User:Janet B. Matsen: Difference between revisions
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== Tools to Share == | == Tools to Share == | ||
*[https://www.dropbox.com/s/ | *[https://www.dropbox.com/s/yntqb2cizfluci7/APE_AnnotationFeatureLibraryCreator.R Ape Annotation Feature Library Creator] | ||
** 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: | ** 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: | ||
***trims out sequences not intended for sequencing such as Gibson assembly primers | ***trims out sequences not intended for sequencing such as Gibson assembly primers | ||
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***assigns colors in APE that communicate whether it primers in the forward direction or the reverse direction. | ***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. | ***saves the info in the format APE needs, with the date it was generated in the title. | ||
** Here is a [https://www.dropbox.com/s/780e32xer5j3wjo/2013-03-29_Primers_Colored-JanetMatsen.csv sample output file]. | |||
** 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! | ** 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. | ** I am happy to help friends modify this script to be useful with their own primer libraries! No R experience is necessary. | ||
Revision as of 06:52, 29 March 2013
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Department of Chemical Engineering jmatsen@uw.edu
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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.
Research Interests
- metabolic engineering
- synthetic biology
- transcriptomics
- chemical engineering
Education
PhD University of Washington, Seattle
- Chemical Engineering, expected graduation: 2015
- Lidstrom Lab
B.S. University of California, Berkeley
- Chemical Engineering, 2010
Awards & Activities
- 2012 honorable mention for the National Science Foundation's Graduate Research Fellowship Program
- 2011-2012 Outreach Coordinator for the Puget Sound chapter of the American Institute of Chemical Engineers
- 2010-2011 Outreach Coordinator for the University of Washington chapter of the American Chemical Engineering Society
My Personal Pages
- Lab Tips & Tricks
- Open Lab Questions
- Closed Lab Questions
- Best Lab Practices
- Useful Links
- Personal Notes for Thesis Project
- Fruit Foraging at the University of Washington
- Guide to Gibson Assembly (incomplete)
- 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.
- Here is a sample output file.
- 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.
- 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:
Skills I'm developing
- molecular biology
- mass spectrometry based metabolomics
- R & ggplot2
- Inkscape
- Gibson cloning
