OpenWetWare - Recent changes [en]

2020(S10) Lecture:week 2

2010-02-09T17:30:36Z

Why are we doing this??:

←Older revision		Revision as of 17:30, 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"

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

20.109(S10):Journal club (Day8)

2010-02-09T17:30:24Z

Methodology/Technology:

←Older revision		Revision as of 17:30, 9 February 2010
(One intermediate revision not shown.)
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	#Vuyisich and Beal. Controlling protein activity with ligand-regulated RNA aptamers. Chem Biol (2002) vol. 9 (8) pp. 907-13		#Vuyisich and Beal. Controlling protein activity with ligand-regulated RNA aptamers. Chem Biol (2002) vol. 9 (8) pp. 907-13
	#Cox and Ellington. Automated selection of anti-protein aptamers. Bioorg Med Chem (2001) vol. 9 (10) pp. 2525-31		#Cox and Ellington. Automated selection of anti-protein aptamers. Bioorg Med Chem (2001) vol. 9 (10) pp. 2525-31
-	#Mi et al. In vivo selection of tumor-targeting RNA motifs. Nat Chem Biol (2010) vol. 6 (1) pp. 22-4 <font color = orange><b>[AK/WF/Orange]</b></font color>	+	#Mi et al. In vivo selection of tumor-targeting RNA motifs. Nat Chem Biol (2010) vol. 6 (1) pp. 22-4 <font color = orange><b>[AK/WF/Orange]</b></font color> <font color = blue><b>[PL/TR/Blue]</b></font color>
		+
	== Headline text ==		== Headline text ==

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	#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9		#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9
	#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6 <font color = pink><b>[TS/MW/Pink]</b></font color>		#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6 <font color = pink><b>[TS/MW/Pink]</b></font color>
-	#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 ~~<font color = blue><b>[PL/TR/Blue]</b></font color>~~	+	#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78
	#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123		#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123
	#Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23		#Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23

User talk:Nicholas Swenson

2010-02-09T17:29:37Z

New page

Hello, Nicholas Swenson! 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:Nicholas Swenson|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!

== Personal/Lab Info ==
We have gone ahead and filled in some information you provided us in your membership application on your [[User:Nicholas Swenson|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:Nicholas Swenson|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:Nicholas Swenson|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.

User:Nicholas Swenson

2010-02-09T17:29:37Z

New page

{{New user}}

==Contact Info==
[[Image:OWWEmblem.png|thumb|right|Nicholas Swenson (an artistic interpretation)]]

*Nicholas Swenson
*MIT
*Address 1
*Address 2
*City, State, Country etc.
*[[Special:Emailuser/Nicholas Swenson|Email me through OpenWetWare]]

I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from class, and I've joined because class.

==Education==

* Year, PhD, Institute
* Year, MS, Institute
* Year, BS, Institute

==Research interests==

# Interest 1
# Interest 2
# Interest 3

==Publications==

<biblio>
#Paper1 pmid=6947258
#Paper2 pmid=13718526
// leave a comment about a paper here
#Book1 isbn=0879697164
</biblio>

==Useful links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[Help|OpenWetWare help pages]]

20.109(S10):Journal club (Day8)

2010-02-09T17:29:12Z

Applications:

←Older revision		Revision as of 17:29, 9 February 2010
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	#Mayer et al. An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro. RNA (2008) vol. 14 (3) pp. 524-34		#Mayer et al. An RNA molecule that specifically inhibits G-protein-coupled receptor kinase 2 in vitro. RNA (2008) vol. 14 (3) pp. 524-34
	#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9		#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9
-	#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6	+	#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6 <font color = pink><b>[TS/MW/Pink]</b></font color>
	#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 <font color = blue><b>[PL/TR/Blue]</b></font color>		#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 <font color = blue><b>[PL/TR/Blue]</b></font color>
	#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123		#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123

KP Ramirez Week 3

2010-02-09T17:23:42Z

Outline:

←Older revision		Revision as of 17:23, 9 February 2010
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	'''Figures & Table'''		'''Figures & Table'''
	*Figure 1		*Figure 1
-	Indicates the diversity, divergence and cell count for the 15 individuals	+	Indicates the diversity, divergence and cell count for the 15 individuals. Presents the divergence of the viral variance from the initial visit. The CD4 T cell count lay across the vertical axis and presented the separation between the progressors. Presented steady progression for the moderate progressors. Presents an inverse relationship.
	*Figure 2		*Figure 2
	Indicates the "mean slope" of diversity and differences of each progressor category and indicates significant differences.		Indicates the "mean slope" of diversity and differences of each progressor category and indicates significant differences.

