Team:Edinburgh/Links

Links

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

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

• iGEM
  • iGEM 2011
  • Recent Changes to the Wiki
  • Previous iGEM competitions
  • This year's judging criteria
  • Calander of Events (i.e. deadlines)
• [http://partsregistry.org/Main_Page Parts Registry]
  • [http://partsregistry.org/Help Help]
  • [http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix BioBrick prefix and suffix]
  • [http://dspace.mit.edu/bitstream/handle/1721.1/45139/BBFRFC12.txt?sequence=1 RFC 12]
  • [http://dspace.mit.edu/bitstream/handle/1721.1/32535/PhillipsSilverFusion.pdf?sequence=1 RFC 23]
• [http://www.wired.com/wired/archive/13.01/mit.html Life Reinvented] (article on the origins of 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]