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Ryan N. Willhite Week 4

Ryan N. Willhite — Tue, 09 Feb 2010 19:27:26 GMT

change link name

←Older revision		Revision as of 19:27, 9 February 2010
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	===Activity 1, Part 3===		===Activity 1, Part 3===

-	[[Media:ClustWweek4treediagram.gif]]	+	[[Media:ClustWweek4treediagram.gif\|Clustal W tree diagram]]

J'aime C. Moehlman's Week 4

J'aime C. Moehlman — Tue, 09 Feb 2010 19:27:02 GMT

←Older revision		Revision as of 19:27, 9 February 2010
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	#Saved my FASTA data into the Biology Workbench		#Saved my FASTA data into the Biology Workbench
	#Viewed the Help page for using the ClustalW tool in the nucleic tools.		#Viewed the Help page for using the ClustalW tool in the nucleic tools.
-	#*	+	#*It shows how this tool helps to perform multiple sequence alignment on protein or nucleic sequences.
		+	===Activity 2: Part 1===
		+	#added all of the first visit nucleic acid sequences.
		+	#Data Table:
		+	#*'''Subject: Clone:'''
		+	#* 1 -------- 1,2,3
		+	#* 2 -------- 1,2,3
		+	#* 3 --------- 1,2,3
		+	#* 4 -------- 1,2,3

Ryan N. Willhite Week 4

Ryan N. Willhite — Tue, 09 Feb 2010 19:26:53 GMT

add tree diagram of clustal w

←Older revision		Revision as of 19:26, 9 February 2010
Line 10:		Line 10:
	* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.		* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.
	===Activity 1, Part 3===		===Activity 1, Part 3===
		+
		+	[[Media:ClustWweek4treediagram.gif]]

Image:KAH 020810 gel1.tif

Karmella Haynes — Tue, 09 Feb 2010 19:26:42 GMT

uploaded "[[Image:KAH 020810 gel1.tif]]"

New page

Alex J. George Week 4

Alex J. George — Tue, 09 Feb 2010 19:26:20 GMT

←Older revision		Revision as of 19:26, 9 February 2010
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	* This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.		* This sequence was taken from the first visit of Subject 1. This information is given in the title of the sequence.
	[[Media:FASTA sequences.doc\| FASTA sequences]]		[[Media:FASTA sequences.doc\| FASTA sequences]]
		+
		+	====Part 3: Biology Workbench====
		+	* Registered for Workbench, followed "Nucleic Tools" link to add a sequence.
		+	* Uploaded sequences successfully, realizing it is best to keep the file saved as a ".fasta" file
		+	* CLUSTALW Tool performs multiple sequence alignment on protein or nucleic sequences
		+	*Example: gi:33187149 and gi:33187151 are on the same side of the tree because their differences from the other sequences are most similar. For example, in the 21st and 22nd base pairs, these sequences show "AA" whereas the other three show "CC"
		+
		+	=== Activity 2: Looking at sources of HIV across subjects===
		+	* Goal: Determine if the isolated HIV from subgroups comes from a common source
		+	* Multiple sequence alignment: comparing nucleotide positions for many sequences
		+
		+	====Part 1: Clustering across subjects====

	{{Alex J. George}}		{{Alex J. George}}

Image:ClustWweek4treediagram.gif

Ryan N. Willhite — Tue, 09 Feb 2010 19:25:48 GMT

uploaded "[[Image:ClustWweek4treediagram.gif]]" Part 3 Clustal W tree diagram

New page

User:Karmella Haynes/Notebook/BioBrick cloning/2010/02/08

Karmella Haynes — Tue, 09 Feb 2010 19:25:16 GMT

mm/dd/yy:

←Older revision		Revision as of 19:25, 9 February 2010
Line 8:		Line 8:
	==mm/dd/yy==		==mm/dd/yy==
	<!-- Precede finished items with a checkmark ✓ -->		<!-- Precede finished items with a checkmark ✓ -->
-	* ~~Line item 1~~	+	* Minipreps: KAH80 (2)
-	* Line item 2	+