20.109(S10):Journal club (Day8)

2010-02-09T17:23:39Z

Applications:

←Older revision		Revision as of 17:23, 9 February 2010
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	#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9		#Homann et al. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen (2006) vol. 9 (7) pp. 491-9
	#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6		#An et al. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA (2006) vol. 12 (5) pp. 710-6
-	#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78	+	#Hicke et al. Tumor targeting by an aptamer. J Nucl Med (2006) vol. 47 (4) pp. 668-78 <font color = blue><b>[PL/TR/Blue]</b></font color>
	#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123		#Cerchia et al. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) vol. 3 (4) pp. e123
	#Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23		#Collett et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal Biochem (2005) vol. 338 (1) pp. 113-23
Line 78:		Line 78:
	\|-		\|-
	\|4		\|4
-	\|	+	\|Pei Lin
	\|		\|
	\|Alicia Kaestli		\|Alicia Kaestli

IC Bioinfs/Project1/Tomcat

2010-02-09T17:00:55Z

tUTORIAL LINKS...:

←Older revision		Revision as of 17:00, 9 February 2010
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	[[Image:Sample_servlet1.jpg]]<br>		[[Image:Sample_servlet1.jpg]]<br>
	==tUTORIAL LINKS...==		==tUTORIAL LINKS...==
		+	*[http://www.roseindia.net/flex/compiling_flex_on_eclipse.shtml Compiling FLEX in eclipse]
	*[http://www.roseindia.net/servlets/index.shtml Index of servlet tutorials]		*[http://www.roseindia.net/servlets/index.shtml Index of servlet tutorials]
	*[http://docstore.mik.ua/orelly/java-ent/servlet/ch05_03.htm yet more tutorials on java servlet programming]		*[http://docstore.mik.ua/orelly/java-ent/servlet/ch05_03.htm yet more tutorials on java servlet programming]
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	*[http://web.bvu.edu/faculty/schweller/internetprog/classForNameDemo.htm How servlets talk to databases...]		*[http://web.bvu.edu/faculty/schweller/internetprog/classForNameDemo.htm How servlets talk to databases...]
	*[http://www.roseindia.net/servlets/databaseconnectionservlet.shtml Another link to connect servlet to mysql]		*[http://www.roseindia.net/servlets/databaseconnectionservlet.shtml Another link to connect servlet to mysql]
		+
	==Servlet on hash tables...==		==Servlet on hash tables...==
	*[http://en.wikipedia.org/wiki/Hash_tabe What is a hash table]		*[http://en.wikipedia.org/wiki/Hash_tabe What is a hash table]

User:Anthony Salvagno/Notebook/Research/2010/02/09/Tethering prior to BPS2010

2010-02-09T16:55:53Z

How to Sonciate Beads in our Sonicator:

←Older revision		Revision as of 16:55, 9 February 2010
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	[[Category:Ant Tethering]]I am making this page a day early so I can get a good jump tomorrow on getting this done in the am.		[[Category:Ant Tethering]]I am making this page a day early so I can get a good jump tomorrow on getting this done in the am.
	==Procedure==		==Procedure==
		+	===How to Sonciate Beads in our Sonicator===
		+	According to sources, beads are properly sonicated when you see little splashes on the side walls of the microcentrifuge tube. Here is what I did and what got me results:
		+	*Water heigh halfway between min and max - no splashes
		+	*Messed with tube height in water - no splashes
		+	*Water level at minimum with tips of tubes barely in water - getting some splashes
		+	It seems that last option works the best. I am giving up for now because I think the transducer is heating the water. I sonicated for a total of 12 min messing around with the above options. I will try again another time.
		+
		+	===Protocol===
	{{ShowGoogleExcel\|id=tew-yWtbyz9c3O52ly6o-4g\|width=500\|height=300}}		{{ShowGoogleExcel\|id=tew-yWtbyz9c3O52ly6o-4g\|width=500\|height=300}}
		+
	==Results==		==Results==
	I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...		I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...

IC Bioinfs/Project1/toydatabase

2010-02-09T16:30:24Z

Toy Database:

←Older revision		Revision as of 16:30, 9 February 2010
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	=Toy Database=		=Toy Database=

-	An SQL database created from the DAS and FASTA output of the MIT Parts Registry.	+	An SQL database created from the [http://partsregistry.org/Registry_API DAS and FASTA output] of the MIT Parts Registry.

