Lidstrom:Back Door:Useful Links

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Back to [[Lidstrom:Back Door|Back Door]]
Back to [[Lidstrom:Back Door|Back Door]]
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To [[Lidstrom:Protocols|Protocols]]
==General==
==General==
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*** Mitochondrial DNA, Mendelian Genetics, Molecular Facts and Figures, Protein Synthesis, microRNAs, DNA Replication, A Brief History of DNA, What is an Oligo  
*** 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:
** Molecular Biology Techniques:
-
*** The Polymerase Chain Reaction, Gel Electrophoresis , Restriction Endonucleases , DNA Sequencing , Antisense Technologies , A Basic PCR Protocol ,
+
*** The Polymerase Chain Reaction, Gel Electrophoresis , Restriction Endonucleases , DNA Sequencing , Antisense Technologies , A Basic PCR Protocol  
 +
*[http://www.gene-quantification.de/Qiagen-BenchGuide.pdf Qiagen Bench Guide]
 +
** cell culture & DNA
==Microbiology==
==Microbiology==
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*[http://ecosal.org/ EcoSal]  !!subscription required!!  (not available at UW)
*[http://ecosal.org/ EcoSal]  !!subscription required!!  (not available at UW)
*[http://openwetware.org/wiki/Arking:JCAOligoTutorial8 origins of replication]
*[http://openwetware.org/wiki/Arking:JCAOligoTutorial8 origins of replication]
 +
*[http://regulondb.ccg.unam.mx/index.jsp RegulonDB] A curated database of E. coli regulation.
==Molecular Biology==
==Molecular Biology==
===DNA/RNA Tools===
===DNA/RNA Tools===
 +
==== plasmid annotations ====
 +
*[http://biologylabs.utah.edu/jorgensen/wayned/ape/ APE] free plasmid editor
 +
*[http://serialbasics.free.fr/Serial_Cloner.html Serial Cloner] free equivalent to Vector NTI
 +
*[http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper]
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** 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 ====
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* [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]
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** Requires more selections, so is less simple than the IDT one.
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* [http://www.genscript.com/cgi-bin/tools/rare_codon_analysis Genscript Rare Codon Analysis]
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===== codon frequency tables for E. coli =====
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* [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm from HÉNAUT and DANCHIN:Analysis and Predictions from Escherichia coli sequences]
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** Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C.
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** Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth.
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* [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 ====
 +
*[http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html Agarose gel electrophoresis basics]
*[http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html Agarose gel electrophoresis basics]
*[http://www.genewiz.com/ Genewiz DNA sequencing]
*[http://www.genewiz.com/ Genewiz DNA sequencing]
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*[http://www.ebi.ac.uk/Tools/psa/ EBI Sequence Alignment]
*[http://www.ebi.ac.uk/Tools/psa/ EBI Sequence Alignment]
*[http://blast.ncbi.nlm.nih.gov/ BLAST! Sequence Alignment]
*[http://blast.ncbi.nlm.nih.gov/ BLAST! Sequence Alignment]
 +
** The most commonly used nucleotide/protein alignment tool. 
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** start [http://www.digitalworldbiology.com/BLAST/index.html here] (animated web intro)
 +
** Practical intro: [http://www.ncbi.nlm.nih.gov/books/NBK21097/pdf/ch16.pdf 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 +."
*[https://salis.psu.edu/software/ RBS strength calculator/engineering tool]  
*[https://salis.psu.edu/software/ RBS strength calculator/engineering tool]  
 +
** Another: [http://www.garlandscience.com/res/pdf/practicalbioinformatics_ch3.pdf link]
** Accuracy stated by [https://salis.psu.edu/software/static/faq.html 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.
** Accuracy stated by [https://salis.psu.edu/software/static/faq.html 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.
*[http://www.finnzymes.fi/tm_determination.html Finnzyme Tm calculator]: use if you use Phusion DNA polymerase
*[http://www.finnzymes.fi/tm_determination.html Finnzyme Tm calculator]: use if you use Phusion DNA polymerase
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*[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html Replicons and Compatibility]
*[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html Replicons and Compatibility]
*[http://www.nanodrop.com/ND1/NucleicAcid-Booklet.html Nanodrop Info]
*[http://www.nanodrop.com/ND1/NucleicAcid-Booklet.html Nanodrop Info]
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*[http://www.nupack.org/ NuPack] Nucleic acid secondary structure predictor
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=== BioBricks ===
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*[http://partsregistry.org/Help:Plasmids/Nomenclature backbone & origins: naming]
===Protein Tools===
===Protein Tools===
-
*Size Estimation
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==== 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]
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*Visualization
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**[http://www.pymol.org/ Pymol]
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==== Visualization ====
-
**[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
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[http://www.pymol.org/ Pymol]
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*Structure Prediction
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* Tutorials:
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**[http://swissmodel.expasy.org/ Swiss Model]
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** [http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners pymol for beginners]
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**[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
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** [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf bioquest.org]
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*Alignment
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** [http://www.doe-mbi.ucla.edu/CHEM125/pymol_tutorial_060418.pdf UCLA]: concise less basic review
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**[http://fatcat.burnham.org/ FATCAT]
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** [http://bioquest.org/nimbios2010/wp-content/blogs.dir/files/2010/07/pymol_tutorial3.pdf Madison Tutorial]
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* Cheat sheets:
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** intermediate level: [http://www.medschool.lsuhsc.edu/biochemistry/docs/PyMOL-QuickRef-0905.pdf AMAZING Cheat Sheet]
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** [http://www.doe-mbi.ucla.edu/CHEM125/PymolRef.pdf UCLA], 2 pages of text
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* tips/examples:
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** [http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol figure tips]
 +
 
