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2015 Lennon Lab Jim Holland Summer Science Research Program (SSRP 2015)

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 SSRP 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

data: a folder containing plate-reader output from EcoPlate experiments. Each .txt file in this folder respresents a single 96-well plate (8 rows, 12 columns), 'tab' separated values. Each well is an absorbance reading at 590 nm, which corresponds to the utilization of a specific resource in the corresponding well of the resource matrix (ecoplate.info/resource_matrix.txt). Resources are distributed on plates in triplicate (cols 1-4 repeated three times).

ecoplate.info: a folder containing the text file resource_matrix.txt. Resources are distributed on plates in triplicate (cols 1-4 repeated three times).

bin: a folder containing scripts for parsing relevant info from a .txt file generated by the plate-reader software (bin/ecoplate_parser.R). This script takes the raw output of the plate reader (as a .txt file), and writes another tab-separated .txt file into the same folder, with _parsed appended to the original filename.

File names:

“3C”--stands for “from experimental tube 3. Also indicates that the derived

"0723"--the organism

pilot-- parsed--

For data files, the last three capital letters are initials of whomever generated it.

Contributors

Dakayla Calhoun: SSRP Student,

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

Dr. Ken Locey: co-Principle Investigator, Postdoctoral Fellow in the Lennon Lab

Dr. Megan Behringer: Postdoctoral Fellow in the Lennon Lab

Jared Brewer: REU Researcher, Undergraduate, Department of Biology, Transylvania University.

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

Megan Larsen: Ph.D. candidate in the Lennon Lab

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

Nathan Wisnoski: Ph.D. candidate in the Lennon Lab

Will Shoemaker: 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.

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Jim Holland Summer Science Research Program

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