User:Karmella Haynes/Notebook/Polycomb project/2010/02/09

2010-02-09T16:21:06Z

02/09/10:

←Older revision		Revision as of 16:21, 9 February 2010
Line 8:		Line 8:
	==02/09/10==		==02/09/10==
	<!-- Precede each finished task with a checkmark ✓ -->		<!-- Precede each finished task with a checkmark ✓ -->
-	* U2OS Flp-in T-REx: add dox to Dox+ wells (6-well plate from 2/08)	+	* ✓ U2OS Flp-in T-REx: add dox to Dox+ wells (6-well plate from 2/08)
-	* RT-PCR: Optimization on new cDNA samples	+
	* Transfection: Gal4-EED constructs in HEK293 luc reporter line		* Transfection: Gal4-EED constructs in HEK293 luc reporter line
		+	* Polycomb-ATF lines: frozen stocks for 90% confluent plats (3 total)

		+	----
		+	'''Transfection'''<br>
		+	> HEK293 cells + Gal4-EED constructs (KAH139, 140, 141/V0201)<br>
		+	> Use Fugene, 24-well format<br>
		+	> Serial dilutions of plasmids: 800 - 25 ng in 5 μL<br>
		+	--> Start with 1600 ng in 10 μL OptiMEM
		+	{\| class="wikitable" border="0" cellspacing="5"
		+	\| <u>Plasmid</u> \|\| <u>ng/μL</u> \|\| <u>Add (μL)...</u> \|\| <u>to OptiMEM (μL)</u>
		+	\|-
		+	\| 1. KAH139/V0201 \|\| 454.2 \|\| 3.5 \|\| 7.5
		+	\|-
		+	\| 2. KAH140/V0201 \|\| 342.3 \|\| 4.7 \|\| 5.3
		+	\|-
		+	\| 3. KAH141/V0201 \|\| 388.8 \|\| 4.1 \|\| 5.9
		+	\|}
		+	--> Add 5 μL plasmid to 5 μL OptiMEM for each dilution step
		+
		+	{\| class="wikitable" border="0" cellspacing="5" <!-- Transfection table -->
		+	\|-
		+	\| <u>Wells</u> \|\| <u>Plasmid</u> \|\| <u>DNA</u> \|\| <u>Volume</u> \|\| <u>Fugene</u> \|\| <u>Opti-MEM</u>
		+	\|-
		+	\| 1-6 \|\| KAH139/V0201 \|\| 25, 50, 100, 200, 400, 800 ng \|\| 5.0 μL \|\| 1.8 μL \|\| 18.2 μL
		+	\|-
		+	\| 7-12 \|\| KAH140/V0201 \|\| " \|\| " \|\| " \|\| "
		+	\|-
		+	\| 13-18 \|\| KAH141/V0201 \|\| " \|\| " \|\| " \|\| "
		+	\|-
		+	\| 19-24 \|\| no DNA \|\| " \|\| " \|\| " \|\| "
		+	\|}
		+
		+	> Master mix: 90 μL Fugene + 910 μL Opti-MEM --> R.T/ 5 min. <br>
		+	> Add 20 μL Fugene mix to DNA --> R.T./ 20 min. <br>
		+	> Add 25 μL complexes to each well (1 ml med. each); Grow cells at 37°C <br>
		+	> Assay Luc after 18-24 hours

Manalis:Orders

2010-02-09T16:19:00Z

Orders Placed, to be processed:

←Older revision		Revision as of 16:19, 9 February 2010
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	*12/18 (rec 1/5), Edmund Optics (filter), $1,675.00 + s&h, acct 6918047 --Francisco 10:05, 05 January 2010 (EDT)		*12/18 (rec 1/5), Edmund Optics (filter), $1,675.00 + s&h, acct 6918047 --Francisco 10:05, 05 January 2010 (EDT)
	*01/05 (rec 1/8), Thorlabs, $799.72, acct 6918047 --Francisco 09:15, 08 January 2010 (EDT)		*01/05 (rec 1/8), Thorlabs, $799.72, acct 6918047 --Francisco 09:15, 08 January 2010 (EDT)
-	*01/18 (rec -/-), Digikey, $320.39, acct 6918047 --Francisco 18:50, 18 January 2010 (EDT)	+	*01/18 (rec 2/8), Digikey, $320.39, acct 6918047 --Francisco 18:50, 18 January 2010 (EDT)
	*01/19 (rec 1/25), Upchurch, $823.73, acct 6918047 --Francisco 18:50, 18 January 2010 (EDT)		*01/19 (rec 1/25), Upchurch, $823.73, acct 6918047 --Francisco 18:50, 18 January 2010 (EDT)
-	*01/27 (rec -/-), VWR, $206.72, acct 6919767 --Francisco 18:50, 18 January 2010 (EDT)	+	*01/27 (rec 2/8), VWR, $206.72, acct 6919767 --Francisco 18:50, 18 January 2010 (EDT)
-	*02/04 (rec -/-), Thorlabs $403.92, acct 6919767 --[[User:Francisco Feijo Delgado\|Francisco]] 18:25, 4 February 2010 (EST)	+	*02/04 (rec 2/8), Thorlabs $403.92, acct 6919767 --[[User:Francisco Feijo Delgado\|Francisco]] 18:25, 4 February 2010 (EST)

