Measuring Microbial Growth Rates in a Plate Reader

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:
  • Duration: 16-24 hours (as appropriate for your experiment)
  • Kinetic interval: every 10 minutes
    • Orbital Shaking: 420 seconds at amplitude 3
    • Wait: 5 seconds
    • Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

1) Inoculate an overnight culture of each strain being tested. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate.

4) Begin heating the plate reader to the desired growth temperature using the “Temp. control...” button in the “Start Measurement” dialog box.

• The plate reader needs to be turned on before the computer is booted up to allow the computer to recognize it.

• To export data in Magellan you must first click on the "Data Export" tab, check the "Raw data" box, and then click the right-facing arrow to move "Raw data" to the export column. Then you can select "Export to Excel" from the "File" drop-down menu.

Formatting the data

In order to run Growthcurver, you need to create a tab-delimited file in the following arrangement (see example file below):

• Column 1, "time": The time each measurement was taken.
  
• Column 2, "blank": an average of the blank measurements at each time point.
  
• Columns 3+: the measurements from each sample at each time point, one column per well.
  

• growth_data_example.tsv: Example Growthcurver input file

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

Growthcurver can be run on the formatted tab-delimited file with the following code. The variable "r" contains the growth rate and is extracted once the model has been fit to the data. Note that the units of the growth rate will be based on the units of your file, i.e. if your time is in seconds and the growth measurements are in OD600 the growth rate will be expressed in OD600/second and may need to be converted to other units.

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

library("dplyr")
gc_out %>% filter(note != "")

Additionally, a histogram of the variance of the data can be produced with the following code. Poorly fit samples will appear as outliers on the histogram as in the example below.

gc_out = as_data_frame(gc_out)
hist(gc_out$sigma, main="Histogram of sigma values", xlab = "sigma")

Calculating growth rates using the Grofit R package

Growth curves can also be fit using Grofit, however this package is no longer supported by the current version of R.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring the optical density (OD600) of the culture over time. This protocol is written specifically for a Tecan Infinite® M200 Pro plate reader combined with the Magellan™ data analysis software and thus may require alteration for other machines. The Nunc™ MicroWell™ 96-Well Optical-Bottom Plates (black wells with clear bottoms) are ideal for this assay.

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:
  • Duration: 16-24 hours (as appropriate for your experiment)
  • Kinetic interval: every 10 minutes
    • Orbital Shaking: 420 seconds at amplitude 3
    • Wait: 5 seconds
    • Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

1) Inoculate an overnight culture of each strain being tested. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate.

4) Begin heating the plate reader to the desired growth temperature using the “Temp. control...” button in the “Start Measurement” dialog box.

• The plate reader needs to be turned on before the computer is booted up to allow the computer to recognize it.

• To export data in Magellan you must first click on the "Data Export" tab, check the "Raw data" box, and then click the right-facing arrow to move "Raw data" to the export column. Then you can select "Export to Excel" from the "File" drop-down menu.

Formatting the data

In order to run Growthcurver, you need to create a tab-delimited file in the following arrangement (see example file below):

• Column 1, "time": The time each measurement was taken.
  
• Column 2, "blank": an average of the blank measurements at each time point.
  
• Columns 3+: the measurements from each sample at each time point, one column per well.
  

• growth_data_example.tsv: Example Growthcurver input file

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

Growthcurver can be run on the formatted tab-delimited file with the following code. The variable "r" contains the growth rate and is extracted once the model has been fit to the data. Note that the units of the growth rate will be based on the units of your file, i.e. if your time is in seconds and the growth measurements are in OD600 the growth rate will be expressed in OD600/second and may need to be converted to other units.

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

library("dplyr")
gc_out %>% filter(note != "")

gc_out = as_data_frame(gc_out)
hist(gc_out$sigma, main="Histogram of sigma values", xlab = "sigma")

Calculating growth rates using the Grofit R package

Growth curves can also be fit using Grofit, however this package is no longer supported by the current version of R.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring the optical density (OD600) of the culture over time. This protocol is written specifically for a Tecan Infinite® M200 Pro plate reader combined with the Magellan™ data analysis software and thus may require alteration for other machines. The Nunc™ MicroWell™ 96-Well Optical-Bottom Plates (black wells with clear bottoms) are ideal for this assay.

