Growth analysis

Scripts for Biolog (Biolog.py) and other bacterial growth (Justgrowth.py) experiment analysis in multiwell plates.

• Calculates bacterial growth parameters such as integral (AUC) and growth rate
• Plots curves for growth, growth in log scale and growth rate (dOD/dt)
• Exports tidy data as time series, summary and experiement description

Configuration

MacOS

• Install Xcode from App Store and open it to accept license (might ask to update your OS to most recent version).
• Install Homebrew by running in Terminal:

  /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

• Install git version control system using brew:

  brew install git

• Install Python using brew:

  brew install python

• Configure your Python:

  brew unlink python && brew link python;
  brew doctor

  In some cases might require mannually setting default Python to Homebrew version:

  echo "export PATH=/usr/local/bin:/usr/bin:$PATH" >> ~/.bash_profile;
  cp /usr/local/bin/python2 /usr/local/bin/python

• Install necessary Python packages:

  pip install numpy, scipy, matplotlib

• Clone Growth_analysis GitHub repository into selected <location>:

  cd <location>;
  git clone git@github.com:PNorvaisas/Growth_analysis.git

• Make sure scripts are executable by running:

  chmod +x *.py

• Add <location> to your PATH:

  echo "export PATH=<location>:$PATH" >> .bash_profile

• Log Out & Log In
• Test scripts by running in any directory:

  Biolog.py -h
  Justgrowth.py -h

• Script should ask you to install the necessary packages that are missing.
• If you can't run these scripts in any directory, there might be a problem with the way you have set PATH. To test this, try running scripts in the <location> where you have cloned git repository. If you still can't do that, there might be other problems.

Windows

• Install Anaconda
  • Choose Anaconda instead of Miniconda (reduced functionality)
  • You need to add Anaconda to your PATH!
• Install git for Windows
• Navigate to a selected <location> using Command Prompt
• Clone Growth_analysis GitHub repository into a selected <location>:

  cd <location>;
  git clone git@github.com:PNorvaisas/Growth_analysis.git

• In this <location> try running:

  python Biolog.py -h
  python Justgrowth.py -h

• If everything is correct, scripts should automatically check for missing packages and install them.

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Biolog.py

• Biolog.py uses Design.xlsx and Biolog_metabolites.csv tables to generate output to a selected folder (defaults to Output).
• Design (template: Biolog_Design_template.xlsx) file can be any table (.xls, .xlsx, .csv) that contains columns:
  • File - name of the plate reader file.
  • Plate - name of the Biolog plate as present in the Biolog_metabolites_EcoCycU.csv table.
  • Reader - name of the reader used to collect data: Tecan or Biotek.
  • Strain - bacterial strain used in an experiment.
  • Type - experiment type: Control/Treatment. Defines line color in generated plots.
  • Replicate - biological replicate of the experiment. Defines linetype in generated plots.
  • Any additional variables of interest which can be applied to the whole plate, like Replicate, Drug, etc.
• As a rule of a thumb, experiment description in Design file should be as detailed as possible.

Running in MacOS, Unix:

• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Terminal and run:

  Biolog.py -i Design.xlsx -d Biolog_metabolites_EcoCycU.csv -o Output_dir

• To get information about input arguments:

  Biolog.py -h

Running in Windows

• Copy both Biolog.py and Biolog_metabolites_EcoCycU.csv to where your plate reader and Design.xlsx files are.
• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Command Prompt and run:

  python Biolog.py -i Design.xlsx -d Biolog_metabolites_EcoCycU.csv -o Output_dir

• To get information about input arguments:

  python Biolog.py -h

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Justgrowth.py

• Justgrowth.py uses Design.xlsx and Pattern.xlsx tables to generate output to a selected folder (defaults to Output).
• Design (template: Justgrowth_Design_template.xlsx) file can be any table (.xls, .xlsx, .csv) that contains columns:
  • File - names of the plate reader files.
  • Pattern - names of Pattern tables, which contain information about the variables investigated in a particular plate
  • Reader - name of the reader used to collect data: Tecan or Biotek
  • Any additional variables of interest which can be applied to the whole plate, like Replicate, Date, etc.
• Pattern (template Justgrowth_Pattern_template.xlsx) file can be any Excel table (.xls, .xlsx) with multiple sheets, each of which describes different variable in the plate and particular value assigned to each well:
  • Strain, Drug, Drug_conc, etc.
• As a rule of a thumb, experiment description in Design file should be as detailed as possible
• Design file can be used to describe variables which are shared in the whole plate.
• Pattern file can be used to describe variable which are unique to each well in the plate.

Runnig in MacOS, Unix

• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Terminal and run:

  Justgrowth.py -i Design.xlsx -o Output_dir

• To get information about input arguments:

  Justrowth.py -h

Windows

• Copy Justgrowth.py to where your plate reader and Design.xlsx files are.
• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Command Prompt and run:

  python Justgrowth.py -i Design.xlsx -o Output_dir

• To get information about input arguments:

  python Justgrowth.py -h

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Growth.py

• Growth.py is a script that combines the functionality of both Justgrowth.py and Biolog.py. It uses the same input files as the previous scripts and generates the same output. Given that most of the functions are shared between Justgrowth.py and Biolog.py, it only makes sense to join them into one, more consistent framework.
• Growth.py uses growth or biolog flags at the end of the command argument to choose Justgrowth.py or Biolog.py functionality correspondingly.
• Growth.py also has full flag, which generates more extensive output in terms of data tables and figures.

Runnig in MacOS, Unix

• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Terminal:
• For regular reads which are used with Pattern files (like Justgrowth.py):

  Growth.py -i Design.xlsx -o Output_dir growth

  For more extensive output:

  Growth.py -i Design.xlsx -o Output_dir growth full

• For Biolog reads which are used with Biolog_meabolites.csv table (like Biolog.py):

  Growth.py -i Design.xlsx -m Biolog_metabolites.csv -o Output_dir biolog

  For more extensive output:

  Growth.py -i Design.xlsx -m Biolog_metabolites.csv -o Output_dir <biolog/growth> full

• To get information about input arguments:

  Growth.py -h

Windows

• Copy Growth.py to where your plate reader and Design.xlsx files are.
• Navigate to the working directory (where your plate reader and Design.xlsx files are) in Command Prompt:
• For regular reads which are used with Pattern files (like Justgrowth.py):

  python Growth.py -i Design.xlsx -o Output_dir growth

  For more extensive output:

  python Growth.py -i Design.xlsx -o Output_dir growth full

• For Biolog reads which are used with Biolog_meabolites.csv table (like Biolog.py):

  python Growth.py -i Design.xlsx -m Biolog_metabolites.csv -o Output_dir biolog

  For more extensive output:

  python Growth.py -i Design.xlsx -m Biolog_metabolites.csv -o Output_dir <biolog/growth> full

• To get information about input arguments:

  python Growth.py -h

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Output

• Description to be added..