	----		----
Line 18:		Line 17:
	\|-valign="top"		\|-valign="top"
	\| <u>Reagent</u> \|\| <u>Volume</u>		\| <u>Reagent</u> \|\| <u>Volume</u>
-	\| rowspan="7" \| <u>Expected:</u><br>1~~. BB 1 = size<br>~~2. ~~BB2~~ = ~~size<br>~~	+	\| rowspan="7" \| <u>Expected:</u><br>1,2. KAH80 = 1474
-	\| rowspan="7" \| ~~<!--~~ [[Image:~~GelImage~~.~~jpg~~\|400px\|Hover name]]<br>15 μL/lane; 1% agarose ~~-->~~	+	\| rowspan="7" \| [[Image:KAH_020810_gel1.tif\|400px\|Hover name]]<br>15 μL/lane; 1% agarose
	\|-		\|-
	\| DNA(plasmid) \|\| 2.0 μL		\| DNA(plasmid) \|\| 2.0 μL
Line 32:		Line 31:
	\|-		\|-
	\|   \|\| 15 μL --> 37°C/ ~15 min.		\|   \|\| 15 μL --> 37°C/ ~15 min.
-	\|}
-
-	~~----~~
-	~~'''Assemblies'''~~
-	~~# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size~~
-	~~# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size~~
-
-	~~> Digests (Fermentas FD)<br>~~
-	~~--> Specific notes<br>~~
-
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Digest rxn. table -->~~
-	~~\|-valign="top"~~
-	~~\| <u>Reagent</u> \|\| <u>Volume</u> \|\|  ~~
-	~~\| rowspan="9" \| <!-- [[Image:GelImage.jpg\|270px\|Hover name]]<br>30 μL/lane, 1% agarose -->~~
-	\|-
-	~~\| DNA (plasmid) \|\| up to 25 μL~~
-	\|-
-	~~\| 10x buffer \|\| 3.0~~
-	\|-
-	~~\| enzyme 1 \|\| 1.0~~
-	\|-
-	~~\| enzyme 2 \|\| 1.0~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| ---~~
-	\|-
-	~~\|   \|\| 30 μL --> 37°C/ ~30 min.~~
-	\|}
-
-
-	~~> Measure conc.'s~~
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- [DNA] table -->~~
-	\|-
-	~~\| <u>Sample</u> \|\| <u>OD260</u> \|\| <u>260/280</u> \|\| <u>ng/μL</u>~~
-	\|-
-	~~\| 1. Digested part (a/b) \|\| --- \|\| --- \|\| ---~~
-	\|-
-	~~\| 2. Digested part (c/d) \|\| --- \|\| --- \|\| ---~~
-	\|}
-
-
-	~~> Dephosphorylation (Roche)~~
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Dephos table -->~~
-	\|-
-	~~\| <u>Reagent</u> \|\| <u>Volume</u>~~
-	\|-
-	~~\| DNA (clean digest) \|\| up to 17 μL (500 ng)~~
-	\|-
-	~~\| 10x buffer d.p. \|\| 2.0~~
-	\|-
-	~~\| phosphatase \|\| 1.0~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| ---~~
-	\|-
-	~~\|   \|\| 20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL~~
-	\|}
-
-
-	~~> Ligations~~
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Ligations table -->~~
-	~~\| <u>Ligation</u> \|\| <font color="blue"><u>Plate results (lig : neg crtl)</u> mm/dd/yy</font>~~
-	\|-
-	~~\| 1. insert(a/b)/size, ## ng + vector(c/d)/size, ## ng \|\| <font color="blue">new BioBrick #:1 (Pick #)</font>~~
-	\|-
-	~~\| 2. vector(c/d)/ ## ng \|\|  ~~
-	\|}
-
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Ligation rxn table -->~~
-	~~\|   \|\| 1 \|\| 2 \|\|~~
-	\|-
-	~~\| Insert DNA \|\| ### \|\| --- \|\|~~
-	\|-
-	~~\| Vector DNA \|\| ### \|\| ### \|\|~~
-	\|-
-	~~\| 2x lgn buf (Roche) \|\| ### \|\| ### \|\|~~
-	\|-
-	~~\| T4 ligase (NEB) \|\| 1.0 \|\| 1.0 \|\|~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| ### \|\| ### \|\|~~
-	\|-
-	~~\|   \|\| # μL \|\| # μL \|\|~~
-	\|}
-
-	~~----~~
-	~~'''Oligo annealing'''~~
-	~~# New BB 1~~
-	~~# New BB 2~~
-
-	~~{\| class="wikitable" border="0" cellspacing="3" <!-- Oligo annealing rxn table -->~~
-	~~\| DNA (oligos, 100 μM) \|\| up to 18 μL (3 μL ea.)~~
-	\|-
-	~~\| 10x annealing buffer \|\| 2.0~~
-	\|-
-	~~\| dH<sub>2</sub>O \|\| ---~~
-	\|-
-	~~\|   \|\| 20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight~~
	\|}		\|}

SBB10Ntbk-WeiChunHsu

Wei-Chun Hu — Tue, 09 Feb 2010 19:24:58 GMT

←Older revision		Revision as of 19:24, 9 February 2010
Line 1:		Line 1:
	=Computational Part Design=		=Computational Part Design=
		+
		+	==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 14:24, 9 February 2010 (EST)==
		+
		+	===The following protocols are relevant for me:===
		+
		+	[[Template:SBB-Protocols_PCR2 \| Cloning by PCR]]<br>
		+	[[Template:SBB-Protocols_PCR3 \| SOEing PCR]]<br>
		+	[[Template:SBB-PCA \| PCA Gene Synthesis]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Zymo1 \| Regular Zymo Cleanup]]<br>
		+	[[Template:SBB-Protocols_Zymo3 \| Zymo Gel Purification]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Enz2 \| EcoRI/BamHI Digest of PCR Products]]<br>
		+	[[Template:SBB-Protocols_Enz4 \| Ligation of EcoRI/BamHI digests]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Micro1 \| Transformation by heat-shock]]<br>
		+	[[Template:SBB-Protocols_Micro2 \| Picking of colonies]]<br>
		+	[[Template:SBB-Protocols_Micro3 \| Miniprep purification of DNA]]<br>

	==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 01:45, 4 February 2010 (EST)==		==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 01:45, 4 February 2010 (EST)==

Ryan N. Willhite Week 4

Ryan N. Willhite — Tue, 09 Feb 2010 19:24:56 GMT

part 3

←Older revision		Revision as of 19:24, 9 February 2010
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	# [[Media:Wk4sequences.txt\|FASTA sequences]]		# [[Media:Wk4sequences.txt\|FASTA sequences]]
	* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.		* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.
		+	===Activity 1, Part 3===

