Janet B. Matsen:Useful Links - Revision history

Janet B. Matsen: /* Useful Links */

Janet B. Matsen — Sun, 27 Jan 2013 18:34:25 GMT

Useful Links

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	*[http://www.finnzymes.fi/java_applets/multiple_primer_analyzer.html Finnzyme Primer Dimer Predictor]		*[http://www.finnzymes.fi/java_applets/multiple_primer_analyzer.html Finnzyme Primer Dimer Predictor]
	**Enter yours here see predicted dimers		**Enter yours here see predicted dimers
		+	*[http://partsregistry.org/Help:Plasmids/Nomenclature backbone & origins: naming]
		+	** decipher compatibility between BioBrick vector backbone and other vectors
	*[http://bitesizebio.com/ BitesizeBio]		*[http://bitesizebio.com/ BitesizeBio]
	**They have short but useful articles on lab technique and often include references. I am not a fan of all the advertising.		**They have short but useful articles on lab technique and often include references. I am not a fan of all the advertising.

Janet B. Matsen — Thu, 20 Dec 2012 14:26:04 GMT

Software

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	*APE (A Plasmid Editor; free)		*APE (A Plasmid Editor; free)
	*Mendeley (free)		*Mendeley (free)
		+	*Mathematica (not free)
		+	** [http://www.wolfram.com/learningcenter/tutorialcollection/MathematicsAndAlgorithms/MathematicsAndAlgorithms.pdf Excellent equation solving tutorial ]
	*InkScape (free)		*InkScape (free)
	**Can get beautiful color paletes from [http://colorbrewer2.org/ ColorBrewer]		**Can get beautiful color paletes from [http://colorbrewer2.org/ ColorBrewer]

Janet B. Matsen — Sun, 18 Nov 2012 02:07:38 GMT

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	Back to [[User:Janet B. Matsen\|Janet]]		Back to [[User:Janet B. Matsen\|Janet]]

-	As of 11/2012, I'm not maintaining this list. Instead, I'm posting to [[Lidstrom:Back_Door:Useful_Links\|My lab's links page]], a list curated by myself and [[User:Amanda_L_Smith\|Amanda Smith]].	+	'''As of 11/2012, I'm not maintaining this list.''' Instead, I'm posting to [[Lidstrom:Back_Door:Useful_Links\|My lab's links page]], a list curated by myself and [[User:Amanda_L_Smith\|Amanda Smith]].

	===Useful Links===		===Useful Links===

Janet B. Matsen — Sun, 18 Nov 2012 02:06:39 GMT

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	Back to [[User:Janet B. Matsen\|Janet]]		Back to [[User:Janet B. Matsen\|Janet]]
		+
		+	As of 11/2012, I'm not maintaining this list. Instead, I'm posting to [[Lidstrom:Back_Door:Useful_Links\|My lab's links page]], a list curated by myself and [[User:Amanda_L_Smith\|Amanda Smith]].

	===Useful Links===		===Useful Links===

Janet B. Matsen — Wed, 11 Jul 2012 23:04:54 GMT

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	*InkScape (free)		*InkScape (free)
	**Can get beautiful color paletes from [http://colorbrewer2.org/ ColorBrewer]		**Can get beautiful color paletes from [http://colorbrewer2.org/ ColorBrewer]
		+
		+	== Induction Levels ==
		+	These can help give an idea of how much inducer to add to various inducible promoters. Of course, there are infinite variables that make your circumstances different than these examples, but they probably don't have a huge effect.
		+	*[http://www.expressys.com/main_applications.html expressys] (from Austin Moon)
		+	*[http://openwetware.org/wiki/IGEM:IMPERIAL/2007/Projects/Hrp_System/Parts 2007 iGem team] (from Austin Moon)

Janet B. Matsen — Tue, 10 Jul 2012 13:50:49 GMT

Useful Links

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	** Recomended by Amanda Smith via Rob Egbert		** Recomended by Amanda Smith via Rob Egbert
	** probably accurate within an order of magnitude		** probably accurate within an order of magnitude
-	** If you use the forward engineering mode, check your solution in the reverse engineering mode (include ~ 75 bp on either side of the start codon) and make sure it still agrees with it's solution~~. I have been finding these solutions can differ by an order of magnitude~~.	+	** If you use the forward engineering mode, check your solution in the reverse engineering mode (include ~ 75 bp on either side of the start codon) and make sure it still agrees with it's solution.
	**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!		**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!

Janet B. Matsen — Tue, 10 Jul 2012 13:30:25 GMT

Useful Links

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	** Recomended by Amanda Smith via Rob Egbert		** Recomended by Amanda Smith via Rob Egbert
	** probably accurate within an order of magnitude		** probably accurate within an order of magnitude
		+	** If you use the forward engineering mode, check your solution in the reverse engineering mode (include ~ 75 bp on either side of the start codon) and make sure it still agrees with it's solution. I have been finding these solutions can differ by an order of magnitude.
	**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!		**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!

Janet B. Matsen — Mon, 02 Jul 2012 22:34:31 GMT

Useful Links

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	*[https://salis.psu.edu/software/reverse RBS strength calculator]		*[https://salis.psu.edu/software/reverse RBS strength calculator]
	** Recomended by Amanda Smith via Rob Egbert		** Recomended by Amanda Smith via Rob Egbert
		+	** probably accurate within an order of magnitude
	**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!		**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!

Janet B. Matsen — Mon, 02 Jul 2012 18:16:15 GMT

Useful Links

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	** an E. Coli & Salmonella reference website (originally, this info was published in books)		** an E. Coli & Salmonella reference website (originally, this info was published in books)
	*[https://salis.psu.edu/software/reverse RBS strength calculator]		*[https://salis.psu.edu/software/reverse RBS strength calculator]
-	** Recomended by Amanda Smith ~~(she says the Klavins lab uses a different one)~~	+	** Recomended by Amanda Smith via Rob Egbert
-	**The sequence matters a lot! (If using the Elowitz RBS, the sequence between this part & the ATG matters!	+	**The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!
-	** Elowitz RBS + BioBrick Scar site + ATG --> ~ 14000 units of transcription, I think.	+

	==Equipment==		==Equipment==

Janet B. Matsen — Wed, 27 Jun 2012 18:04:56 GMT

Useful Links

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	*[http://ecosal.org/ EcoSal] !!subscription required!! (I don't have it at UW)		*[http://ecosal.org/ EcoSal] !!subscription required!! (I don't have it at UW)
	** an E. Coli & Salmonella reference website (originally, this info was published in books)		** an E. Coli & Salmonella reference website (originally, this info was published in books)
		+	*[https://salis.psu.edu/software/reverse RBS strength calculator]
		+	** Recomended by Amanda Smith (she says the Klavins lab uses a different one)
		+	**The sequence matters a lot! (If using the Elowitz RBS, the sequence between this part & the ATG matters!
		+	** Elowitz RBS + BioBrick Scar site + ATG --> ~ 14000 units of transcription, I think.

	==Equipment==		==Equipment==