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:
  • Duration: 16-24 hours (as appropriate for your experiment)
  • Kinetic interval: every 10 minutes
    • Orbital Shaking: 420 seconds at amplitude 3
    • Wait: 5 seconds
    • Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

1) Inoculate an overnight culture of each strain being tested. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate.

4) Begin heating the plate reader to the desired growth temperature using the “Temp. control...” button in the “Start Measurement” dialog box.

• The plate reader needs to be turned on before the computer is booted up to allow the computer to recognize it.

• To export data in Magellan you must first click on the "Data Export" tab, check the "Raw data" box, and then click the right-facing arrow to move "Raw data" to the export column. Then you can select "Export to Excel" from the "File" drop-down menu.

Formatting the data

• Column 1, "time": The time each measurement was taken.
  
• Column 2, "blank": an average of the blank measurements at each time point.
  
• Columns 3+: the measurements from each sample at each time point, one column per well.
  

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

Growthcurver can be run on the formatted tab-delimited file with the following code. The variable "r" contains the growth rate and is extracted once the model has been fit to the data. Note that the units of the growth rate will be based on the units of your file, i.e. if your time is in seconds and the growth measurements are in OD600 the growth rate will be expressed in OD600/second and may need to be converted to other units.

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

library("dplyr")
gc_out %>% filter(note != "")

gc_out = as_data_frame(gc_out)
hist(gc_out$sigma, main="Histogram of sigma values", xlab = "sigma")

Calculating growth rates using the Grofit R package

Growth curves can also be fit using Grofit, however this package is no longer supported by the current version of R.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring the optical density (OD600) of the culture over time. This protocol is written specifically for a Tecan Infinite® M200 Pro plate reader combined with the Magellan™ data analysis software and thus may require alteration for other machines. The Nunc™ MicroWell™ 96-Well Optical-Bottom Plates (black wells with clear bottoms) are ideal for this assay.

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:
  • Duration: 16-24 hours (as appropriate for your experiment)
  • Kinetic interval: every 10 minutes
    • Orbital Shaking: 420 seconds at amplitude 3
    • Wait: 5 seconds
    • Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

1) Inoculate an overnight culture of each strain being tested. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate.

4) Begin heating the plate reader to the desired growth temperature using the “Temp. control...” button in the “Start Measurement” dialog box.

• The plate reader needs to be turned on before the computer is booted up to allow the computer to recognize it.

• To export data in Magellan you must first click on the "Data Export" tab, check the "Raw data" box, and then click the right-facing arrow to move "Raw data" to the export column. Then you can select "Export to Excel" from the "File" drop-down menu.

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:
  • Duration: 16-24 hours (as appropriate for your experiment)
  • Kinetic interval: every 10 minutes
    • Orbital Shaking: 420 seconds at amplitude 3
    • Wait: 5 seconds
    • Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

Growthcurver can be run with the following code. The input file should be a tab-delimited file, which can be created from the Excel spreadsheet. The variable "r" contains the growth rate and is extracted once the model has been fit to the data.

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

gc_out %>% filter(note != "")
gc_fit$vals$note

library(dplyr)
gc_out = as_data_frame(gc_out)
hist(gc_out$sigma, main="Histogram of sigma values", xlab = "sigma")

Calculating Growth Rates using Grofit R package

Growth curves can also be fit using Grofit, however this package is no longer supported by the current version of R.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring the optical density (OD600) of the culture over time. This protocol is written specifically for a Tecan Infinite M200 Pro plate reader combined with the Magellan data analysis software and thus may require alteration for other machines.

Program set-up

The parameters used by the Barrick Lab are:

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:

Reviving cultures (2 days before experiment)

1) Grow an overnight culture of each strain being tested. Inoculate 2 μl of frozen glycerol stocks of each strain into 5 ml of media. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

2) Inoculate 5 μl of each overnight culture into fresh media to precondition. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.
3) Place the media you will use for the assay in an incubator at the correct growth temperature overnight to pre-warm.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate. Clear Costar 96-well plates are a good brand to use.