Image:Mpina visit 1 S10 S15.txt

Michael R. Pina — Tue, 09 Feb 2010 19:23:50 GMT

uploaded "[[Image:Mpina visit 1 S10 S15.txt]]"

New page

2020(S10) Lecture:week 2

Nkuldell — Tue, 09 Feb 2010 19:21:12 GMT

Challenge: extra credit for extra parts?:

←Older revision		Revision as of 19:21, 9 February 2010
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	\| Stephanie, Grant, Judy		\| Stephanie, Grant, Judy
	\| 23		\| 23
-	\|	+	\| nope, but it looked good
	\|-		\|-
	\| 2		\| 2
	\| Aditya, Colin, Ranheetha		\| Aditya, Colin, Ranheetha
	\| 25		\| 25
-	\|	+	\| nope, but w/o Ranheetha the notes were missing
	\|-		\|-
	\| 3		\| 3
	\| Nancy, Logan, Stephanie		\| Nancy, Logan, Stephanie
	\| 49		\| 49
-	\|	+	\| nope, but needed more time with soldering iron
	\|-		\|-
	\| 4		\| 4
	\| Ben, Will, Lizzie		\| Ben, Will, Lizzie
	\| 35		\| 35
-	\|	+	\| earphones worked! (3 reusable parts...)
	\|-		\|-
	\|}		\|}
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	At the end of the 1/2 hour we will spend some time tallying the successes of the groups.		At the end of the 1/2 hour we will spend some time tallying the successes of the groups.
		+
	==<font color = blue>'''Why are we doing this??'''==		==<font color = blue>'''Why are we doing this??'''==
	Even if you were only partially successful in reassembling your tape player, there are probably a lot of things you've learned...things that would help you or the next person to successfully reassemble a tape player, things that reflect back on the take-apart exercise, aspects of the exercise that are common to any scientific or engineering effort (and remember your work this term will have elements of both!). We'll work as a class to add more ideas, questions and thoughts to this list.</font color>		Even if you were only partially successful in reassembling your tape player, there are probably a lot of things you've learned...things that would help you or the next person to successfully reassemble a tape player, things that reflect back on the take-apart exercise, aspects of the exercise that are common to any scientific or engineering effort (and remember your work this term will have elements of both!). We'll work as a class to add more ideas, questions and thoughts to this list.</font color>

User:Karmella Haynes/Notebook/BioBrick cloning/2010/02/08

Karmella Haynes — Tue, 09 Feb 2010 19:19:39 GMT

Autocreate 2010/02/08 Entry for User:Karmella_Haynes/Notebook/BioBrick_cloning

New page

{|{{table}} width="800"
|-
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Project name
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]] {{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>      </html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|-
| colspan="2"|

==mm/dd/yy==

* Line item 1
* Line item 2

----
'''Minipreps''' 
> Check with E/P digests

{| class="wikitable" border="0" cellspacing="3" 
|-valign="top"
| Reagent || Volume
| rowspan="7" | Expected: 1. BB 1 = size 2. BB2 = size 
| rowspan="7" | 
|-
| DNA(plasmid) || 2.0 μL
|-
| 10X buffer || 1.5
|-
| EcoRI || 1.0
|-
| PstI || 1.0
|-
| dH2O || 9.5
|-
|   || 15 μL --> 37°C/ ~15 min.
|}

----
'''Assemblies'''
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size

> Digests (Fermentas FD) 
--> Specific notes 

{| class="wikitable" border="0" cellspacing="3" 
|-valign="top"
| Reagent || Volume ||  
| rowspan="9" | 
|-
| DNA (plasmid) || up to 25 μL
|-
| 10x buffer || 3.0
|-
| enzyme 1 || 1.0
|-
| enzyme 2 || 1.0
|-
| dH2O || ---
|-
|   || 30 μL --> 37°C/ ~30 min.
|}

> Measure conc.'s
{| class="wikitable" border="0" cellspacing="3" 
|-
| Sample || OD260 || 260/280 || ng/μL
|-
| 1. Digested part (a/b) || --- || --- || ---
|-
| 2. Digested part (c/d) || --- || --- || ---
|}

> Dephosphorylation (Roche)
{| class="wikitable" border="0" cellspacing="3" 
|-
| Reagent || Volume
|-
| DNA (clean digest) || up to 17 μL (500 ng)
|-
| 10x buffer d.p. || 2.0
|-
| phosphatase || 1.0
|-
| dH2O || ---
|-
|   || 20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL
|}

> Ligations
{| class="wikitable" border="0" cellspacing="3" 
| Ligation || Plate results (lig : neg crtl) mm/dd/yy
|-
| 1. insert(a/b)/size, ## ng + vector(c/d)/size, ## ng || new BioBrick #:1 (Pick #)
|-
| 2. vector(c/d)/ ## ng ||  
|}

{| class="wikitable" border="0" cellspacing="3" 
|   || 1 || 2 ||
|-
| Insert DNA || ### || --- ||
|-
| Vector DNA || ### || ### ||
|-
| 2x lgn buf (Roche) || ### || ### ||
|-
| T4 ligase (NEB) || 1.0 || 1.0 ||
|-
| dH2O || ### || ### ||
|-
|   || # μL || # μL ||
|}