	==To Be Ordered==		==To Be Ordered==

IC Bioinfs/Project1/toydatabase

2010-02-09T16:17:53Z

Toy Database:

←Older revision		Revision as of 16:17, 9 February 2010
Line 9:		Line 9:
	The toy database has been established on codon.		The toy database has been established on codon.

-	Database name: '''msc_09_das'''	+	*Database name: '''msc_09_das'''
-	Username/password: as above.	+	*Username/password: as above.
-	Host name: db-bss.lesc.doc.ic.ac.uk	+	*Host name: db-bss.lesc.doc.ic.ac.uk

	===Access Via Codon===		===Access Via Codon===
Line 23:		Line 23:
	At the prompt:		At the prompt:

-	mysql -u msc_09_das -p -h db-bss.lesc.doc.ic.ac.uk	+	mysql msc_09_das -u msc_09_das -p -h db-bss.lesc.doc.ic.ac.uk

User:Nuri Purswani/Notebook/ICBioinfp1/2010/02/08

2010-02-09T16:16:21Z

AIM- HOW DO OUR COMPONENTS CONNECT?::

←Older revision		Revision as of 16:16, 9 February 2010
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	*NURI: JSPs.Connection - we talk Geraint.		*NURI: JSPs.Connection - we talk Geraint.

		+	==Other==

		+	Zabeen: I updated the toy database schema [http://openwetware.org/wiki/IC_Bioinfs/Project1/toydatabase#Version_2]. Huntley has granted us some webspace for our database on codon. Tables have been created and populated with data [http://openwetware.org/wiki/IC_Bioinfs/Project1/toydatabase#Online_Database].

	<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

User:Anthony Salvagno/Notebook/Research/2010/02/09/Tethering prior to BPS2010

2010-02-09T16:15:27Z

Results:

←Older revision		Revision as of 16:15, 9 February 2010
Line 5:		Line 5:
	I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...		I definitely need a smartphone or maybe a live feed note taker program. Basically I don't want to drag the laptop around with me everywhere I need to to be able to get to take notes on OWW. Maybe I should look into getting the Droid asap, or maybe we can get a tablet pc soon. The iPad is a let down, but maybe the courier will be for real and awesome. Anyways...
	:[[User:Steven J. Koch\|Steve Koch]] 00:50, 9 February 2010 (EST): What about the iphone that doesn't have a phone? (can't rememember what it's called, itouch?). How expensive are those?		:[[User:Steven J. Koch\|Steve Koch]] 00:50, 9 February 2010 (EST): What about the iphone that doesn't have a phone? (can't rememember what it's called, itouch?). How expensive are those?
		+	==In Other News==
		+	I had this weird dream last night that I had to write a bunch of scripts for windows. One of which was the turn pictures b&w and invert them. Another one was to add gaussian blur to photos. There were more, but I can't remember what other scripts I had to write. I do want to do all this, but I need time and right now, I do not have this. After BPS though... we'll see!

Nagrath:People

2010-02-09T16:14:52Z

←Older revision		Revision as of 16:14, 9 February 2010
Line 31:		Line 31:

	Nadege Bellance		Nadege Bellance
		+
		+	PhD, Inserm, France

	'''Email:''' nvb1<at>rice.edu		'''Email:''' nvb1<at>rice.edu
Line 36:		Line 38:
	Thasni Karedath		Thasni Karedath

-	PhD Rajiv Gandhi Centre for Biotechnology, India	+	PhD, Rajiv Gandhi Centre for Biotechnology, India

	'''Email:''' tk9<at>rice.edu		'''Email:''' tk9<at>rice.edu

IC Bioinfs/Project1/toydatabase

2010-02-09T16:12:46Z

Toy Database:

←Older revision		Revision as of 16:12, 9 February 2010
Line 5:		Line 5:


