Lidstrom:Back Door:Useful Links

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General

• 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

Microbiology

• KEGG
• Metacyc
• bacterial gene & knockout nomenclature

E. coli

• Working with E. coli
• coli Genome Stock Center
• Ecocyc
• EcoSal  !!subscription required!! (not available at UW)
• origins of replication
• RegulonDB A curated database of E. coli regulation.

Molecular Biology

DNA/RNA Tools

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.

other

• Agarose gel electrophoresis basics
• Genewiz DNA sequencing
• IDT DNA oligos
• EBI Sequence Alignment
• BLAST! Sequence Alignment
• RBS strength calculator/engineering tool
  • Accuracy stated by FAQ: "on average, the predictions of the RBS Calculator are accurate to within a factor of 2.3, equivalent to an error of 1.82 kcal/mol in the thermodynamic model. There is a 47% chance that a synthetic ribosome binding site will be accurate to within 2-fold of its predicted translation initiation rate." So you can estimate it to have accuracy within an order of magnitude. Pretty sensitive to the amount of upstream & downstream sequence info you provide. Check your forward engineering designs with more bp included in the reverse engineering mode.
• Finnzyme Tm calculator: use if you use Phusion DNA polymerase
• Finnzyme multiple primer analyzer looks for primer dimers (check before ordering primers)
• Replicons and Compatibility
• Nanodrop Info
• NuPack Nucleic acid secondary structure predictor

BioBricks

• backbone & origins: naming

Protein Tools

• Size Estimation
  • Protein MW Calculator
  • Protein Mass to Mol Converter
• Visualization
  • Pymol
  • Chimera
• Structure Prediction
  • Swiss Model
  • Phyre
• Alignment
  • FATCAT

Synthetic Biology

• Std Parts Registry
• SBOL (synthetic biology open language) visual format
  • Or look at this

Mass Spec

• Scripps Mass Spec Book
• Ion Suppression

HPLC

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

Programming/Scripting

• R
  • cheat sheet

Misc

• Mathematica (not free)
  • Excellent equation solving tutorial

Presentations/Posters

• Website to see how colorblind people will see your slides
• University Art Pack Download: a collection of University of Washington logos

University of Washington

• UW Chemical Engineering Department
• UW Microbiology Department
• UW Synthetic Biology
• UW IGEM 2011

UW Resources

• MyChem
• Biochem Store

Safety/Lab Technique

• Sample video: sterile technique

Graphics

• inkscape - SVG (vector) drawings, free. Loved by Janet & Amanda
  • Inkscape: Guide to a Vector Drawing use examples
• GIMP - pixels (like photoshp), free
  • website about the interface
  • http://www.gimp.org/release-notes/gimp-2.8.html - shows the location plus download link
• drawing chemical structures: (ask Amanda about either of these)
  • chemsketch (free)
  • chemdraw (seems to cost $)

Misc

• 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