4) Add 195 μl of pre-warmed media to each well being used for cultures and additional wells for blanks.
5) Inoculate each test well with 5 μl of overnight culture.
6) Place the plate into the plate reader. The lid can be removed (we've had no problems with contamination, as seen on wells with LB blanks, with this).
7) Start your program.
8) Once the program has finished, export the data as an Excel spreadsheet.

Fitting growth curves with Growthcurver in R

Growthcurver is an R package that analyzes the optical density data by fitting it to a logistic function from which the growth rate, doubling time, and carrying capacity can be calculated. Growthcurver can be installed with the command: install.packages("growthcurver")

Growthcurver can be run with the following code. The input file should be a tab-delimited file, which can be created from the Excel spreadsheet. The variable "r" contains the growth rate and is extracted once the model has been fit to the data.

library("growthcurver")

#import data
growth = read.table("/path/to/your/file/data.tsv", header=T, sep="\t", stringsAsFactors=F)

#calculate growth rate
gc_out = SummarizeGrowthByPlate(growth, bg_correct="blank")
gc_out$r

gc_out %>% filter(note != "")
gc_fit$vals$note

library(dplyr)
gc_out = as_data_frame(gc_out)
hist(gc_out$sigma, main="Histogram of sigma values", xlab = "sigma")

Calculating Growth Rates using Grofit R package

Growth curves can also be fit using Grofit, however this package is no longer supported by the current version of R.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

Program set-up

• Temperature: Appropriate for growth of your organism
• Kinetic Cycle:

Duration: 16-24 hours (as appropriate for your experiment)

Kinetic interval: every 10 minutes

Orbital Shaking: 420 seconds at amplitude 3

Wait: 5 seconds

Absorbance reading: 600 nm, 25 flashes, 50 ms settle time

It's important for the program to shake for most of the time that you are not making measurements. Less shaking leads to slower growth.

Reviving cultures (2 days before experiment)

1) Grow an overnight culture of each strain being tested. Inoculate 2 μl of frozen glycerol stocks of each strain into 5 ml of media. Prepare a separate tube of uninoculated media as a control for contamination. Incubate overnight.

Preconditioning cultures (1 day before experiment)

Preconditioning acclimates the strains to the media. Additionally, on this day you should pre-warm your media as it takes a long time for the plate reader to warm up media. Not doing this will lead to inconsistent lag time.

Growing cells in plate reader and measuring OD600

All strains tested should have at least have 3 replicates, although more replicates should be performed as long as there is available space on the plate. Evaporation can occur in the outermost wells, so if there are few enough samples the outer ring of wells should be skipped. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are distributed randomly across the plate. Clear Costar 96-well plates are a good brand to use.

References

1. Growthcurver publication: https://link.springer.com/article/10.1186/s12859-016-1016-7
2. Growthcurver manual: https://cran.r-project.org/web/packages/growthcurver/vignettes/Growthcurver-vignette.html

Contributors

• Isaac Gifford
• Julie Perreau
• Gabriel Suárez

Measuring Microbial Growth Rates in a Plate Reader

Growing cells in plate reader and measuring OD600

Converting your file with OD data to the proper format

• yourdatafile.csv: Example spreadsheet of your OD600 data file

Create a "times only" csv file

• timesonlyworksheet.csv: Times only worksheet for Grofit

Calculating Growth Rates using Grofit R package

setwd("C:/.../R_GrowthData") #sets the working directory to the folder (here named R_GrowthData) you'll be working on your computer
install.packages(c("grofit", "tidyr", "reshape2"))
library(grofit)
library(tidyr)
library(reshape2)

growthdata <- read.csv("yourdatafile.csv",sep=",", header=TRUE, check.names = FALSE) <br/> timedata <- read.csv("timesonlyworksheet.csv", sep=",", header=TRUE, check.names = FALSE) <br/> gro <- grofit(timedata, growthdata) #runs grofit <br/>
summary_table<-summary.gcFit(gro$gcFit) #makes a summary table <br/> write.csv(summary_table,"FinalTable.csv") #makes a csv file of the summary table

Accepting/declining model fits:

Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

Growing cells in plate reader and measuring OD600

All strains tested should at least have 3 replicates. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are randomly located at different wells. Set up 200 µL cultures with 2 µL from a pre-conditioned (same media as actual test) overnight culture. These 100-fold dilutions should be good enough for OD600 measurements that will give out reliable information for lag phase, exponential phase and stationary phase. To allow cultures to aerate properly, set the plate reader to shake (1 mm radius) at least every 5 minutes; normally this would be before and after taking reads.

