Barrick Lab :: Reference Information

Getting Started in Lab

• Getting Started with Lab Techniques
• Synthetic Biology 101
  Background on what synthetic biology is and how to get started in the field.
• Resources to Learn Biocomputing
  Resources for learning the command line, R, Python, GitHub, etc.

Templates and Spreadsheets

• Circular and Rectangular Tube Labels
  Templates for printing cryotube labels.
• Petri Dish Patch Templates
  Grids that can be used to divide up petri dishes.

Writing

• Barrick Lab Style Guide
  How to format manuscript files.
• Unicode Tables
  Complete catalog of symbols that can be used in manuscripts.
• Subtle Grammatical Usage Rules
  Common grammatical mistakes and confused words.
• Accessing Journal Articles
  Methods for finding, discovering, and accessing various journal articles, including when off-campus.
• Publicly Archive Data
  Uploading data and obtaining an accession number from GenBank, SRA, Zenodo, and Dryad repositories.
• How to write a response to reviewers (Rich Lenski)

Presenting

• How to Graph Data
  Preferred conventions for presenting data of different kinds.
• Presentation Advice
  Advice on how to present your research in different venues.

Experimental Design and Statistics

• Introduction to Experimental Design
  How to design effective experiments.

Bacteria

• E. coli Genotypes (OWW)
  Common genotypes, genetic markers, and alleles.
• Acinetobacter baylyi ADP1 Genome Resources: BLAST | BioCyc | tdk/kanR sequence
  
• Characteristics of the E. coli Genome
• Commonly Used Plasmids
• Bacterial Genetic Code
  Translation table and codon nomenclature.

Computation

General Setup and Getting Started Guides

• Computer Setup
  How to get your computer ready for bioinformatics and computational biology.
• Computing Environment Setup
  Advice for setting up your Linux/Unix environment for bioinformatics and computational biology.
• Learn Biocomputing
  Resources for learning the command line, R, Python, GitHub, etc.
• Bioinformatics Master List
  A master list of bioinformatics software frequently used in the lab

Specific Topics/Workflows

• Unix Commands Quick Reference
  Collection of useful Unix commands.
• SSH Public Key Authentication
  How to set up login without typing password between Linux machines.
• Command Line File Transfer to UT Box
  How to directly transfer files to/from TACC or other computers to UT Box using LFTP.
• Useful Python snippets for biology
  Short code blocks for performing common tasks in Python

User Guides and Manuals

• TACC – Resources at the Texas Advanced Computing Center.
  • Lonestar6 - high performance cluster user guide
• Genome Sequencing

Deprecated

• Retired Computation Pages
  Older topics that are likely out of date!

Miscellaneous and Humor

• Link List
  Miscellaneous links of interest.
• Science Quotations
  Memorable and humorous sayings related to our research.