----
'''Oligo annealing'''
# New BB 1
# New BB 2

{| class="wikitable" border="0" cellspacing="3" 
| DNA (oligos, 100 μM) || up to 18 μL (3 μL ea.)
|-
| 10x annealing buffer || 2.0
|-
| dH2O || ---
|-
|   || 20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight
|}


|}

__NOTOC__

2020(S10) Lecture:week 2

Nkuldell — Tue, 09 Feb 2010 19:16:31 GMT

Why are we doing this??:

←Older revision		Revision as of 19:16, 9 February 2010
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	* from 2009: secrets to success: ''"good notes, Duct tape, didn't try rebuild as it was"''		* from 2009: secrets to success: ''"good notes, Duct tape, didn't try rebuild as it was"''
	* from 2009: advice to next year's students: ''"bring a camera, don't lose things, know which direction the springs go in, not all parts are needed"''		* from 2009: advice to next year's students: ''"bring a camera, don't lose things, know which direction the springs go in, not all parts are needed"''
-	* from 2010: took pictures, ~~labelled~~ parts, talked about orientation~~, the~~ thing that would have helped would have been to cut the wire in a sensible place, What if we had 5 of these? could take them apart to different stages, not themselves modular..~~.can~~'t test the sub-parts, definition of modularity relates to testability, mapping to biology may involve placing in proxy organism"	+	* from 2010: ''"we took pictures, labeled parts, talked about orientation...it still didn't work!" "The thing that would have helped would have been to cut the wire in a sensible place" What if we had 5 of these? we could take them apart to different stages, and reuse modules from each." "The tape players themselves were not themselves modular, e.g. we couldn't test the sub-parts independently." "The definition of modularity relates to testability, and mapping modularity to biology may involve placing module in proxy organism"''

	=='''Homework''' for tomorrow's studio session==		=='''Homework''' for tomorrow's studio session==

User:Brian P. Josey/Notebook/2010/02/09

Brian P. Josey — Tue, 09 Feb 2010 19:16:23 GMT

Entry title:

←Older revision		Revision as of 19:16, 9 February 2010
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	\| colspan="2"\|		\| colspan="2"\|
	<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
-	==~~Entry title~~==	+	==Yesterday==
-	* Insert content here...	+	I didn't come in yesterday because I have a paper for my history class that was giving me grief. I took yesterday to go through everything that I needed to do to get the paper taken care of and out of my hair.
		+
		+	==Tomorrow==
		+	So tomorrow, I want to try two things. The first is that I want to try diluting the ferritin, and seeing if I can move it in the tube. On Friday, when I was playing with the magnetic beads, I noticed a couple of things:
		+	#. When I mixed them up, the tube became cloudy as the beads when into solution from mixing.
		+	#. Placing a magnet next to makes the solution more clear.
		+	#. Leaving the magnet next to the tube for a long time, about an hour, makes the tube completely clear, and all of the beads clump together as close to the magnet as possible.
		+
		+	Have to go to class, I'll finish in the afternoon.

User:Tong Zhou

Tong Zhou — Tue, 09 Feb 2010 19:15:40 GMT

Education:

←Older revision		Revision as of 19:15, 9 February 2010
Line 4:		Line 4:
	*Tong Zhou		*Tong Zhou
	*Center for Computational Biology and Bioinformatics and Section of Integrative Biology		*Center for Computational Biology and Bioinformatics and Section of Integrative Biology
-	*The University of Texas at Austin	+	*The University of Texas at Austin, Austin, Texas 78712
-	*Austin, Texas 78712	+
	*[[Special:Emailuser/Tong Zhou\|Email me through OpenWetWare]]		*[[Special:Emailuser/Tong Zhou\|Email me through OpenWetWare]]

	==Education==		==Education==
	<!--Include info about your educational background-->		<!--Include info about your educational background-->
-	* ~~Year~~, PhD, ~~Institute~~	+	* 2006, PhD, Southeast University, China
-	* ~~Year~~, MS, ~~Institute~~	+	* 2002, MS, Southeast University, China
-	* ~~Year~~, BS, ~~Institute~~	+	* 2000, BS, Southeast University, China

	==Research interests==		==Research interests==

Bobak Seddighzadeh Week 4

Bobak Seddighzadeh — Tue, 09 Feb 2010 19:12:50 GMT

←Older revision		Revision as of 19:12, 9 February 2010
Line 1:		Line 1:
		+	===Activity 1===
		+
	Part 2: GenBank		Part 2: GenBank

Line 4:		Line 6:
	* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.		* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.
	*[[Media:HIVSequences.txt\|HIV Sequences]]		*[[Media:HIVSequences.txt\|HIV Sequences]]
		+
		+
		+	Part 3: Introduction to the Biology Workbench

User:Tong Zhou

Tong Zhou — Tue, 09 Feb 2010 19:12:12 GMT

Contact Info:

←Older revision		Revision as of 19:12, 9 February 2010
Line 3:		Line 3:

