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:
- NSF: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1442246&HistoricalAwards=false
- Dimensions Repo: https://github.com/LennonLab/Dimensions
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Aim 1.)
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Aim 2.)
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Aim 3.)
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analyses:
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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.
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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
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figures:
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** notse:**
- EcoPlate_Info: Informational datasheet for the BioLog EcoPlate.
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.