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*[http://www.cgl.ucsf.edu/chimera/download.html Chimera]
 +
 
 +
==== Structure Prediction ====
 +
*[http://swissmodel.expasy.org/ Swiss Model]
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*[http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Phyre]
 +
 
 +
==== Alignment ====
 +
*[http://fatcat.burnham.org/ FATCAT]
 +
 
 +
=== Enzymes ===
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* Databases:
 +
** [http://sabio.villa-bosch.de/newSearch/index Sabio-RK]: biochemical reaction kinetics database
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** [http://www.brenda-enzymes.org/index.php4 BRENDA]:  (BRaunschweig ENzyme DAtabase)
==Synthetic Biology==
==Synthetic Biology==
*[http://partsregistry.org/Main_Page Std Parts Registry]
*[http://partsregistry.org/Main_Page Std Parts Registry]
 +
*[https://docs.google.com/document/d/1QY9Y7A-2YpTOBt9M3LDOTrmlX4Broz7AjVdhDYIxGsw/edit SBOL (synthetic biology open language) visual format]
 +
** Or look at [http://dspace.mit.edu/bitstream/handle/1721.1/49523/RFC_16_SBOLv_Specification.pdf?sequence=1 this]
==Mass Spec==
==Mass Spec==
*[http://masspec.scripps.edu/book_toc.php Scripps Mass Spec Book]
*[http://masspec.scripps.edu/book_toc.php Scripps Mass Spec Book]
*[http://www.chromatographyonline.com/lcgc/article/articleDetail.jsp?id=327354 Ion Suppression]
*[http://www.chromatographyonline.com/lcgc/article/articleDetail.jsp?id=327354 Ion Suppression]
 +
 +
== HPLC ==
 +
* Shimadzu [http://www.ssi.shimadzu.com/LC_VirtualAdvisor/LCVA.htm Virtual Advisor].
 +
** Ask Nicole, Amanda, or Janet for the lab log-in.
 +
 +
== Programming/Scripting ==
 +
R
 +
* tutorials:
 +
** [https://www.datacamp.com/ R tutorial]
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** From [https://github.com/raphg/Biostat-578 Biostat 578]
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*** [http://tim-smith.us/arrgh/ aRrgh: a newcomer's (angry) guide to R]
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** [http://www.amazon.com/Introductory-Statistics-R-Computing/dp/0387790535 Introductory Statistics (R)] by Peter Dalgaard
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** [http://www.cyclismo.org/tutorial/R/ R tutorial]
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* references:
 +
** [http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html cheat sheet]
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** [http://cran.r-project.org/doc/contrib/Short-refcard.pdf reference card]
 +
** [http://adv-r.had.co.nz/ Advanced R] by the author of ggplot, etc. (Hadley Wickham)
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* [http://r-project.org Bioconductor]
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* [http://www.cookbook-r.com/Graphs/] amazing reference for making ggplot graphs!
 +
 +
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
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* 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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==Safety/Lab Technique==
==Safety/Lab Technique==
*[http://www.benchfly.com/video/33/working-with-sterile-technique/ Sample video]: sterile technique
*[http://www.benchfly.com/video/33/working-with-sterile-technique/ Sample video]: sterile technique
 +
*[http://www.ehs.washington.edu/ohsreslab/maincampuschart.pdf biohazard waste stream flow chart UW]
== Graphics ==
== Graphics ==
* [http://inkscape.org/ inkscape] - SVG (vector) drawings, free.  Loved by Janet & Amanda
* [http://inkscape.org/ inkscape] - SVG (vector) drawings, free.  Loved by Janet & Amanda
 +
** [http://www.idea2ic.com/Manuals/Inkscape.pdf Inkscape: Guide to a Vector Drawing] use examples
* [http://www.gimp.org/ GIMP] - pixels (like photoshp), free
* [http://www.gimp.org/ GIMP] - pixels (like photoshp), free
** [http://arstechnica.com/business/2012/05/hands-on-testing-the-gimp-28-and-its-new-single-window-interface/ website] about the interface
** [http://arstechnica.com/business/2012/05/hands-on-testing-the-gimp-28-and-its-new-single-window-interface/ website] about the interface
** http://www.gimp.org/release-notes/gimp-2.8.html  - shows the location plus download link
** 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)
 +
** [http://www.acdlabs.com/resources/freeware/chemsketch/ chemsketch]  (free)
 +
** [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ chemdraw]  (seems to cost $)
 +
 +
== Statistics ==
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=== Multiple linear regression ===
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* [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]
 +
=== Statistical testing ===
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*[http://www.statisticsdonewrong.com/introduction.html Statistics done wrong] Good explanation of p-value
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 +
==Industry==
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* [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==
*[http://www.mendeley.com/ Mendeley] : reference/paper manager that's awesome
*[http://www.mendeley.com/ 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]]
*[[Endy:Victor3_plate_reader/filters Filters for Fluorescence]]
*[http://equilibrator.weizmann.ac.il/ Equilibrator]
*[http://equilibrator.weizmann.ac.il/ Equilibrator]
*[http://bionumbers.hms.harvard.edu BioNumbers]: a collection of useful bionumbers
*[http://bionumbers.hms.harvard.edu BioNumbers]: a collection of useful bionumbers
*[http://www.emolecules.com/ emolecules Chemical Lookup]
*[http://www.emolecules.com/ emolecules Chemical Lookup]

Current revision

Back to Back Door

To Protocols

Contents

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

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

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

Statistical testing

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
Personal tools