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 ,

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

Molecular Biology

DNA/RNA Tools

• 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

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

Mass Spec

• Scripps Mass Spec Book
• Ion Suppression

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
• 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

Misc

• Mendeley : reference/paper manager that's awesome
• Endy:Victor3_plate_reader/filters Filters for Fluorescence
• Equilibrator
• BioNumbers: a collection of useful bionumbers
• emolecules Chemical Lookup