-	==~~Codon~~==	+	==Online Database==

-	The toy database has been established on codon~~, under the~~ name: '''msc_09_das'''.	+	The toy database has been established on codon.
-	~~To access it, login~~ to your codon account, then enter the following command at the prompt:	+
		+	Database name: '''msc_09_das'''
		+	Username/password: as above.
		+	Host name: db-bss.lesc.doc.ic.ac.uk
		+
		+	===Access Via Codon===
		+
		+	Login to your codon account, then enter the following command at the prompt:

	mysql msc_09_das -u msc_09_das -p		mysql msc_09_das -u msc_09_das -p

-	~~The password is~~ the ~~same as the database name~~.	+	===Access via Other Servers===
		+
		+	At the prompt:
		+
		+	mysql -u msc_09_das -p -h db-bss.lesc.doc.ic.ac.uk

SBB10IndivCombined

2010-02-09T16:07:32Z

←Older revision		Revision as of 16:07, 9 February 2010
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	{{SBB09Indiv-ChrisAnderson}}<br>		{{SBB09Indiv-ChrisAnderson}}<br>
-	~~[[Template:SBB09Indiv-ChrisAnderson]]~~
	{{SBB10Indiv-11097}}<br>		{{SBB10Indiv-11097}}<br>
	{{SBB10Indiv-11956}}<br>		{{SBB10Indiv-11956}}<br>

Template:SBB09Indiv-ChrisAnderson

2010-02-09T16:07:09Z

←Older revision		Revision as of 16:07, 9 February 2010
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	'''Chris Anderson'''<br>		'''Chris Anderson'''<br>
-	Assistant Professor in UC Berkeley's Department of Bioengineering and instructor of SynBio Bootcamp (aka BioE140L). For more information about my lab, visit our website at andersonlab.qb3.berkeley.edu.	+	Assistant Professor in UC Berkeley's Department of Bioengineering and instructor of SynBio Bootcamp (aka BioE140L). For more information about my lab, visit our website at http://andersonlab.qb3.berkeley.edu

SBB10IndivCombined

2010-02-09T16:06:11Z

←Older revision		Revision as of 16:06, 9 February 2010
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	{{SBB09Indiv-ChrisAnderson}}<br>		{{SBB09Indiv-ChrisAnderson}}<br>
		+	[[Template:SBB09Indiv-ChrisAnderson]]
	{{SBB10Indiv-11097}}<br>		{{SBB10Indiv-11097}}<br>
	{{SBB10Indiv-11956}}<br>		{{SBB10Indiv-11956}}<br>

Yeo lab:meetings

2010-02-09T15:53:46Z

←Older revision		Revision as of 15:53, 9 February 2010
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	\|1/22/10 \|\|''9-10:30AM'' \|\|RHPH 554 \|\| Journal club (Emily)		\|1/22/10 \|\|''9-10:30AM'' \|\|RHPH 554 \|\| Journal club (Emily)
	\|-		\|-
-	\|2/12/10 \|\|9-10:30AM \|\|''JNSN (Nursing) B002'' \|\| Journal club (Basma)	+	\|2/12/10 \|\|9-10:30AM \|\|JNSN (Nursing) B002 \|\| Journal club (Basma)
	\|-		\|-
-	\|2/26/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Yan)	+	\|2/26/10 \|\|9-10:30AM \|\|JNSN (Nursing) B002 \|\| Journal club (Yan)
	\|-		\|-
	\|3/12/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Gaurav)		\|3/12/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Gaurav)
	\|-		\|-
-	\|3/26/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Min)	+	\|3/26/10 \|\|9-10:30AM \|\|JNSN (Nursing) B002\|\| Journal club (Min)
	\|-		\|-
-	\|4/9/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Hillary)	+	\|4/9/10 \|\|9-10:30AM \|\|JNSN (Nursing) B002\|\| Journal club (Hillary)
	\|-		\|-
	\|4/23/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Karen)		\|4/23/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Karen)

20.109(S10):Purify aptamer-encoding DNA (Day2)

2010-02-09T15:52:58Z

Part 1: Run PCR products on gel:

←Older revision		Revision as of 15:52, 9 February 2010
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	\|-		\|-
	\| 1		\| 1
-	\| [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (15 μL)	+	\| [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (load 15 μL)
	\| 6		\| 6
-	\| [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (15 μL)	+	\| [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (load 15 μL)
	\|-		\|-
	\| 2		\| 2

