsheet Feedback ==

Kam D. Dahlquist: added Week 12 journal feedback

2013-04-18T15:47:27Z

added Week 12 journal feedback

←Older revision		Revision as of 15:47, 18 April 2013
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		+	== Week 12 Journal Feedback ==
		+
		+	* Thank you for submitting your assignment on time.
		+	* I was unable to check your work with regard to the GO terms and YEASTRACT because you did not post your GO list file and Gene list file on LionShare. Please post the files for profile 45 and send me the link.
		+	* Profile 45 is a profile of genes whose expression is up-regulated at the cold shock time points and then down-regulated at the recovery time points. ''All'' the genes in that profile fit that pattern. Since the GO terms are associated with the genes in that profile, then you can think of them as similarly up-regulated during cold shock and down-regulated during recovery. In other words, each of the GO terms that are associated with that profile contains genes that are up-regulated during cold shock and then down-regulated during recovery.
		+	* Remember that each individual journal page needs to link back to your User page, link to the original assignment page, and needs to have the category BIOL398-03/S13.
		+
	== Week 9 Spreadsheet Feedback ==		== Week 9 Spreadsheet Feedback ==

Kam D. Dahlquist: feedback on week 9 spreadsheet

2013-04-09T05:38:46Z

feedback on week 9 spreadsheet

←Older revision		Revision as of 05:38, 9 April 2013
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		+	== Week 9 Spreadsheet Feedback ==
		+
		+	* I have reviewed the spreadsheet you have submitted for the Week 9 assignment. Unfortunately, you made a typo on your "scaled_centered" worksheet that has affected all of your downstream calculations. In the STDEV calculation, your the range of cells in your formula went to row 9192 instead of 6192. You will need to correct this before going on to the Week 12 assignment.
		+
		+	''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 01:38, 9 April 2013 (EDT)''
		+
	== Week 1 Journal Feedback ==		== Week 1 Journal Feedback ==

Helena M. Olivieri: /* Week 2 Journal Feedback */

2013-02-08T06:20:19Z

Week 2 Journal Feedback

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	'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 13:52, 4 February 2013 (EST)'''		'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 13:52, 4 February 2013 (EST)'''
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-	~~----~~
-	Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.

Helena M. Olivieri: /* Basic Wiki Instructions */

2013-02-08T06:19:54Z

Basic Wiki Instructions

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	----		----
	Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.		Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.
-
-	~~== Basic Wiki Instructions ==~~
-	*'''Don't be afraid to edit!''' As with all pages on the wiki, all versions are saved so its easy to undo. If you have any questions feel free to [[Special:Contact\|send us an email]].
-	~~# Start off by clicking the 'edit' button to the right of this section, or at the top of the page.~~
-	# Now you should see the text of this section as text within an editor box. There are several buttons in the editor box, but don't worry about those for now. Just type something in the box, scroll down to the bottom, and hit the 'Preview' button.
-	~~# 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'!~~
-	# 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]]'''.
-	# 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.)
-
-	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!

Helena M. Olivieri: /* Personal/Lab Info */ delete

2013-02-08T06:19:14Z

Personal/Lab Info: delete

←Older revision		Revision as of 06:19, 8 February 2013
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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!		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!
-
-	~~== Personal/Lab Info ==~~
-	We have gone ahead and filled in some information you provided us in your membership application on your [[User:Helena M. Olivieri\|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]].
-
-	You'll also notice that we have put an 'image' placeholder at the top of your [[User:Helena M. Olivieri\|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 name. After you have uploaded the image, you should see it loaded on its own page. Go back to your [[User:Helena M. Olivieri\|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.

Ben G. Fitzpatrick: bgf added discussion to chemostat week 2 assignment

2013-02-04T18:52:10Z

bgf added discussion to chemostat week 2 assignment

←Older revision		Revision as of 18:52, 4 February 2013
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	'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 14:02, 3 February 2013 (EST)'''		'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 14:02, 3 February 2013 (EST)'''
		+	----
		+
		+	== Week 2 Journal Feedback ==
		+
		+	* For future assignments, please plan ahead and submit 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 the ethanol production as a third differential equation? How might it impact the mortality?
		+
		+	'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 13:52, 4 February 2013 (EST)'''
		+
	----		----
	Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.		Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.

Ben G. Fitzpatrick: bgf answers HMO question.

2013-02-03T19:02:41Z

bgf answers HMO question.

←Older revision		Revision as of 19:02, 3 February 2013
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	Helena, I answered your question on my [[User_talk:Kam_D._Dahlquist \| user talk page]]. ''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 20:04, 24 January 2013 (EST)''		Helena, I answered your question on my [[User_talk:Kam_D._Dahlquist \| user talk page]]. ''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 20:04, 24 January 2013 (EST)''
		+	----
		+	You asked: "Hi Dr. Fitzpatrick, What are some of your hobbies outside of academia? Helena M. Olivieri 01:12, 23 January 2013 (EST)"
		+
		+	My answer: I have quite a few. I like to travel, when I can afford it and make time for it. I (attempt to) play guitar. I do some woodworking, and I like to take pictures.
		+
		+	'''[[User:Ben G. Fitzpatrick\|Ben G. Fitzpatrick]] 14:02, 3 February 2013 (EST)'''
	----		----
	Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.		Hello, Helena M. Olivieri! 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:Helena M. Olivieri\|User Page]] so that we can get to know you better! We've included some tips below to get you started.