Lidstrom:Back Door:Useful Links

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To Protocols

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
• Plasmid guide: Plasmids 101
  • Download from: http://info.addgene.org/download-addgenes-ebook-plasmids-101-1st-edition

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

Cloning guides

• NEB Molecular Cloning Technical Guide: overview and comparison of most types of cloning.

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.

codon optimization

• IDT's web tool to optimize for a given organism
  • Doesn't provide any info about the strategy used for codon optimization. (Boo!) However, IDT is a leading company for DNA technology, so whatever they use is likely fine.
• OPTIMIZER
  • Original paper
  • Requires more selections, so is less simple than the IDT one.
• Genscript Rare Codon Analysis

codon frequency tables for E. coli

• from HÉNAUT and DANCHIN:Analysis and Predictions from Escherichia coli sequences
  • Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C.
  • Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth.
• Table modified from Maloy, S., V. Stewart, and R. Taylor. 1996. Genetic analysis of pathogenic bacteria. Cold Spring Harbor Laboratory Press, NY.

other

• Agarose gel electrophoresis basics
• Genewiz DNA sequencing
• IDT DNA oligos
• EBI Sequence Alignment
• BLAST! Sequence Alignment
  • The most commonly used nucleotide/protein alignment tool.
  • start here (animated web intro)
  • Practical intro: CHS protocols
    • protein alignments: "The line between the two sequences indicates the similarities between the sequences. If the query and the subject have the same amino acid at a given location, the residue itself is shown. Conservative substitutions, as judged by the substitution matrix, are indicated with +."
• RBS strength calculator/engineering tool
  • Another: link
  • 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

• Tutorials:
  • pymol for beginners
  • bioquest.org.
  • UCLA: concise less basic review
  • Madison Tutorial
• Scripting
  • Quickie PyMol Tutorial: great script syntax examples
• Cheat sheets:
  • intermediate level: AMAZING Cheat Sheet
  • UCLA, 2 pages of text
• tips/examples:
  • figure tips

• Chimera

Structure Prediction

• Swiss Model
• Phyre

Alignment

• FATCAT

Enzymes

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

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

• tutorials:
  • Swirl: swirl teaches you R programming and data science interactively, at your own pace, and right in the R console
    • List of courses within Swirl
  • R tutorial
  • From Biostat 578
    • aRrgh: a newcomer's (angry) guide to R
  • Introductory Statistics (R) by Peter Dalgaard
  • R tutorial
• references:
  • cheat sheet
  • reference card
  • Advanced R by the author of ggplot, etc. (Hadley Wickham)
• tools:
  • ggplot:
    • ggplot2 plot menu
    • [1] amazing reference for making ggplot graphs!
  • dplyr (and tidyr)
    • plyr cheat sheet
  • Bioconductor

Python

• Matplotlib
  • tutorial

Regular expressions:

• PyThex. A quick way to test your Python regular expressions.
• Rubular. Website to test regular expressions in Ruby, but works for grep in R. It is possible it works a little differently in Ruby and grep.

GitHub

• GitHub interactive tutorial

Graphics

• Hot & Not: Graphics

Protein Engineering

• Random mutagenesis methods summarized succinctly.
  • Excellent equation solving tutorial
• chemical mutagenesis summary of popular mutagens
• Site directed mutagenesis:
  • QuikChange:
    • The Agilent commercial kits for single and multiple mutations work great. This protocol should deliver the same results with a bit lower efficiency and slower Dpn1 step but is almost free.
  • Free Agilent QuikChange primer design tool (Agilent account required)
  • QuikChange manuals:
    • Lightning, Multi Kit
      • Catalog # 210514 (10 reactions) and #210516 (30 reactions)
      • Academic version of kit (cheaper): Item # 210515 ($321.30, 10 rxns), Item # 210513 ($853.20, 30 rxns)
    • Lightning, Single mutation at a time
      • • Catalog # 210518 (10 reactions) and #210519 (30 reactions). No academic price appears to be available (JM 12 June 2014)
• IDT Mutagenesis Application Guide for mutating genes

Organic Chemistry

• Free downloadable book with focus on biology: download here

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
• Inkscape (free version of Adobe Illustrator)

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
• biohazard waste stream flow chart UW

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
• colors
  • ColorBrewer - provides nice color palettes & helps you create hex colors
  • Hex gradient creator
• drawing chemical structures: (ask Amanda about either of these)
  • chemsketch (free)
  • chemdraw (seems to cost $)

LaTeX

• Draw a character, get the LaTeX translation: Detexify
• Draw an equation, get the whole LaTeX equation: [2]

Statistics

Multiple linear regression

• basics, from an R perspective.
• Relative importance of variables:
  • good lecture slides

Statistical testing

• Statistics done wrong Good explanation of p-value

Industry

• scale up slides from major players

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