Microbes in Spaaaaaaaaaaaaaaaace

Growth data and analysis for microbial playoffs in space

Project MERCCURI

This repository contains all the raw data from both the ground based and in-orbit growth experiments. The instruments used were SpectraMax M5e plate readers, with the device aboard the International Space Station modified by Nanoracks, Inc. All measurements are optical density at 600 nm (OD600).

What is all this stuff?

There are a lot of files here! What's going on?

Notebooks

• SpaceGrowthWinners.ipynb : Generates analytical charts and tables
• SpectraMax M5e OD600.ipynb : Generates charts of raw data
• OD600 Tecan.ipynb : Generates charts for method validation

Raw data

The raw data has been plotted in 12x8 grids of bar charts. Each grid cell represents the well on the plate, and each bar represents one of the nine reads in the well.

Raw data from the ground

Ground Plate 1 : 0, 24, 48, 72, 96 hours

• Groundplate1_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate1_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate1_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate1_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate1_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Ground Plate 2 : 0, 24, 48, 72, 96 hours

• Groundplate2_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate2_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate2_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate2_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate2_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Ground Plate 3 : 0, 24, 48, 72, 96 hours

• Groundplate3_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate3_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate3_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate3_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Groundplate3_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Raw data from Space

Space Plate 1 : 0, 24, 48, 72, 96 hours

• Spaceplate1_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate1_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate1_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate1_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate1_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Space Plate 2 : 0, 24, 48, 72, 96 hours

• Spaceplate2_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate2_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate2_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate2_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate2_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Space Plate 3 : 0, 24, 48, 72, 96 hours

• Spaceplate3_0.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate3_24.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate3_48.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate3_72.{txt,png,pdf} : raw data, PNG chart, PDF chart
• Spaceplate3_96.{txt,png,pdf} : raw data, PNG chart, PDF chart

Method validation run :

• OD600_tecan_raw.{csv,png,pdf} : raw data, PNG chart, PDF chart

• Tecan_final_ground1.csv : raw data from post-experiment plate scan

• Tecan_final_ground2.csv : raw data from post-experiment plate scan

• Tecan_final_ground3.csv : raw data from post-experiment plate scan

• Tecan_final_space1.csv : raw data from post-experiment plate scan

• Tecan_final_space2.csv : raw data from post-experiment plate scan

• Tecan_final_space3.csv : raw data from post-experiment plate scan

Plate mapping files

• platemap_ground1.csv : Map for Ground Plate 1
• platemap_ground2.csv : Map for Ground Plate 2
• platemap_ground3.csv : Map for Ground Plate 3
• platemap_space1.csv : Map for Space Plate 1
• platemap_space2.csv : Map for Space Plate 2
• platemap_space3.csv : Map for Space Plate 3

Sample metadata

• spacebugs.tsv : bug list (index, species, name)
• spacebugsnames_2.txt : bug list (index, site, species, name, source)

Plots, charts and tables

The event data is plotted in 12x4 grids gathering all observations for each organism into one grid cell (two experiments of six wells of nine reads points each of five time points). They are represented as follows :

• Box plots : space data
• Green line : median values, space data
• Brown line : median values, ground data
• Red line : Least squares fit to exponential model

Best Huddle : Highest optical density achieved

• BestHuddle.{png,pdf} : Charts of all results
• BestHuddle_top3.{png,pdf} : Charts of top 3 results
• BestHuddleRankings.tsv : Table of numerical results

Best Tipoff : Largest increase in optical density achieved on the first day

• BestTipoff.{png,pdf} : Charts of all results
• BestTipoff_top3.{png,pdf} : Charts of top 3 results
• BestTipoffRankings.tsv : Table of numerical results

Best Sprint : Largest increase in optical density achieved on any day of the experiment

• BestSprint.{png,pdf} : Charts of all results
• BestSprint_top3.{png,pdf} : Charts of top 3 results
• BestSprintRankings.tsv : Table of numerical results

Space vs. Ground :

The folder Space_v_Ground contains PDfs and PNGs comparing the median optical density of the space-based and ground-based experiments for each individual organism. Files are named according to their sample name as it appears in the mapping files.

• Space_vs_Ground.{png,pdf} : Charts of Spave vs. Ground results
• Space_vs_Ground.tsv : Table of Space vs. Ground rankings

Funding

This work was funded by a grant from the Alphred P. Sloan foundation to Jonathan A. Eisen. Launch costs were supported by Space Florida. Launch integration was performed by Nanorack, Inc. This project would not have been possible without the expert help and guidance of Carl Carruthers at Nanoracks.