	*Tong Zhou		*Tong Zhou
-	*Center for Computational Biology and Bioinformatics and	+	*Center for Computational Biology and Bioinformatics and Section of Integrative Biology
-	Section of Integrative Biology	+
	*The University of Texas at Austin		*The University of Texas at Austin
-	*Austin, ~~TX,~~ 78712	+	*Austin, Texas 78712
	*[[Special:Emailuser/Tong Zhou\|Email me through OpenWetWare]]		*[[Special:Emailuser/Tong Zhou\|Email me through OpenWetWare]]

Angela A. Garibaldi Week 4

Angela A. Garibaldi — Tue, 09 Feb 2010 19:12:07 GMT

Exploring HIV-1 Exercise: add all headers

←Older revision		Revision as of 19:12, 9 February 2010
Line 1:		Line 1:
-	==Exploring HIV-1 ~~Exercise~~==	+	=Exploring HIV-1 Exercises=
		+	==Activity 1==
		+
	===Part 2: GeneBank===		===Part 2: GeneBank===
	#Search NCBI site under GeneBank - Nucleotide with one of the codes used in the Markham paper for the subject's sequence of the env gene.		#Search NCBI site under GeneBank - Nucleotide with one of the codes used in the Markham paper for the subject's sequence of the env gene.
Line 8:		Line 10:

	[[Image:S14_Subject.txt \|List of (6) Subject 14 Sequences]]		[[Image:S14_Subject.txt \|List of (6) Subject 14 Sequences]]
		+
		+	===Part 3: Introduction to the ''Biology Workbench''===
		+
		+	==Activity 2==
		+	===Part 1: Looking at clustering across subjects===
		+	===Part 2: Quantifying diversity within and between subjects===

User:Tong Zhou

Tong Zhou — Tue, 09 Feb 2010 19:11:22 GMT

Contact Info:

←Older revision		Revision as of 19:11, 9 February 2010
Line 3:		Line 3:

	*Tong Zhou		*Tong Zhou
-	*Section of Integrative Biology	+	*Center for Computational Biology and Bioinformatics and
		+	Section of Integrative Biology
	*The University of Texas at Austin		*The University of Texas at Austin
	*Austin, TX, 78712		*Austin, TX, 78712

Bobak Seddighzadeh Week 4

Bobak Seddighzadeh — Tue, 09 Feb 2010 19:11:11 GMT

←Older revision		Revision as of 19:11, 9 February 2010
Line 3:		Line 3:
	*What was the accession number of the sequence you chose? AF089154		*What was the accession number of the sequence you chose? AF089154
	* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.		* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.
-	*	+	*[[Media:HIVSequences.txt\|HIV Sequences]]

KP Ramirez Week 4

Kevin A Paiz-Ramirez — Tue, 09 Feb 2010 19:09:42 GMT

Assignment:

←Older revision		Revision as of 19:09, 9 February 2010
Line 8:		Line 8:
	• Which subject of the study was that HIV sequence from? Which section of		• Which subject of the study was that HIV sequence from? Which section of
	the record contains information about who the HIV was collected from?		the record contains information about who the HIV was collected from?
		+	*S3V5-10 Subject 3, Visit 5, 10th clone. Found under features and source
		+	• Download several (4 to 6) sequences in FASTA format to your local hard drive
		+	by selecting several at the same time in the summary view so they are saved
		+	into a single text file. Be careful to remember where you put the file and what
		+	you name it so that you can find it later.
		+	*Completed
		+	• Open the file that you saved with a word processor to confirm that you have
		+	the sequences and that they are in the FASTA format. In the FASTA format each
		+	sequence is preceeded by a label which begins with the greater than sign (>).
		+	*Completed
		+
		+
		+
		+
		+
		+
		+
		+

	{{Kevin A Paiz-Ramirez}}		{{Kevin A Paiz-Ramirez}}

Salomon Garcia: Week 4

Salomon Garcia Valencia — Tue, 09 Feb 2010 19:09:12 GMT

Activity 1 Part 2: pic added and answered questions.

←Older revision		Revision as of 19:09, 9 February 2010
Line 16:		Line 16:
	# What was the accession number of the sequence you chose?		# What was the accession number of the sequence you chose?
	# Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?		# Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from?
		+	[[Image:Picture 3.jpg\|thumb\|center\|550px]]

-		+	# The accession number was GenBank: AF016760.1.
-	#	+	# This sequence was from subject 1. GenBank and the Fasta both contain where the section of HIV came from.
-	#	+

Image:HIVSequences1.txt

Bobak Seddighzadeh — Tue, 09 Feb 2010 19:08:45 GMT

uploaded "[[Image:HIVSequences1.txt]]" Four HIV Sequences/ Proper file version

New page

Bobak Seddighzadeh Week 4

Bobak Seddighzadeh — Tue, 09 Feb 2010 19:08:15 GMT

New page

Part 2: GenBank

*What was the accession number of the sequence you chose? AF089154
* Which subject of the study was that HIV sequence from? Which section of the record contains information about who the HIV was collected from? The HIV sequence was collected from subject 4. The sequence has a code that contains information about who the HIV was collected from. The code for this subject's particular sequence is S4V2-4 which indicates the clone is from subject four on his second visit, and its his fourth clone.
*