Yeo lab:meetings

2010-02-09T15:52:51Z

←Older revision		Revision as of 15:52, 9 February 2010
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	\|2/12/10 \|\|9-10:30AM \|\|''JNSN (Nursing) B002'' \|\| Journal club (Basma)		\|2/12/10 \|\|9-10:30AM \|\|''JNSN (Nursing) B002'' \|\| Journal club (Basma)
	\|-		\|-
-	\|2/26/10 \|\|9-10:30AM \|\|~~TBA~~ \|\| Journal club (Yan)	+	\|2/26/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Yan)
	\|-		\|-
	\|3/12/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Gaurav)		\|3/12/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Gaurav)
	\|-		\|-
-	\|3/26/10 \|\|9-10:30AM \|\|~~TBA~~ \|\| Journal club (Min)	+	\|3/26/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Min)
	\|-		\|-
-	\|4/9/10 \|\|9-10:30AM \|\|~~TBA~~ \|\| Journal club (Hillary)	+	\|4/9/10 \|\|9-10:30AM \|\|'JNSN (Nursing) B002'' \|\| Journal club (Hillary)
	\|-		\|-
	\|4/23/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Karen)		\|4/23/10 \|\|9-10:30AM \|\|RHPH 554 \|\| Journal club (Karen)

User:Maximilian Peters/TRPharmacalogy

2010-02-09T15:44:57Z

New page: =List of pharmacological activators and inhibitors of Transient Receptor Potential ion channels=

New page

=List of pharmacological activators and inhibitors of Transient Receptor Potential ion channels=

User:Maximilian Peters

2010-02-09T15:44:24Z

←Older revision		Revision as of 15:44, 9 February 2010
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	I learned about [[OpenWetWare]] from google, and I've joined because Learn and contribute.		I learned about [[OpenWetWare]] from google, and I've joined because Learn and contribute.
-	==~~Protocols~~==	+	==Pharmacology of TRP channels==
-		+	[[User:Maximilian_Peters/TRPharmacalogy\|List of antagonists and agonists of TRP channels]]
	==Useful Links==		==Useful Links==
	===Protein-Protein interaction prediction servers===		===Protein-Protein interaction prediction servers===

BIOL398-01/S10:Week 4

2010-02-09T15:40:26Z

week 4 assignment started

New page

{{BIOL398-01/S10}}

<div style="padding: 10px; width: 720px; border: 5px solid #000000;">

{{BIOL398-01/S10:Assignment|week=4|due date=February 15|link=[[BIOL398-01/S10:HIV Evolution | HIV Evolution]]}}

* More specifically, record your notes and answer the questions for the Week 4 [[BIOL398-01/S10:HIV_Evolution#In-class_Activity | In-class Activity]] on your individual journal page.

</div>

BIOL398-01/S10

2010-02-09T15:38:49Z

Schedule: added links to week 4 assignment and class journal

←Older revision		Revision as of 15:38, 9 February 2010
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	[[BIOL398-01/S10:HIV Evolution \| HIV Evolution Project]]		[[BIOL398-01/S10:HIV Evolution \| HIV Evolution Project]]
-	\| Week 4 Assignment	+	\| [[BIOL398-01/S10:Week 4 \| Week 4 Assignment]]

	''Due midnight 2/15''		''Due midnight 2/15''
		+
		+	[[BIOL398-01/S10:Class Journal Week 4]]
	\|--		\|--
	\| '''5'''		\| '''5'''

BIOL398-01/S10:HIV Evolution

2010-02-09T15:37:36Z

un-commented week 4 activity

←Older revision		Revision as of 15:37, 9 February 2010
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	Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.		Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

-	~~<!--~~== Week 4 ==	+	== Week 4 ==

	After Journal Club, you will work with the ''Exploring HIV Evolution'' handout, given out in class on 2/2/10 (an electronic copy of this handout is available on the [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect site]).		After Journal Club, you will work with the ''Exploring HIV Evolution'' handout, given out in class on 2/2/10 (an electronic copy of this handout is available on the [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect site]).
Line 122:		Line 122:
	* For Week 5, you will be working with a partner/group to carry out an HIV Evolution Research project (as described in Activity 3). You should be thinking about questions that you would like to answer in using the Markham et al. (1998) data.		* For Week 5, you will be working with a partner/group to carry out an HIV Evolution Research project (as described in Activity 3). You should be thinking about questions that you would like to answer in using the Markham et al. (1998) data.

