Skip to content

LennonLab/StarvationTraits

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

StarvationTraits: Microbial Starvation Traits

Sub-Project of: Dimensions: Collaborative Research: Microbial seed banks: processes and patterns of dormancy-driven biodiversity

This repository contains open-source code, data, & text files for an REU project related to a National Science Foundation Dimensions of Biodiversity grant (#1442246) awarded to Dr.'s Jay Lennon and Ken Locey of Indiana University (Bloomington) and to Dr. Stuart Jones of the University of Notre Dame (#...).

For information regarding the main project, please visit:

  1. NSF: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1442246&HistoricalAwards=false
  2. Dimensions Repo: https://github.com/LennonLab/Dimensions

Project Goals

  • Aim 1.)

  • Aim 2.)

  • Aim 3.)

Repo Contents

  • analyses:

  • bin:

    • PreSensInteractiveRegression.R: An R script written by Mario Muscarella (Indiana University) containing functions used in the analysis of PreSens oxygen respiration data.
    • ReadSynergy.R: An R script written by Mario Muscarella (Indiana University) containing functions used to import data from BioTek Synergy MX plate reader.
    • ReadAB1.py: A Python script written by Mario Muscarella (Indiana University) used to read raw ABI sequencer files and export *.fasta and *.qual files.
    • TrimMovingAverage.py: A Python script written by Mario Muscarella (Indiana University) used to trim raw sequence files (*.fasta) based on Phred quality scores.
    • MergeSeqs.py: A Python script written by Mario Muscarella (Indiana University) used to merge individual *.fasta files into a multi fasta file.
  • data:

    • Sequences: Contains raw and processed Sanger sequencing files used for colony identifications.
    • Respiration: Contains raw output files (.txt) from PreSens SensorDish Oxygen system
    • GrowthCurves: Contains raw output files (.txt) from BioTek Synergy MX plate reader.
    • DeathCurves: Contains plate count data from long term starvation experiments
  • figures:

  • ** notse:**

    • EcoPlate_Info: Informational datasheet for the BioLog EcoPlate.

Contributors

Rachel Ferrill: REU Research, Undergraduate, Department of Biology, Transylvania University.

Mario Muscarella: Ph.D. candidate in the Lennon Lab

Dr. Jay Lennon: Principle Investigator, Associate Professor, Department of Biology, Indiana University, Bloomington. Head of the Lennon Lab.

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published