Lidstrom:Back Door:Useful Links

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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 ,
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*** 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==
*[http://www.genome.jp/kegg/ KEGG]
*[http://www.genome.jp/kegg/ KEGG]
*[http://metacyc.org/ Metacyc]
*[http://metacyc.org/ Metacyc]
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*[http://mit.edu/7.02/pdfs/nomenclature.pdf bacterial gene & knockout nomenclature]
===E. coli===
===E. coli===
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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]
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*[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===
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==== plasmid annotations ====
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*[http://biologylabs.utah.edu/jorgensen/wayned/ape/ APE] free plasmid editor
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*[http://serialbasics.free.fr/Serial_Cloner.html Serial Cloner] free equivalent to Vector NTI
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*[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.
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==== other ====
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*[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.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===
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==Synthetic Biology==
==Synthetic Biology==
*[http://partsregistry.org/Main_Page Std Parts Registry]
*[http://partsregistry.org/Main_Page Std Parts Registry]
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*[https://docs.google.com/document/d/1QY9Y7A-2YpTOBt9M3LDOTrmlX4Broz7AjVdhDYIxGsw/edit SBOL (synthetic biology open language) visual format]
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** 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]
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== HPLC ==
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* Shimadzu [http://www.ssi.shimadzu.com/LC_VirtualAdvisor/LCVA.htm Virtual Advisor].
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** Ask Nicole, Amanda, or Janet for the lab log-in.
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== Programming/Scripting ==
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*R
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** [http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html cheat sheet]
== Misc ==
== Misc ==
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== 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
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** [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
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** [http://arstechnica.com/business/2012/05/hands-on-testing-the-gimp-28-and-its-new-single-window-interface/ website] about the interface
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** http://www.gimp.org/release-notes/gimp-2.8.html  - shows the location plus download link
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* drawing chemical structures:  (ask Amanda about either of these)
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** [http://www.acdlabs.com/resources/freeware/chemsketch/ chemsketch]  (free)
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** [http://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/ chemdraw]  (seems to cost $)
==Misc==
==Misc==
*[http://www.mendeley.com/ Mendeley] : reference/paper manager that's awesome
*[http://www.mendeley.com/ Mendeley] : reference/paper manager that's awesome
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** 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

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.

other

BioBricks

Protein Tools

Synthetic Biology

Mass Spec

HPLC

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

Programming/Scripting

Misc

Presentations/Posters

University of Washington

UW Resources

Safety/Lab Technique

Graphics

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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