Difference between revisions of "Lidstrom:Back Door:Useful Links"

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(Protein Tools)
(Protein Tools)
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**[http://www.pymol.org/ Pymol]
**[http://www.pymol.org/ Pymol]
** tutorial: [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners]
** tutorial: [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners]
* tutorial: [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org]
** concise less basic review
** tips/examples: [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips]
** tips/examples: [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips]
**[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
**[http://www.cgl.ucsf.edu/chimera/download.html Chimera]

Revision as of 05:13, 27 September 2013

Back to Back Door


  • general biology/biotech basics from Integrated DNA Technologies (IDT)
    • Molecular Biology Background:
      • Mitochondrial DNA, Mendelian Genetics, Molecular Facts and Figures, Protein Synthesis, microRNAs, DNA Replication, A Brief History of DNA, What is an Oligo
    • Molecular Biology Techniques:
      • The Polymerase Chain Reaction, Gel Electrophoresis , Restriction Endonucleases , DNA Sequencing , Antisense Technologies , A Basic PCR Protocol
  • Qiagen Bench Guide
    • cell culture & DNA


E. coli

Molecular Biology


plasmid annotations

  • APE free plasmid editor
  • Serial Cloner free equivalent to Vector NTI
  • PlasMapper
    • The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format.



Protein Tools


  • Databases:
    • Sabio-RK: biochemical reaction kinetics database
    • BRENDA: (BRaunschweig ENzyme DAtabase)

Synthetic Biology

Mass Spec


  • Shimadzu Virtual Advisor.
    • Ask Nicole, Amanda, or Janet for the lab log-in.




University of Washington

UW Resources

Safety/Lab Technique



  • Mendeley : reference/paper manager that's awesome
    • Janet's workflow: (1) discover papers via google scholar saved search, (2) save them to Mendeley in the appropriate nested folder regardless of whether you intend to read it now or "some day when I'm thinking about that topic" (3) read in Mendeley, which makes a green dot (indicating unread) go away.
    • You can highlight and keep notes on top of your PDFs enabling quicker review of topics.
    • Imagine being able to query all of the papers you have ever read for a topic of interest! You can also see whether you have ever read a paper or not, potentially saving yourself time.
    • I also like the idea that I will never lose track of a paper I want to tell someone about. It isn't uncommon for someone to tell me about a paper but be unable to find it and send it to me. This should never happen for a dedicated Mendeley user.
  • Endy:Victor3_plate_reader/filters Filters for Fluorescence
  • Equilibrator
  • BioNumbers: a collection of useful bionumbers
  • emolecules Chemical Lookup