-	== Week 5 ==	+	<!--== Week 5 ==

	== Week 6 ==-->		== Week 6 ==-->

BIOL398-01/S10

2010-02-09T15:36:32Z

Announcements: updated seminars and took down old announcements

User:Stephanie Senna

2010-02-09T15:33:44Z

←Older revision		Revision as of 15:33, 9 February 2010
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-	~~<!-- Delete this entire line as part of your first edit of your user page --> {{New user}}~~	+	===Registration/Questionnaire: 20.109 Spring 2010===

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

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

-	~~I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from From my instructor, and I've joined because For a class~~.	+	===Course/Minor===
		+	Major: Course 20 (Biological Engineering)
		+	===Year of Graduation===
		+	2012
		+	===Telephone #===
		+	650-238-7668
		+	===Email===
		+	senna@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)
		+	\|Yes; Fall 2009
		+	\|-
		+	\|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~~	+	\|Yes
-	~~#Book1 isbn~~=~~0879697164~~	+	\|-
-	~~</biblio>~~	+	\|Molecular biology (electrophoresis, PCR, etc)
		+	\|Yes
		+	\|-
		+	\|}
		+
		+	===Please briefly describe any previous laboratory experience===
		+	I have worked as a UROP in the Jacks Lab (Koch Institute for Integrative Cancer Research) since Fall 2008. My previous work includes some ImmunoHistoChemistry work, mammalian cell culture (derived from mice small cell lung cancer), maintaining the rodents in the lab, and some molecular biology techniques (genotyping; DNA extraction, PCR, gel electrophoresis). My current project is to study a potential gene involved in the formation and metastases of small cell lung cancer.
		+
		+	===Anything else you would like us to know?===
		+	I want to be a doctor one day! :)
		+
		+	===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]].''
		+
		+
		+	Stephanie Senna

	==Useful links==		==Useful links==
	*[[OpenWetWare:Welcome\|Introductory tutorial]]		*[[OpenWetWare:Welcome\|Introductory tutorial]]
	*[[Help\|OpenWetWare help pages]]		*[[Help\|OpenWetWare help pages]]

User:Jenny Zhou

2010-02-09T15:13:05Z

←Older revision		Revision as of 15:13, 9 February 2010
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-	~~<!-- Delete this entire line as part of your first edit of your user page --> {{New user}}~~

	==Contact Info==		==Contact Info==
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	I currently also work in the Griffith Lab at MIT. I study the migration of human bone marrow-derived, multipotential stromal cells (MSCs).		I currently also work in the Griffith Lab at MIT. I study the migration of human bone marrow-derived, multipotential stromal cells (MSCs).
-

User:Karmella Haynes/Notebook/Polycomb project/2010/02/09

2010-02-09T15:04:55Z

02/09/10:

New page

{|{{table}} width="800"
|-
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#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"|

==02/09/10==

* U2OS Flp-in T-REx: add dox to Dox+ wells (6-well plate from 2/08)
* RT-PCR: Optimization on new cDNA samples
* Transfection: Gal4-EED constructs in HEK293 luc reporter line


|}

__NOTOC__

User:Jacqueline Soegaard

2010-02-09T14:35:23Z

←Older revision		Revision as of 14:35, 9 February 2010
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	*[[OpenWetWare:Welcome\|Introductory tutorial]]		*[[OpenWetWare:Welcome\|Introductory tutorial]]
	*[[Help\|OpenWetWare help pages]]		*[[Help\|OpenWetWare help pages]]
		+
		+
		+	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==
		+
		+	===Last Name===
		+	Soegaard
		+	===First Name===
		+	Jacqueline
		+
		+	===Preferred name (if not first)===
		+
		+	===Course/Minor===
		+	Major: Course 20 (Biological Engineering); Potential Minor: Management Science in Course 15, French
		+	===Year of Graduation===
		+	2012
		+	===Telephone #===
		+	787.548.7440
		+	===Email===
		+	jmsoe@mit.edu
		+	===Potentially Relevant Background===
		+
		+	{\| border="1"
		+	\|Have you taken/are you taking...
		+	\|Answer yes/no/when
		+	\|-
		+	\|7.05/5.07 (Biochemistry)
		+	\|No
		+	\|-
		+	\|7.06 (Cell Biology)
		+	\|No
		+	\|-
		+	\|7.03 (Genetics)
		+	\|Yes; Spring 2010
		+	\|-
		+	\|7.02 (General Biology Lab)
		+	\| No
		+	\|-
		+	\| 5.310 (General Chemistry Lab)
		+	\| No
		+	\|-
		+	\|}
		+
		+	<br style="clear:both;"/>
		+
		+	{\| border="1"
		+	\|Do you have experience with...
		+	\|Answer yes/no/type
		+	\|-
		+	\|Cell culture (microbial/mammalian/yeast?)
		+	\|Yes, mammalian.
		+	\|-
		+	\|Molecular biology (electrophoresis, PCR, etc)
		+	\|Yes, PCR, electrophoresis, ELISA.
		+	\|-
		+	\|}
		+
		+	===Please briefly describe any previous laboratory experience===
		+	I worked at the Broad Institute during a summer genomics course as part of the MIT MITES program. Last semester I UROPed at the Khademhosseini Lab, where I worked on a project which aimed at designing a chip device for detecting cardiotoxicity using a miniaturized ELISA and in-chip cell cultures.
		+
		+	===Anything else you would like us to know?===
		+	I have NEVER seen such a gorgeous lab before!
		+
		+	===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]].''
		+
		+
		+	Jing Jing Gong

