<!-- Preferences start here * Set PAGETITLE = Barrick Lab :: Reference Information Preferences end here --> ---+ Barrick Lab :: Reference Information ---++ Templates and Spreadsheets * [[ProceduresLabelTemplates][Circular and Rectangular Tube Labels]] <br> Templates for printing cryotube labels. * [[ProceduresPetriDishPatchTemplates][Petri Dish Patch Templates]] <br> Grids that can be used to divide up petri dishes. ---++ Writing and Presenting * [[ProtocolsStyleGuide][Barrick Lab Style Guide]] <br> How to format manuscript files. * [[IntroductionToExperimentalDesign][Introduction to Experimental Design]] <br> How to design effective experiments. * [[ProtocolsGraphGuide][How to Graph Data]] <br> Preferred conventions for presenting data of different kinds. * [[http://www.alanwood.net/unicode/][Unicode Tables]] <br> Complete catalog of symbols that can be used in manuscripts. * [[SubtleGrammar][Subtle Grammatical Usage Rules]] <br> Common grammatical mistakes and confused words. * [[ScienceQuotations][Science Quotations]] <br> Memorable and humorous sayings related to our research. ---++ Bacteria * [[http://openwetware.org/wiki/E._coli_genotypes][ _E. coli_ Genotypes (OWW)]] <br> Common genotypes, genetic markers, and alleles. * [[LenskiLongTerms][Lenski Long-Term <i>E. coli</i> Lines]]<br>Brief summary of stories and idiosyncrasies of each of the 12 lines. * _Escherichia coli_ REL606 Genome Resources: [[http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?ORGANISM=413997&INPUT_SEQUENCE=NC_012967.1&log$=seqview_list_primer][Design Primers]] | [[http://www.ncbi.nlm.nih.gov//genomes/geblast.cgi?gi=24777][Blast]] | [[http://www.ncbi.nlm.nih.gov/nuccore/254160123][Genbank]] | [[http://www.ncbi.nlm.nih.gov/nuccore/NC_012967.1?report=graph][Browser]] |[[http://www.ecocyc.org/ECOL413997/][BioCyc]] * _Acinetobacter baylyi_ ADP1 Genome Resources: [[http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&USER_FORMAT_DEFAULTS=on&PAGE=MegaBlast&PROGRAM=blastn&GAPCOSTS=0%200&MATCH_SCORES=1,-2&BLAST_SPEC=MicrobialGenomes_62977&EQ_MENU=Acinetobacter%20sp.%20ADP1%20%28taxid%3A62977%29&DATABASE=Complete_Genomes&BLAST_PROGRAMS=megaBlast&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=10&WORD_SIZE=28&TEMPLATE_TYPE=0&TEMPLATE_LENGTH=0&FILTER=L&FILTER=m&DB_GROUP=AllMG&SUBGROUP_NAME=All_genomes&DB_SUBGROUP=Complete_Genomes&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&GET_SEQUENCE=on&NUM_OVERVIEW=100&DESCRIPTIONS=100&ALIGNMENTS=100&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&OLD_BLAST=false][BLAST]] | [[http://biocyc.org/organism-summary?object=ASP62977][BioCyc]] <br> * [[http://openwetware.org/wiki/User:Gabriel_A._Suarez/Notebook/ADP1_Baylyi_reference tdk/kan sequence]] as used by Berardinis et al., 2012. <br> * [[ReferenceEColiGenome][Characteristics of the <i>E. coli</i> Genome]] * [[ReferencePlasmids][Commonly Used Plasmids]] * [[BacterialGeneticCode][Bacterial Genetic Code]] <br> Translation table and codon nomenclature. ---++ Computation * Manuals * [[http://www.ee.surrey.ac.uk/Teaching/Unix/index.html][Introduction to Unix]] * [[http://tldp.org/LDP/abs/html/][Bash shell scripting]] * [[http://hgbook.red-bean.com/read/][Mercurial: The Definitive Guide]] * [[http://www.eng.cam.ac.uk/help/tpl/textprocessing/][LaTeX]] * [[http://www.tacc.utexas.edu/][TACC]] – [[https://www.tacc.utexas.edu/user-services/user-guides/lonestar-user-guide][Lonestar]] | [[https://www.tacc.utexas.edu/user-services/user-guides/stampede-user-guide][Stampede]] | [[https://www.tacc.utexas.edu/user-services/user-guides/corral-user-guide][Corral]] | [[https://www.tacc.utexas.edu/user-services/user-guides/ranch-user-guide][Ranch]] <br> Resources at the Texas Advanced Computing Center. * [[ReferenceGenomeSequencing][Genome Sequencing]] * [[http://python.org/][Python]] * [[http://biopython.org/wiki/Main_Page][Biopython]] and [[http://www.biopython.org/DIST/docs/tutorial/Tutorial.html][the Biopython Tutorial]] * [[http://sphinx.pocoo.org][Sphinx documentation generator]] * [[http://www.ncbi.nlm.nih.gov/books/NBK25501/][NCBI E-utils]] * [[http://guide.macports.org][MacPorts Guide]] ---++ Statistics * [[http://books.google.com/books?id=N6KCNw5NHNkC&pg=PA821&lpg=PA821&dq=tukey+jackknife+procedure+sokal+and+rolf&source=bl&ots=ohiXDXXleM&sig=2wGOZ3qXtd9cUVjdsdtj8n5HblM&hl=en&ei=fo1cTdapOIT68AbFwIz8DQ&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBMQ6AEwAA#v=onepage&q&f=false][Tukey's Jackknife]]
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Topic revision: r41 - 2014-11-13 - GabrielSuarez