User:Kwyllie - Revision history

Kwyllie: Cut and pasted my protcol to the week 3 assignment, as instructed in class.

2015-09-18T18:51:30Z

Cut and pasted my protcol to the week 3 assignment, as instructed in class.

Kwyllie: Added mention of LMU symposium and WCBSURC as instructed in my week 1 assignment feedback.

2015-09-15T05:56:43Z

Added mention of LMU symposium and WCBSURC as instructed in my week 1 assignment feedback.

Kwyllie: Continued fixing the template.

2015-09-15T05:46:50Z

Continued fixing the template.

Kwyllie: Oops, that didn't work. Fixing it now.

2015-09-15T05:46:08Z

Oops, that didn't work. Fixing it now.

Kwyllie: Edited the name of template as instructed in my week 1 assignment feedback.

2015-09-15T05:45:44Z

Edited the name of template as instructed in my week 1 assignment feedback.

Kwyllie: Fixed a typo.

2015-09-15T05:43:05Z

Fixed a typo.

Kwyllie: Fixed a typo and added a small detail to my protocol.

2015-09-15T05:42:29Z

Fixed a typo and added a small detail to my protocol.

Kwyllie: Added my protocol for the week 2 individual assignment.

2015-09-15T05:41:02Z

Added my protocol for the week 2 individual assignment.

Kwyllie: Adjusted my headers as instructed in my Week 1 feedback.

2015-09-15T03:50:13Z

Adjusted my headers as instructed in my Week 1 feedback.

Kwyllie: Attempted syntax fix.

2015-09-15T03:45:43Z

Attempted syntax fix.

← Older revision		Revision as of 18:51, 18 September 2015
Line 65:		Line 65:
	{{Template:KwyllieJournalLinks}}		{{Template:KwyllieJournalLinks}}
	[[Template:KwyllieJournalLinks]]		[[Template:KwyllieJournalLinks]]
−
−	~~==Electronic Lab Notebook==~~
−
−	~~===Week 2 Individual Journal Assignment===~~
−
−	~~# First, using the given DNA strand, write out the sequence for the complementary strand. A's pair with T's, while C's pair with G's.~~
−	#* Remember that although you may have written the new strand from left to right, due to DNA's antiparallel characteristic, it will be ''read'' in the reverse direction, assuming you designated that this new strand was the "bottom strand." To remind yourself of this, add the 5' and 3' notation as done for the original strand, although remember that the sides for either will be reversed.
−	~~# To avoid errors when using the amino acids translation chart (discussed below), you should write out the mRNA transcript for all six of the frames.~~
−	## Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
−	## Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
−	~~## For the "+3" frame, start by deleting the first two nucleotides and continue as normal.~~
−	## For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). This may be tedious, but it can get very confusing to read the strand in reverse. After that, as before, group the nucleotides into groups of three.
−	~~## Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.~~
−	~~# Finally, translate each frame.~~
−	~~#* Use the amino acid translator chart to convert each codon into an amino acid. [https://www.manylabs.org/file/lessonMedia/69/geneticCode.png Here's an amino acids chart from ManyLabs.org]~~
−	~~#* If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicate the beginning and end of the chain with the "Nter" and "Cter" notation.~~
−	~~#** "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.~~
−	~~#* If a frame does not contain a STOP codon, then it referred to as an "open reading frame."~~

@@ Line 34: / Line 34: @@
 *** Publication
 :Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science; Phage Hunters Integrating Research and Education; Mycobacterial Genetics Course. April, 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife.
 ** Dahlquist Lab (2014 to present)
 *** Mentor: Dr. Kam D. Dahlquist
 *** Investigating transcription factors involved in the cold stress response in ''Saccharomyces cerevisiae'' via DNA microarray analysis and growth experiments.[http://openwetware.org/wiki/Kevin_Wyllie's_Electronic_Lab_Notebook (See my electronic lab notebook for microarray data normalization)]
 * [[Media:KevinWyllieCV2015.pdf|See my full curriculum vitae]]

@@ Line 63: / Line 63: @@
 * [[Class Journal Week 1]]
-{{Template:JournalLinks}}
+{{Template:KwyllieJournalLinks}}
-[[Template:JournalLinks]]
+[[Template:KwyllieJournalLinks]]
 ==Electronic Lab Notebook==

@@ Line 63: / Line 63: @@
 * [[Class Journal Week 1]]
-{{Template:KwyllieJournalLinks}}
+{{Template:JournalLinks}}
-[[Template:KwyllieJournalLinks]]
+[[Template:JournalLinks]]
 ==Electronic Lab Notebook==

