Janet B. Matsen:Useful Links

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Back to [[User:Janet B. Matsen|Janet]]
Back to [[User:Janet B. Matsen|Janet]]
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==Useful Links==
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'''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]].
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===Useful Links===
*[http://bionumbers.hms.harvard.edu BioNumbers]
*[http://bionumbers.hms.harvard.edu BioNumbers]
**Save time searching for cell facts such as cellular volume or concentration of ATP
**Save time searching for cell facts such as cellular volume or concentration of ATP
*[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]  
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**Enter yours here & it will show you likely dimers
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**Enter yours here see predicted dimers
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*[http://partsregistry.org/Help:Plasmids/Nomenclature backbone & origins: naming]
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** decipher compatibility between BioBrick vector backbone and other vectors
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*[http://bitesizebio.com/ BitesizeBio]
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**They have short but useful articles on lab technique and often include references.  I am not a fan of all the advertising.
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*[http://www.emolecules.com/ emolecules]
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**See who sells compounds you want to buy.  Will help you shop around & give more options when your default supplier shows a compound as being back-ordered.
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*BenchFly: free science videos
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**[http://www.benchfly.com/video/33/working-with-sterile-technique/ Sample video]: sterile technique
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*[http://ecosal.org/ EcoSal]  !!subscription required!!  (I don't have it at UW)
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** an E. Coli & Salmonella reference website (originally, this info was published in books)
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*[https://salis.psu.edu/software/reverse RBS strength calculator]
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** Recomended by Amanda Smith via Rob Egbert
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** probably accurate within an order of magnitude
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** 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.
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**The sequence matters a lot!  High translation is ~___.  (If using the Elowitz RBS, the sequence between this part & the ATG matters!
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==Equipment==
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*[http://www.bio.davidson.edu/projects/gcat/protocols/NanoDrop_tip.pdf NanoDrop basics] (nucleic acid concentration measurements)
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==Software==
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*APE (A Plasmid Editor; free)
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*Mendeley (free)
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*Mathematica (not free)
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** [http://www.wolfram.com/learningcenter/tutorialcollection/MathematicsAndAlgorithms/MathematicsAndAlgorithms.pdf Excellent equation solving tutorial ]
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*InkScape (free)
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**Can get beautiful color paletes from [http://colorbrewer2.org/ ColorBrewer]
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== Induction Levels ==
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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.
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*[http://www.expressys.com/main_applications.html expressys] (from Austin Moon)
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*[http://openwetware.org/wiki/IGEM:IMPERIAL/2007/Projects/Hrp_System/Parts 2007 iGem team] (from Austin Moon)

Current revision

Back to Janet

As of 11/2012, I'm not maintaining this list. Instead, I'm posting to My lab's links page, a list curated by myself and Amanda Smith.

Contents

Useful Links

  • BioNumbers
    • Save time searching for cell facts such as cellular volume or concentration of ATP
  • Finnzyme Primer Dimer Predictor
    • Enter yours here see predicted dimers
  • backbone & origins: naming
    • decipher compatibility between BioBrick vector backbone and other vectors
  • BitesizeBio
    • They have short but useful articles on lab technique and often include references. I am not a fan of all the advertising.
  • emolecules
    • See who sells compounds you want to buy. Will help you shop around & give more options when your default supplier shows a compound as being back-ordered.
  • BenchFly: free science videos
  • EcoSal  !!subscription required!! (I don't have it at UW)
    • an E. Coli & Salmonella reference website (originally, this info was published in books)
  • RBS strength calculator
    • Recomended by Amanda Smith via Rob Egbert
    • 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.
    • The sequence matters a lot! High translation is ~___. (If using the Elowitz RBS, the sequence between this part & the ATG matters!

Equipment

Software

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.

Personal tools