-1OR3974-974-1=0001 < Lab

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---+!! Barrick Lab :: Reference Information

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---++ Getting Started in Lab

   * [[ProtocolsGettingStarted][Getting Started with Lab Techniques]]
   * [[SynBio101][Synthetic Biology 101]] %BR% Background on what synthetic biology is and how to get started in the field.
   * [[ProtocolsLearnBiocomputing][Resources to Learn Biocomputing]] %BR% Resources for learning the command line, R, Python, GitHub, etc.

---++ 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

   * [[ProtocolsStyleGuide][Barrick Lab Style Guide]] <br> How to format manuscript files.
   * [[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.
   * [[ProtocolsJournalArticleAccess][Accessing Journal Articles]] <br />Methods for finding, discovering, and accessing various journal articles, including when off-campus.
   * [[PubliclyArchivingData][Publicly Archive Data]]<br />Uploading data and obtaining an accession number from GenBank, SRA, Zenodo, and Dryad repositories.
   * [[https://telliamedrevisited.wordpress.com/2020/07/15/how-to-write-a-response-to-reviewers-in-ten-easy-steps/][How to write a response to reviewers (Rich Lenski)]]

---++ Presenting

   * [[ProtocolsGraphGuide][How to Graph Data]] <br> Preferred conventions for presenting data of different kinds.
   * [[ProtocolsMakingPresentations][Presentation Advice]] <br />Advice on how to present your research in different venues.

---++ Experimental Design and Statistics

   * [[IntroductionToExperimentalDesign][Introduction to Experimental Design]] <br> How to design effective experiments.

---++ Bacteria

   * [[http://openwetware.org/wiki/E._coli_genotypes][ _E. coli_ Genotypes (OWW)]] <br> Common genotypes, genetic markers, and alleles.
   * _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]] | [[http://openwetware.org/wiki/User:Gabriel_A._Suarez/Notebook/ADP1_Baylyi_reference <i>tdk</i>/<i>kanR</i> sequence]]<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

---+++ General Setup and Getting Started Guides
   * [[ProtocolsComputerSetup][Computer Setup]] %BR% How to get your computer ready for bioinformatics and computational biology.
   * [[ProtocolsComputingEnvironmentSetup][Computing Environment Setup]] %BR% Advice for setting up your Linux/Unix environment for bioinformatics and computational biology.
   * [[ProtocolsLearnBiocomputing][Learn Biocomputing]] %BR% Resources for learning the command line, R, Python, GitHub, etc.
   * [[ListofBioinformatics][Bioinformatics Master List]] %BR% A master list of bioinformatics software frequently used in the lab 

---+++ Specific Topics/Workflows
   * [[ProtocolsUnixCommandsQuickReference][Unix Commands Quick Reference]] <br />Collection of useful Unix commands.
   * [[ProtocolsSSHPublicKeyAuthentication][SSH Public Key Authentication]] <br /> How to set up login without typing password between Linux machines.
   * [[CommandLineBox][Command Line File Transfer to UT Box]]  <br />How to directly transfer files to/from TACC or other computers to UT Box using LFTP.
   * [[ProtocolsPythonSnippets][Useful Python snippets for biology]] %BR% Short code blocks for performing common tasks in Python

---+++ User Guides and Manuals
   * [[http://www.tacc.utexas.edu/][TACC]] –  Resources at the Texas Advanced Computing Center.
      * [[https://docs.tacc.utexas.edu/hpc/lonestar6/][Lonestar6]] - high performance cluster user guide
   * [[ReferenceGenomeSequencing][Genome Sequencing]]

---+++ Deprecated
   * [[RetiredComputationPages][Retired Computation Pages]] %BR% Older topics that are likely out of date!

---++ Miscellaneous and Humor

   * [[%INCLUDINGWEB%.LinkList][ %MAKETEXT{"Link List"}%]] %ICON{external}% <br> Miscellaneous links of interest.
   * [[ScienceQuotations][Science Quotations]] <br> Memorable and humorous sayings related to our research.
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Topic revision: r59 - 2025-09-16 - TWikiGuest