Image:Picture 3.jpg

Salomon Garcia Valencia — Tue, 09 Feb 2010 19:07:25 GMT

uploaded "[[Image:Picture 3.jpg]]" Fasta pic of gene

New page

Angela A. Garibaldi Week 4

Angela A. Garibaldi — Tue, 09 Feb 2010 19:07:02 GMT

Part 2: GeneBank: add file

←Older revision		Revision as of 19:07, 9 February 2010
Line 6:		Line 6:
	#Click on FASTA to get the FASTA format		#Click on FASTA to get the FASTA format
	#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.		#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.
		+
		+	[[Image:S14_Subject.txt \|List of (6) Subject 14 Sequences]]

User:Brian P. Josey/Notebook/2010/02/09

Brian P. Josey — Tue, 09 Feb 2010 19:04:58 GMT

Autocreate 2010/02/09 Entry for User:Brian_P._Josey/Notebook

New page

Image:S14 Subject.txt

Angela A. Garibaldi — Tue, 09 Feb 2010 19:03:37 GMT

uploaded "[[Image:S14 Subject.txt]]" Angela's list of 6 FASTA sequences of Subject 14 from the Marham study

New page

J'aime C. Moehlman's Week 4

J'aime C. Moehlman — Tue, 09 Feb 2010 19:02:04 GMT

←Older revision		Revision as of 19:02, 9 February 2010
Line 5:		Line 5:
	FASTA sequences on a word document:		FASTA sequences on a word document:
	[[Media:J'aimes Sequences.doc\| Example FASTA Sequences]]		[[Media:J'aimes Sequences.doc\| Example FASTA Sequences]]
		+
		+	===Activity 1: Part 3===
		+	#Created a workbench account with the user name of jmoehlman.
		+	#Saved my FASTA data into the Biology Workbench
		+	#Viewed the Help page for using the ClustalW tool in the nucleic tools.
		+	#*

Angela A. Garibaldi Week 4

Angela A. Garibaldi — Tue, 09 Feb 2010 19:01:40 GMT

Starting Journal Week 4

New page

==Exploring HIV-1 Exercise==
===Part 2: GeneBank===
#Search NCBI site under GeneBank - Nucleotide with one of the codes used in the Markham paper for the subject's sequence of the env gene.
#The '''Accession number''' of the S14V4-8 sequence is GenBank: AF089617.1
#This first HIV sequence is from Subject 14 from Visit 4, Variant 8. The name code of the sequence in this case indicates who the HIV was collected from.
#Click on FASTA to get the FASTA format
#Copy and paste 6 sequences into a .txt file for easy access. In this way the entire descriptive name of the sequences along with their accession numbers are listed.

Ryan N. Willhite Week 3

Ryan N. Willhite — Tue, 09 Feb 2010 19:00:39 GMT

In-Class Activity:

←Older revision		Revision as of 19:00, 9 February 2010
Line 1:		Line 1:
	==In-Class Activity==		==In-Class Activity==
		+	[[BIOL398-01/S10:Week 3]]

	What I know about HIV		What I know about HIV

Template:SBB10 ConstructionFiles RaffiH sbb33

Raffi Hagopian — Tue, 09 Feb 2010 19:00:13 GMT

New page: '''Construction of Gentamicin resistance gene (sbb33) BglBrick Part''' PCR rh03F/rh05R on pLoxGen4 (576 bp, gp = A) PCR rh04F/rh06R on pLoxGen4 (284 bp, gp = B) ---- PCR rh03...

New page

'''Construction of Gentamicin resistance gene (sbb33) BglBrick Part'''
PCR rh03F/rh05R on pLoxGen4 (576 bp, gp = A)
PCR rh04F/rh06R on pLoxGen4 (284 bp, gp = B)
----
PCR rh03F/rh06R on A+B (bp 833, EcoRI/BamHI)
Sub into pBjk2741-Bca1144 (EcoRI/BamHI, 2170+910, L)
Product is pBjk2741-sbb33 {Promoter.rbs.GenR}
----
rh03F Forward EcoRI for BglBricking GenR ctctgGAATTCatgAGATCTctagcgcgtcgacataagcc
rh04F Removing the BglII site from GenR cgcgtagtgagatAtatatctatgatc
rh05R Removing the BglII site from GenR gatcatagatataTatctcactacgcg
rh06R Reverse BamHI for BglBricking GenR gcaaaGGATCCctagcgcgtcggccgggaag

Ryan N. Willhite Week 4

Ryan N. Willhite — Tue, 09 Feb 2010 18:59:57 GMT

add link to assignment

←Older revision		Revision as of 18:59, 9 February 2010
Line 1:		Line 1:
	==In-Class Activity==		==In-Class Activity==
-		+	[[BIOL398-01/S10:Week 4]]
	===Activity 1, Part 2===		===Activity 1, Part 2===

Line 7:		Line 7:
	* In order to get to the FASTA format, on he NCBI website the displau drop down menu allowed me to view the selected sequences in FASTA format.		* In order to get to the FASTA format, on he NCBI website the displau drop down menu allowed me to view the selected sequences in FASTA format.
	*uploaded file as (.txt), it is the FASTA file sequences from downloading sequences to the local hard drive.		*uploaded file as (.txt), it is the FASTA file sequences from downloading sequences to the local hard drive.
-		+	# [[Media:Wk4sequences.txt\|FASTA sequences]]
	* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.		* Ran into some trouble opening the FASTA file since there was no type it recognized. In order to overcome this issue, i saved as a .txt file extension and then opened it in notepad.