@@ Line 63: / Line 63: @@
 * [[Class Journal Week 1]]
-{{Template:JournalLinks}}
+{{Template:KwyllieJournalLinks}}
-[[Template:JournalLinks]]
+[[Template:KwyllieJournalLinks]]
-−
 ==Electronic Lab Notebook==

@@ Line 81: / Line 81: @@
 # Finally, translate each frame.
 #* Use the amino acid translator chart to convert each codon into an amino acid. [https://www.manylabs.org/file/lessonMedia/69/geneticCode.png Here's an amino acids chart from ManyLabs.org]
-#* If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicated the beginning and end of the chain with the "Nter" and "Cter" notation.
+#* If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicate the beginning and end of the chain with the "Nter" and "Cter" notation.
 #** "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.
 #* If a frame does not contain a STOP codon, then it referred to as an "open reading frame."

@@ Line 76: / Line 76: @@
 ## Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
 ## Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
-## For the "+3" frame, start by deleted the first two nucleotides and continue as normal.
+## For the "+3" frame, start by deleting the first two nucleotides and continue as normal.
-## For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). After that, as before, group the nucleotides into groups of three.
+## For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). This may be tedious, but it can get very confusing to read the strand in reverse. After that, as before, group the nucleotides into groups of three.
 ## Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.
 # Finally, translate each frame.

← Older revision		Revision as of 05:41, 15 September 2015
Line 65:		Line 65:
	{{Template:JournalLinks}}		{{Template:JournalLinks}}
	[[Template:JournalLinks]]		[[Template:JournalLinks]]
		+
		+
		+	==Electronic Lab Notebook==
		+
		+	===Week 2 Individual Journal Assignment===
		+
		+	# First, using the given DNA strand, write out the sequence for the complementary strand. A's pair with T's, while C's pair with G's.
		+	#* Remember that although you may have written the new strand from left to right, due to DNA's antiparallel characteristic, it will be ''read'' in the reverse direction, assuming you designated that this new strand was the "bottom strand." To remind yourself of this, add the 5' and 3' notation as done for the original strand, although remember that the sides for either will be reversed.
		+	# To avoid errors when using the amino acids translation chart (discussed below), you should write out the mRNA transcript for all six of the frames.
		+	## Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
		+	## Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
		+	## For the "+3" frame, start by deleted the first two nucleotides and continue as normal.
		+	## For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). After that, as before, group the nucleotides into groups of three.
		+	## Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.
		+	# Finally, translate each frame.
		+	#* Use the amino acid translator chart to convert each codon into an amino acid. [https://www.manylabs.org/file/lessonMedia/69/geneticCode.png Here's an amino acids chart from ManyLabs.org]
		+	#* If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicated the beginning and end of the chain with the "Nter" and "Cter" notation.
		+	#** "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.
		+	#* If a frame does not contain a STOP codon, then it referred to as an "open reading frame."

@@ Line 5: / Line 5: @@
 [[image:Kevinwyllie.jpg|thumb|right]]
-===Contact===
+====Contact====
 kwyllie@lion.lmu.edu
@@ Line 11: / Line 11: @@
 LMU Dr. 90045, MSB 7967
-===Education===
+====Education====
 * Major: Biochemistry
@@ Line 26: / Line 26: @@
 *# Biological databases [[Main Page|(See the course's Main Page)]]
-===Career===
+====Career====
 * After completing my B.S. in biochemistry, I plan to participate in post-grad service. Following one or two years of service, I hope to attend medical school.
 * Research Experience:
@@ Line 40: / Line 40: @@
 * [[Media:KevinWyllieCV2015.pdf|See my full curriculum vitae]]
-===Work Experience===
+====Work Experience====
 * Paralegal's assistant, Omikron IP Law (Summer 2011 through Summer 2012)
 ** Managed transmittance of patent information between paralegal and clients
@@ Line 46: / Line 46: @@
 ** Managed check-out and check-in of books and media
 ** Carried and some clerical, customer information and financial duties
-===Personal Interests===
+====Personal Interests====
 * Service and social justice - particularly restorative justice
 * Running
 * Experimental/progressive/multi-genre music
-===More Information===
+====More Information====
 * My favorite thing about biology is that it forces us to see ourselves as being just as embedded in nature as the life forms we study. As a species that sees itself as being highly complex and sophisticated, we often fall victim to human exceptionalism. Biology reminds us that we, as organisms, are at the mercy of the same fundamental principles as the most primordial prokaryote.
 * I have very little background in computer science, but what I most appreciate about the field is its contribution to the well-being of humanity.
-===Wiki Syntax Help===
+====Wiki Syntax Help====
 To help me complete this assignment, I used [https://en.wikipedia.org/wiki/Help:Cheatsheet this page].
-===Journal Assignments===
+====Journal Assignments====
 * [[Class Journal Week 1]]