User:Janet B. Matsen

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My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation.  Currently I am helping engineer E. coli to make biofuel precursors from electricity and CO<sub>2</sub>.   
My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation.  Currently I am helping engineer E. coli to make biofuel precursors from electricity and CO<sub>2</sub>.   
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I started the [[Lidstrom|Lidstrom Lab OWW wiki]] and am addicted to posting what I learn!  [[User:Amanda_L_Smith|Amanda Smith]] is significant contributor as well.
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I started the [[Lidstrom|Lidstrom Lab OWW wiki]] and am addicted to posting what I learn!  [[User:Amanda_L_Smith|Amanda Smith]] is significant contributor as well. It has been a lot of fun for me to record what I have learned about lab techniques.  It is also a fun place me to share tips/tricks and experiments that probe how important variables in a protocol are.
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== Research Interests ==
== Research Interests ==
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== Education==
== Education==
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<blockquote>PhD University of Washington, Seattle <br>
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<blockquote>PhD (in progress) University of Washington, Seattle <br>
*Chemical Engineering, expected graduation: 2015
*Chemical Engineering, expected graduation: 2015
*[[Lidstrom| Lidstrom Lab]]
*[[Lidstrom| Lidstrom Lab]]
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*[[Janet B. Matsen:Thesis Project|Personal Notes for Thesis Project]]
*[[Janet B. Matsen:Thesis Project|Personal Notes for Thesis Project]]
*[[Janet B. Matsen:Fruit Foraging at the University of Washington|Fruit Foraging at the University of Washington]]
*[[Janet B. Matsen:Fruit Foraging at the University of Washington|Fruit Foraging at the University of Washington]]
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*[[Janet B. Matsen:Guide to Gibson Assembly|Guide to Gibson Assembly]]
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*[[Janet B. Matsen:Guide to Gibson Assembly|Guide to Gibson Assembly]] (incomplete)
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<br>
</blockquote>
</blockquote>
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== Tools to Share ==
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*[https://www.dropbox.com/s/yntqb2cizfluci7/APE_AnnotationFeatureLibraryCreator.R Ape Annotation Feature Library Creator]
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** This is an R script that converts the info in [https://docs.google.com/spreadsheet/ccc?key=0AlVxrZi130nMdHlsaml2OGFDUW9zRlVBdkRKaXVEbkE#gid=22 my list of primers] into a file that I can use to annotate DNA files in APE with.  It:
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***trims out sequences not intended for sequencing such as Gibson assembly primers
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***makes a label that combines the unique primer number, the melting temperature, and the letter F or R for forward or reverse
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***assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction. 
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***saves the info in the format APE needs, with the date it was generated in the title.
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** This allows me to instantly see where all of the primers I own bind to a DNA sequence for a given project I am working on.  It also allows me to share these primers very easily; by sharing the file it outputs allows my lab mates to instantly see if I have any primers that can be used in their project.  It has been very handy for them!
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** I am happy to help friends modify this script to be useful with their own primer libraries!  No R experience is necessary.
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** Anyone can access my most current primer "Annotation Feature Library" [https://www.dropbox.com/sh/5w53jl3jhbdddvp/iW7cOtZ2Wd here].  You can also see the files used to generate it there.
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== Skills I'm developing ==
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*molecular biology
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*mass spectrometry based metabolomics
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*R & ggplot2
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*Inkscape
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*Gibson cloning

Revision as of 12:22, 1 April 2013


Image:Janet_Matsen.png


Janet B. Matsen

Department of Chemical Engineering
Seattle, Washington

jmatsen@uw.edu

I am a 3rd year Chemical Engineering PhD student at the University of Washington working at Mary Lidstrom's Lab and it is so fun!

My first year was spent investigating methanotrophic metabolism in pure cultures and a model ecosystem in a team that combined transcriptomics, metabolomics, and single-cell observation. Currently I am helping engineer E. coli to make biofuel precursors from electricity and CO2.

I started the Lidstrom Lab OWW wiki and am addicted to posting what I learn! Amanda Smith is significant contributor as well. It has been a lot of fun for me to record what I have learned about lab techniques. It is also a fun place me to share tips/tricks and experiments that probe how important variables in a protocol are.

Contents

Research Interests

  • metabolic engineering
  • synthetic biology
  • transcriptomics
  • chemical engineering

Education

PhD (in progress) University of Washington, Seattle
B.S. University of California, Berkeley
  • Chemical Engineering, 2010

Awards & Activities

My Personal Pages


Tools to Share

  • Ape Annotation Feature Library Creator
    • This is an R script that converts the info in my list of primers into a file that I can use to annotate DNA files in APE with. It:
      • trims out sequences not intended for sequencing such as Gibson assembly primers
      • makes a label that combines the unique primer number, the melting temperature, and the letter F or R for forward or reverse
      • assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction.
      • saves the info in the format APE needs, with the date it was generated in the title.
    • This allows me to instantly see where all of the primers I own bind to a DNA sequence for a given project I am working on. It also allows me to share these primers very easily; by sharing the file it outputs allows my lab mates to instantly see if I have any primers that can be used in their project. It has been very handy for them!
    • I am happy to help friends modify this script to be useful with their own primer libraries! No R experience is necessary.
    • Anyone can access my most current primer "Annotation Feature Library" here. You can also see the files used to generate it there.

Skills I'm developing

  • molecular biology
  • mass spectrometry based metabolomics
  • R & ggplot2
  • Inkscape
  • Gibson cloning
Personal tools