Template:SBB10 ConstructionFiles RaffiH sbb09

Raffi Hagopian — Tue, 09 Feb 2010 18:57:04 GMT

←Older revision		Revision as of 18:57, 9 February 2010
Line 1:		Line 1:
-	'''Construction of sbb09 BglBrick Part'''	+	'''Construction of Tn5 3'TR (sbb09) BglBrick Part'''
	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)		EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
	Product is pBjk2741-sbb09 {Tn5 3'TR}		Product is pBjk2741-sbb09 {Tn5 3'TR}

Image:HIVSequences.txt

Bobak Seddighzadeh — Tue, 09 Feb 2010 18:57:03 GMT

uploaded "[[Image:HIVSequences.txt]]" Four different HIV sequences

New page

KP Ramirez Week 4

Kevin A Paiz-Ramirez — Tue, 09 Feb 2010 18:56:24 GMT

←Older revision		Revision as of 18:56, 9 February 2010
Line 1:		Line 1:
	come up with a question to email about what you felt should be asked in this paper?		come up with a question to email about what you felt should be asked in this paper?
		+
		+
		+	I began by loading up the Markham paper from PubMed then clicking on the nucleotides links. From there I could access GenBank. I noted that the links seemed to be invalid however I was able to access them through a different browser.
		+	==Assignment==
		+	• What was the accession number of the sequence you chose?
		+	*AF089141
		+	• Which subject of the study was that HIV sequence from? Which section of
		+	the record contains information about who the HIV was collected from?
		+
	{{Kevin A Paiz-Ramirez}}		{{Kevin A Paiz-Ramirez}}

Salomon Garcia: Week 4

Salomon Garcia Valencia — Tue, 09 Feb 2010 18:55:37 GMT

Activity 1 Part 1:

←Older revision		Revision as of 18:55, 9 February 2010
Line 6:		Line 6:
	# What oher ways might you have searched?		# What oher ways might you have searched?
	# What other types of related information are available?		# What other types of related information are available?
-		+	[[Image:search 1.jpg\|thumb\|center\|550px\|Pubmed search]]

	# I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.		# I searched for the original paper by typing in the entire title of the research paper into the search box and the window showed the paper that was written in 1998.
	# Another way I could have searched for it was by doing an advanced search and using the authors name on the search.		# Another way I could have searched for it was by doing an advanced search and using the authors name on the search.
	# There were other information that was useful as was the information that described what HIV-1 is.		# There were other information that was useful as was the information that described what HIV-1 is.
-

	====Activity 1 Part 2====		====Activity 1 Part 2====

Template:SBB10 ConstructionFiles RaffiH sbb09

Raffi Hagopian — Tue, 09 Feb 2010 18:55:19 GMT

←Older revision		Revision as of 18:55, 9 February 2010
Line 1:		Line 1:
-	~~<pre>~~	+	'''Construction of sbb09 BglBrick Part'''
-	~~<b>~~Construction ~~File for~~ sbb09 BglBrick Part~~</b>~~	+	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)
-	EIPCR rh01F/rh02R on pBjk2741-Bca1144 (2230 bp, BglII)	+	Product is pBjk2741-sbb09 {Tn5 3'TR}
-	Product is pBjk2741-sbb09 {Tn5 3'TR}	+	----
-	----	+	rh01F EIPCR construction of Tn5 3'TR basic part ccataAGATCTggttgagatgtgtataagagacagtcgacGGATCCtaactcgctcctcag
-	rh01F EIPCR construction of Tn5 3'TR basic part	+	rh02R Reverse BglII oligo for pBjk2741 EIPCR ccaatAGATCTcatGAATTCcacttcag
-	ccataAGATCTggttgagatgtgtataagagacagtcgacGGATCCtaactcgctcctcag	+
-	rh02R Reverse BglII oligo for pBjk2741 EIPCR	+
-	ccaatAGATCTcatGAATTCcacttcag	+
-	~~</pre>~~	+

User:Patricio Velez

Patricio Velez — Tue, 09 Feb 2010 18:54:58 GMT

←Older revision		Revision as of 18:54, 9 February 2010
Line 1:		Line 1:
-	~~<!-- Delete~~ this ~~entire line as part of your first edit of~~ your user page --> ~~{{New~~ user}}	+	Please copy the source code from this page to your user page, fill in the answers and print out a copy for next time.<br>
		+	You do not need to keep the information on your user page once you've printed it out.
		+	==Registration/Questionnaire: 20.109 Spring 2010==

-	==~~Contact Info~~==	+	===Last Name===
-	~~[[Image:OWWEmblem.png\|thumb\|right\|Patricio~~ Velez ~~(an artistic interpretation)]]~~	+	Velez
		+	===First Name===
		+	Patricio

-	*Patricio Velez	+	===Preferred name (if not first)===
-	*MIT	+	PJ
-	*Address 1	+
-	*Address 2	+
-	*City, State, Country etc.	+
-	*[[Special:Emailuser/Patricio Velez\|Email me through OpenWetWare]]	+

-	~~I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from My class., and I've joined because I am in~~ 20.~~109 and the class website is on openwetware..~~	+	===Course/Minor===
		+	Major: Course 20 (Biological Engineering); Potential Minor: 5(Chemistry)
		+	===Year of Graduation===
		+	2012
		+	===Telephone #===
		+	813-541-4025
		+	===Email===
		+	pjvelez@mit.edu
		+	===Potentially Relevant Background===