Converting your file with OD data to the proper format

• yourdatafile.csv: Example spreadsheet of your OD600 data file

Create a "times only" csv file

• timesonlyworksheet.csv: Times only worksheet for Grofit

Calculating Growth Rates using Grofit R package

setwd("C:/.../R_GrowthData") #sets the working directory to the folder (here named R_GrowthData) you'll be working on your computer
install.packages(c("grofit", "tidyr", "reshape2"))
library(grofit)
library(tidyr)
library(reshape2)

growthdata <- read.csv("yourdatafile.csv",sep=",", header=TRUE, check.names = FALSE) <br/> timedata <- read.csv("timesonlyworksheet.csv", sep=",", header=TRUE, check.names = FALSE) <br/> gro <- grofit(timedata, growthdata) #runs grofit <br/>
summary_table<-summary.gcFit(gro$gcFit) #makes a summary table <br/> write.csv(summary_table,"FinalTable.csv") #makes a csv file of the summary table

Accepting/declining model fits:

Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

Contributors

• Gabriel Suárez
• Julie Perreau

Download and install "R" and "R studio"

Growing cells in plate reader and measuring OD600

Converting your file with OD data to the proper format

• yourdatafile.csv: Example spreadsheet of your OD600 data file

Create a "times only" csv file

• timesonlyworksheet.csv: Times only worksheet for Grofit

Accepting/declining model fits:

Reading summary table results:

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

Contributors

• Gabriel Suárez
• Julie Perreau

Converting your file with OD data to the proper format

• yourdatafile.csv: Example spreadsheet of your OD600 data file

Create a "times only" csv file

• timesonlyworksheet.csv: Times only worksheet for Grofit

Calculating Growth Rates using Grofit R package

setwd("C:/.../R_GrowthData") #sets the working directory to the folder (here named R_GrowthData) you'll be working on your computer
install.packages(c("grofit", "tidyr", "reshape2"))
library(grofit)
library(tidyr)
library(reshape2)

growthdata <- read.csv("yourdatafile.csv",sep=",", header=TRUE, check.names = FALSE)
timedata <- read.csv("timesonlyworksheet.csv", sep=",", header=TRUE, check.names = FALSE)
gro <- grofit(timedata, growthdata) #runs grofit

summary_table<-summary.gcFit(gro$gcFit) #makes a summary table
write.csv(summary_table,"FinalTable.csv") #makes a csv file of the summary table

Accepting/declining model fits:

Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

Contributors

• Gabriel Suárez
• Julie Perreau

Download and install "R" and "R studio"

You'll need to download and install R on your computer. Once R is installed, you can then download and install "R studio" which is easier to work with.

You can download "R" here: https://cran.r-project.org/mirrors.html
You can download "R studio" here: https://www.rstudio.com/

Growing cells in plate reader and measuring OD600

All strains tested should at least have 3 replicates. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are randomly located at different wells.

Converting your file with OD data to the proper format

Create a "times only" csv file

Accepting/declining model fits:

Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

Growing cells in plate reader and measuring OD600

All strains tested should at least have 3 replicates. Due to small variations in temperature throughout a 96-well plate, best results will be obtained if replicates are randomly located at different wells. Set up 200µL cultures with 2µL from a pre-conditioned (same media as actual test) overnight culture. These 100-fold dilutions should be good enough for OD600 measurements that will give out reliable information for lag phase, exponential phase and stationary phase. To allow cultures to aerate properly, set the plate reader to shake (1mm radious) at least every 5 minutes; normally this would be before and after taking reads.

Converting your file with OD data to the proper format

Create a "times only" csv file

Calculating Mutation Rates using Grofit R package

setwd("C:/.../R_GrowthData") #sets the working directory to the folder (here named R_GrowthData) you'll be working on your computer

Accepting/declining model fits:

Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

References

1. https://www.jstatsoft.org/article/view/v033i07
2. https://cran.r-project.org/web/packages/grofit/index.html

-- Main.GabrielSuarez - 15 Dec 2016