←Older revision		Revision as of 15:36, 9 February 2010
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	== Announcements ==		== Announcements ==

-	* I've answered your questions posted on my [[User_talk:Kam D. Dahlquist \| user talk page]]. Please take a look! ''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 23:20, 27 January 2010 (EST)''	+	<!--* I've answered your questions posted on my [[User_talk:Kam D. Dahlquist \| user talk page]]. Please take a look! ''— [[User:Kam D. Dahlquist\|Kam D. Dahlquist]] 23:20, 27 January 2010 (EST)''
-	* Bring the ''Bioinformatics for Dummies'' book to class on Tuesday 2/2/2010.	+	* Bring the ''Bioinformatics for Dummies'' book to class on Tuesday 2/2/2010.-->
	* Record your Windows and Mac tips & tricks in the course [[BIOL398-01/S10:Help#Tips_.26_Tricks \| Help page]].		* Record your Windows and Mac tips & tricks in the course [[BIOL398-01/S10:Help#Tips_.26_Tricks \| Help page]].
-	* The Week 1 point assignments are available in the [https://mylmuconnect.lmu.edu/ MyLMUConnect] Grade Center under "Week 1". Feedback on your Week 1 assignments are available on your respective User_talk pages.	+	<!--* The Week 1 point assignments are available in the [https://mylmuconnect.lmu.edu/ MyLMUConnect] Grade Center under "Week 1". Feedback on your Week 1 assignments are available on your respective User_talk pages. -->

	=== Upcoming Seminars ===		=== Upcoming Seminars ===
Line 17:		Line 17:
	<!--* '''Thursday, January 21, 12:15PM, Seaver 200:''' Kristopher B. Karsten, Ph.D., ''Integrating behavior, physiology, and evolution: an example using a short-lived chameleon from Madagascar''		<!--* '''Thursday, January 21, 12:15PM, Seaver 200:''' Kristopher B. Karsten, Ph.D., ''Integrating behavior, physiology, and evolution: an example using a short-lived chameleon from Madagascar''
	* '''Thursday, January 28, 12:15PM, Seaver 200:''' Dr. Peter Zani, ''Connecting the physiological and ecological responses of lizards to climate change''		* '''Thursday, January 28, 12:15PM, Seaver 200:''' Dr. Peter Zani, ''Connecting the physiological and ecological responses of lizards to climate change''
-	* '''Tuesday, February 2, 12:15PM, Seaver 200:''' Dr. Heather Watts, ''How environment shapes reproduction: Insights from field and laboratory studies,'' ~~-->~~	+	* '''Tuesday, February 2, 12:15PM, Seaver 200:''' Dr. Heather Watts, ''How environment shapes reproduction: Insights from field and laboratory studies,''
-	* '''Thursday, February 4, 12:15PM, Seaver 200:''' Dr. Mark Running, ''Lipid Modification of Plant Proteins: Mechanism and Function'', ~~pizza lunch will be provided for students that meet with the speaker after the seminar in Seaver 202.~~	+	* '''Thursday, February 4, 12:15PM, Seaver 200:''' Dr. Mark Running, ''Lipid Modification of Plant Proteins: Mechanism and Function'', -->
-	* '''Tuesday, February 9, 12:15PM, Seaver 200:''' ~~Biology Department Seminar~~.	+	* '''Tuesday, February 9, 12:15PM, Seaver 200:''' Dr. A.J. Baucum, ''Identification and validation of novel
		+	spinophilin-associated proteins in rodent striatum using an enhanced ex vivo proteomics approach, lunch will be provided for students that meet with the speaker after the seminar in Seaver 202.
	* '''Thursday, February 11, 12:15PM, Seaver 200:''' Biology Department Seminar.		* '''Thursday, February 11, 12:15PM, Seaver 200:''' Biology Department Seminar.
	* '''Tuesday, February 16, 12:15PM, Seaver 200:''' Biology Department Seminar.		* '''Tuesday, February 16, 12:15PM, Seaver 200:''' Biology Department Seminar.