-	=~~=Education==~~	+	{\| border="1"
-	<!--~~Include info about your educational background~~-->	+	\|Have you taken/are you taking...
-	* Year, PhD, Institute	+	\|Answer yes/no/when
-	* Year, MS, Institute	+	\|-
-	* Year, BS, Institute	+	\|7.05/5.07 (Biochemistry)
		+	\|Yes; Spring 2010
		+	\|-
		+	\|7.06 (Cell Biology)
		+	\|No
		+	\|-
		+	\|7.03 (Genetics)
		+	\|No
		+	\|-
		+	\|7.02 (General Biology Lab)
		+	\| No
		+	\|-
		+	\| 5.310 (General Chemistry Lab)
		+	\|No
		+	\|-
		+	\|}

-	=~~=Research interests==~~	+	<br style="clear:both;"/>
-	~~<!-- Feel free to add brief descriptions to your research interests as well --~~>	+
-	~~# Interest 1~~	+
-	~~# Interest 2~~	+
-	~~# Interest 3~~	+

-	=~~=Publications==~~	+	{\| border="1"
-	~~<!-- Replace the PubMed ID's (~~"~~pmid=#######~~"~~) below~~ with ~~the PubMed ID's for your publications~~. ~~You can add or remove lines as needed -->~~	+	\|Do you have experience with...
-	~~<biblio>~~	+	\|Answer yes/no/type
-	~~#Paper1 pmid=6947258~~	+	\|-
-	~~#Paper2 pmid=13718526~~	+	\|Cell culture (microbial/mammalian/yeast?)
-	// ~~leave a comment about a paper here~~	+	\|No
-	~~#Book1 isbn=0879697164~~	+	\|-
-	~~</biblio>~~	+	\|Molecular biology (electrophoresis, PCR, etc)
		+	\|Yes : Minimal
		+	\|-
		+	\|}

-	==~~Useful links~~==	+	===Please briefly describe any previous laboratory experience===
-	*[[OpenWetWare:~~Welcome\|Introductory tutorial]]~~	+	None
-	*[[~~Help~~\|~~OpenWetWare help pages~~]]	+
		+	===Anything else you would like us to know?===
		+	I look forward to skills and habits required to work in a lab so I can apply them to my future endeavors.
		+
		+	===Commitment to academic integrity===
		+
		+	After you print out this page, please sign your name next to the following statement to indicate your agreement:
		+
		+	''I have read and understood the 20.109 [[20.109(S10):Statement_on_Collaboration_and_Integrity \| statement on collaboration and integrity]].''
		+
		+
		+	Patricio J. Velez

Image:Wk4sequences.txt

Ryan N. Willhite — Tue, 09 Feb 2010 18:54:01 GMT

uploaded "[[Image:Wk4sequences.txt]]" Sequences downloaded in FASTA format to hard drive. A summary of all saved in single file.

New page

Amanda N. Wavrin Week 4

Amanda N. Wavrin — Tue, 09 Feb 2010 18:53:17 GMT

added FASTA example doc

New page

====Activity 1, Part 2: GenBank====
*Accesion number of chosen sequence: AF089135
*This sequence was from subject 3
*The definition tells us that the seguence was from S3V5-4
*[[Media:Sequences.doc|Example FASTA sequences]]

Michael R. Pina Week 4

Michael R. Pina — Tue, 09 Feb 2010 18:53:13 GMT

←Older revision		Revision as of 18:53, 9 February 2010
Line 2:		Line 2:
	*The accession number of the sequence is AF016768.		*The accession number of the sequence is AF016768.
	*The sequence comes from subject 1; the definition section of the record contains this information as well as other information such as which visit.		*The sequence comes from subject 1; the definition section of the record contains this information as well as other information such as which visit.
		+	*The Biology Workbench does not seem the most user friendly, but it works just fine and gets the job done. I was able to align 4 sequences acquired from GenBank without any problems.

←Older revision		Revision as of 19:24, 9 February 2010
Line 1:		Line 1:
	=Computational Part Design=		=Computational Part Design=
		+
		+	==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 14:24, 9 February 2010 (EST)==
		+
		+	===The following protocols are relevant for me:===
		+
		+	[[Template:SBB-Protocols_PCR2 \| Cloning by PCR]]<br>
		+	[[Template:SBB-Protocols_PCR3 \| SOEing PCR]]<br>
		+	[[Template:SBB-PCA \| PCA Gene Synthesis]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Zymo1 \| Regular Zymo Cleanup]]<br>
		+	[[Template:SBB-Protocols_Zymo3 \| Zymo Gel Purification]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Enz2 \| EcoRI/BamHI Digest of PCR Products]]<br>
		+	[[Template:SBB-Protocols_Enz4 \| Ligation of EcoRI/BamHI digests]]<br>
		+	<br>
		+	[[Template:SBB-Protocols_Micro1 \| Transformation by heat-shock]]<br>
		+	[[Template:SBB-Protocols_Micro2 \| Picking of colonies]]<br>
		+	[[Template:SBB-Protocols_Micro3 \| Miniprep purification of DNA]]<br>

	==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 01:45, 4 February 2010 (EST)==		==[[User:Wei-Chun Hu\|Wei-Chun Hu]] 01:45, 4 February 2010 (EST)==