Team:Edinburgh/Links

From 2011.igem.org

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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