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Bioinformatics Master List This page is a master list of bioinformatics software frequently used in the lab, and their purposes. It also includes additional notes...

Media amendments Preparation: Generally, prepare 30 50 mL of solution in a 50 mL conical tube. Then, filter sterilize solutions by pushing them through a 50 mL syringe...

Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick...

Handling High Molecular Weight DNA Introduction Long read sequencing, such as Oxford Nanopore or PacBio sequencing, is becoming increasingly important for genome...

General guidelines for sorting bacteria with fluorescence activated cell sorting (FACS) FACS is a powerful tool for high throughput analysis and manipulation of complex...

Barrick Lab :: Laboratory Protocols Updating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki....

Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers...

Barrick Lab :: Research Listen to an introduction to our synthetic biology research:Evolution and Engineering Bee Guts (EBRC in Translation Podcast) Watch a public...

Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota...

Working with Snodgrassella alvi Snodgrassella alvi is a member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated in vitro . Its isolation...

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Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques...

Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing...

Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions...

Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core...

Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated...

Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such...

Isolation of dsRNA from bacteria Materials and Reagents This protocol can be used to validate expression of dsRNA in E. coli (e.g. E.coli HT115(DE3)) or in other...

Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting...

Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology...

Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered...

Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice...

Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded...

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate...

Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation...

LB: Lysogeny Broth / Luria Bertani (Miller) Agar Add dH2O to full volume in an appropriately sized flask. Combine the following, making sure each component fully dissolves...

Retired Protocols Designing a new part Designing a new part for use in the BTK Bee Microbiome Toolkit (BTK) Golden Gate part kit for work in non model bacterial...

Past Barrick Lab Members Olivia Soto Jack Dwenger Elizabeth Manriquez Dan Deathrage Victor Li Matt McGuffie Laurel Miller Aneesa Bhakta Braydin McReynolds Joseph Reitman...

MG: Minimal Glucose agar, aka DM: Davis Mingioli agar Note: When making these plates it is necessary to prepare and autoclave the 3 main parts (salts, agar, and sugar...

TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g...

Bee Microbiome Toolkit The Bee Microbiome Toolkit (BTK) is a Golden Gate compatible toolkit of genetic parts designed for working with newly isolated, non model bacteria...

The University of Texas at Austin :: iGEM Team What is synthetic biology? What is iGEM? `Synthetic biology is the design and construction of biological devices...

Czapek Broth (CB) Combine in a flask: 500 mL 1 L Component 1.5 g 3 g sodium nitrate 0.5 g 1 g potassium phosphate dibasic 0.25 g...

Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli...

breseq breseq is a computational pipeline for finding mutations relative to a reference sequence in short read DNA re sequencing data for haploid microbial sized...

General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol...

SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract...

MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component...

DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.4L 5L Component MW 2.67 g...

Back to Golden Gate Protocols Designing a new part Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA...

LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. Add dH2O to desired...

Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules...

Labeling Glassware and Other Containers All bottles, flasks, tubes, graduated cylinders, and beakers that contain liquid or any substance must be labeled with a description...

Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types...

Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for...

Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Alphabetical Reference cat yourfile.txt Prints the contents of the given...

Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least...