Team:Edinburgh/Links

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Useful information/tools can be found on the following pages:
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<p class="h1">Links</p>
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Useful information/tools, many of which we used regularly, can be found on the following pages:
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===Biology methods===
* [http://www.openwetware.org/wiki/French_Lab Open Wetware: French Lab protocols]
* [http://www.openwetware.org/wiki/French_Lab Open Wetware: French Lab protocols]
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** [http://www.openwetware.org/wiki/Cfrench:bbprimerdesign Primer Design]
* [http://jbei-exwebapp.lbl.gov/j5/j5manual/pages/1.html J5: overview of automated DNA assembly]
* [http://jbei-exwebapp.lbl.gov/j5/j5manual/pages/1.html J5: overview of automated DNA assembly]
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* [http://www.nfstc.org/pdi/Subject04/pdi_s04_m01_02.htm Primer Design] (for forensics, but probably good advice for us too)
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===Genomics===
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* [http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST: Basic Local Alignment Search Tool]
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* [http://en.wikipedia.org/wiki/DNA_codon_table Codon Table]
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* [http://www.ebi.ac.uk/ EMBL]
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* [http://www.ncbi.nlm.nih.gov/sites/gquery Entrez]
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* [http://genepool.bio.ed.ac.uk/sanger/Sanger_troubleshooting_guide_v1.pdf GenePool: Sanger Sequencing Troubleshooting]
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* [http://tools.neb.com/NEBcutter2/index.php NEBcutter] (finds restriction sites; also finds ORFs if they start with M)
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* [http://www.ebi.ac.uk/Tools/psa/ Needle] (and other pairwise alignment tools)
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* [http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement]
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* [http://www.cbs.dtu.dk/services/SignalP/ SignalP]
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* [http://www.straininfo.net/ StrainInfo]
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* [http://www.ebi.ac.uk/Tools/emboss/transeq/ Transeq] (nucleotide to protein conceptual translation)
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* [http://www.uniprot.org/ UniProt]
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===iGEM===
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* [https://igem.org/Main_Page iGEM]
* [https://igem.org/Main_Page iGEM]
** [https://2011.igem.org/Main_Page iGEM 2011]
** [https://2011.igem.org/Main_Page iGEM 2011]
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** [https://2011.igem.org/Special:RecentChanges Recent Changes to the Wiki]
** [https://igem.org/Previous_iGEM_Competitions Previous iGEM competitions]
** [https://igem.org/Previous_iGEM_Competitions Previous iGEM competitions]
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** [https://2011.igem.org/Judging This year's judging criteria]
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** [https://2011.igem.org/Calendar_of_Events Calander of Events] (i.e. deadlines)
* [http://partsregistry.org/Main_Page Parts Registry]
* [http://partsregistry.org/Main_Page Parts Registry]
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** [http://partsregistry.org/Help Help]
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** [http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix BioBrick prefix and suffix]
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** [http://dspace.mit.edu/bitstream/handle/1721.1/45139/BBFRFC12.txt?sequence=1 RFC 12]
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** [http://dspace.mit.edu/bitstream/handle/1721.1/32535/PhillipsSilverFusion.pdf?sequence=1 RFC 23]
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* [http://www.wired.com/wired/archive/13.01/mit.html Life Reinvented] (article on the origins of iGEM)
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===Software===
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* [http://kappalanguage.org/ The Kappa Biological Modeling Language]
* [http://kappalanguage.org/ The Kappa Biological Modeling Language]
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* [http://www.ebi.ac.uk/Tools/emboss/transeq/ Transeq: nucleotide to protein conceptual translation]
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** [http://www.demonsoft.org/SpatialKappa/ Spatial Kappa]
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* [http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST: Basic Local Alignment Search Tool]
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* [https://www.see.ed.ac.uk/auth/teaching/courses/matlab/ MATLAB intro]
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* [http://tools.neb.com/NEBcutter2/index.php NEBcutter: finds restriction sites] (also finds ORFs if they start with M)
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* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE Plasmid Editor]
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* [http://www.geospiza.com/Products/finchtv.shtml FinchTV Chromatogram Viewer]
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===Misc===
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{{:Team:Edinburgh/Template:Navbox}}
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* [https://www.wiki.ed.ac.uk/display/CFrenchLabwiki/iGEM11TeamInfo The old Wiki] (do not use)
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* [http://www.w3schools.com/css/default.asp CSS guide]
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Latest revision as of 20:20, 12 January 2012

Links

Useful information/tools, many of which we used regularly, can be found on the following pages:

Contents

Biology methods

  • [http://www.openwetware.org/wiki/French_Lab Open Wetware: French Lab protocols]
    • [http://www.openwetware.org/wiki/Cfrench:bbprimerdesign Primer Design]
  • [http://jbei-exwebapp.lbl.gov/j5/j5manual/pages/1.html J5: overview of automated DNA assembly]
  • [http://www.nfstc.org/pdi/Subject04/pdi_s04_m01_02.htm Primer Design] (for forensics, but probably good advice for us too)

Genomics

  • [http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST: Basic Local Alignment Search Tool]
  • [http://en.wikipedia.org/wiki/DNA_codon_table Codon Table]
  • [http://www.ebi.ac.uk/ EMBL]
  • [http://www.ncbi.nlm.nih.gov/sites/gquery Entrez]
  • [http://genepool.bio.ed.ac.uk/sanger/Sanger_troubleshooting_guide_v1.pdf GenePool: Sanger Sequencing Troubleshooting]
  • [http://tools.neb.com/NEBcutter2/index.php NEBcutter] (finds restriction sites; also finds ORFs if they start with M)
  • [http://www.ebi.ac.uk/Tools/psa/ Needle] (and other pairwise alignment tools)
  • [http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement]
  • [http://www.cbs.dtu.dk/services/SignalP/ SignalP]
  • [http://www.straininfo.net/ StrainInfo]
  • [http://www.ebi.ac.uk/Tools/emboss/transeq/ Transeq] (nucleotide to protein conceptual translation)
  • [http://www.uniprot.org/ UniProt]

iGEM

Software

  • [http://kappalanguage.org/ The Kappa Biological Modeling Language]
    • [http://www.demonsoft.org/SpatialKappa/ Spatial Kappa]
  • MATLAB intro
  • [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE Plasmid Editor]
  • [http://www.geospiza.com/Products/finchtv.shtml FinchTV Chromatogram Viewer]

Misc

  • The old Wiki (do not use)
  • [http://www.w3schools.com/css/default.asp CSS guide]

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