Lidstrom:Back Door:Useful Links: Difference between revisions

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==General==
==General==
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==== codon optimization ====
==== codon optimization ====
* [http://idtdna.com/CodonOpt 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. 
* [http://genomes.urv.es/OPTIMIZER/ OPTIMIZER]
** [http://nar.oxfordjournals.org/content/35/suppl_2/W126.short Original paper]
** Requires more selections, so is less simple than the IDT one.
* [http://www.genscript.com/cgi-bin/tools/rare_codon_analysis Genscript Rare Codon Analysis]
===== codon frequency tables for E. coli =====
* [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm from HÉNAUT and DANCHIN:Analysis and Predictions from Escherichia coli sequences]  
* [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm 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.
** 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.
** Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth.
* [http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/in-vitro-genetics/codon-usage.html Table modified from Maloy, S., V. Stewart, and R. Taylor. 1996. Genetic analysis of pathogenic bacteria. Cold Spring Harbor Laboratory Press, NY.]


==== other ====
==== other ====
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===Protein Tools===
===Protein Tools===
*Size Estimation
==== Size Estimation====
** [http://www.bioinformatics.org/sms/prot_mw.html Protein MW Calculator]
** [http://www.bioinformatics.org/sms/prot_mw.html Protein MW Calculator]
** [http://molbiol.ru/eng/scripts/01_04.html Protein Mass to Mol Converter]
** [http://molbiol.ru/eng/scripts/01_04.html Protein Mass to Mol Converter]
*Visualization
 
**[http://www.pymol.org/ Pymol]
==== Visualization ====
** tutorial: [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners]
[http://www.pymol.org/ Pymol]
** tutorial: [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org].  Concise less basic review
* Tutorials:
** tips/examples: [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips]
** [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners]
** tutorial: [http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf UCLA]  
** [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org].   
**[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
** [http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf UCLA]: concise less basic review
*Structure Prediction
** [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf Madison Tutorial]
**[http://swissmodel.expasy.org/ Swiss Model]
* Cheat sheets:
**[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
** intermediate level: [http://www.medschool.lsuhsc.edu/biochemistry/docs/PyMOL-QuickRef-0905.pdf AMAZING Cheat Sheet]
*Alignment
** [http://www.doe-mbi.ucla.edu/CHEM125/PymolRef.pdf UCLA], 2 pages of text
**[http://fatcat.burnham.org/ FATCAT]
* tips/examples:
** [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips]
 
*[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
 
==== Structure Prediction ====
*[http://swissmodel.expasy.org/ Swiss Model]
*[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
 
==== Alignment ====
*[http://fatcat.burnham.org/ FATCAT]


=== Enzymes ===
=== Enzymes ===
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== Programming/Scripting ==
== Programming/Scripting ==
*R  
R  
** tutorials:
* tutorials:
*** [https://www.datacamp.com/ R tutorial]
** [https://www.datacamp.com/ R tutorial]
*** From [https://github.com/raphg/Biostat-578 Biostat 578]
** From [https://github.com/raphg/Biostat-578 Biostat 578]
**** [http://tim-smith.us/arrgh/ aRrgh: a newcomer's (angry) guide to R]
*** [http://tim-smith.us/arrgh/ aRrgh: a newcomer's (angry) guide to R]
*** [http://www.amazon.com/Introductory-Statistics-R-Computing/dp/0387790535 Introductory Statistics (R)] by Peter Dalgaard
** [http://www.amazon.com/Introductory-Statistics-R-Computing/dp/0387790535 Introductory Statistics (R)] by Peter Dalgaard
*** [http://www.cyclismo.org/tutorial/R/ R tutorial]
** [http://www.cyclismo.org/tutorial/R/ R tutorial]
** references:
* references:
*** [http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html cheat sheet]
** [http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html cheat sheet]
*** [http://cran.r-project.org/doc/contrib/Short-refcard.pdf reference card]
** [http://cran.r-project.org/doc/contrib/Short-refcard.pdf reference card]
** [http://r-project.org Bioconductor]
** [http://adv-r.had.co.nz/ Advanced R] by the author of ggplot, etc. (Hadley Wickham)
* Regular expressions:
* [http://r-project.org Bioconductor]
**[http://rubular.com/ 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.
 
Regular expressions:
*[http://rubular.com/ 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
* [https://try.github.io/levels/1/challenges/1 GitHub interactive tutorial]
 
== Protein Engineering ==
* [http://bitesizebio.com/252/8-approaches-to-random-mutagenesis/ Random mutagenesis methods] summarized succinctly.
** [http://www.wolfram.com/learningcenter/tutorialcollection/MathematicsAndAlgorithms/MathematicsAndAlgorithms.pdf Excellent equation solving tutorial]
* [http://www.fgsc.net/neurosporaprotocols/How%20to%20use%20chemical%20mutagenesis.pdf chemical mutagenesis summary] of popular mutagens
* Site directed mutagenesis:
** QuikChange:
*** The Agilent commercial kits for single and multiple mutations work great.  [[Richard_Lab:Site_Directed_Mutagenesis|This protocol]] should deliver the same results with a bit lower efficiency and slower Dpn1 step but is almost free.
** Free [https://www.genomics.agilent.com/primerDesignProgram.jsp Agilent QuikChange primer design tool] (Agilent account required)
** QuikChange manuals:
*** [http://www.chem.agilent.com/library/usermanuals/Public/210514.pdf 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)
*** [http://www.chem.agilent.com/library/usermanuals/Public/210518.pdf Lightning, Single mutation at a time]
***** Catalog # 210518 (10 reactions) and #210519 (30 reactions).  No academic price appears to be available ([[User:Janet B. Matsen|JM]] 12 June 2014)
* [http://eu.idtdna.com/pages/docs/default-source/user-guides-and-protocols/mutagenesis-application-guide.pdf?sfvrsn=9 IDT Mutagenesis Application Guide] for mutating genes


== Misc ==
== Misc ==
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** [http://www.acdlabs.com/resources/freeware/chemsketch/ chemsketch]  (free)
** [http://www.acdlabs.com/resources/freeware/chemsketch/ chemsketch]  (free)
** [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ chemdraw]  (seems to cost $)
** [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ chemdraw]  (seems to cost $)
== Statistics ==
=== Multiple linear regression ===
* [http://math.arizona.edu/~hzhang/waeso/multlr.pdf basics, from an R perspective].
* Relative importance of variables:
** [http://www.unt.edu/rss/class/mike/5710/Multiple%20Regression.pdf good lecture slides]
==Industry==
* [http://www.biofuelsdigest.com/bdigest/2014/05/20/no-shortcuts-to-the-top-a-digest-special-report-on-scale-up-in-industrial-biotechnology/ scale up slides] from major players


==Misc==
==Misc==

Revision as of 07:34, 1 July 2014

Back to Back Door

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

Microbiology

E. coli

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.

codon optimization

codon frequency tables for E. coli

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

Protein Tools

Size Estimation

Visualization

Pymol

Structure Prediction

Alignment

Enzymes

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

Synthetic Biology

Mass Spec

HPLC

Programming/Scripting

R

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

Protein Engineering

Misc

Presentations/Posters

University of Washington

UW Resources

Safety/Lab Technique

Graphics

Statistics

Multiple linear regression

Industry

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
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