SGT-Analyser

• by Riccardo Spott

Cite as

Spott, Riccardo, & Brandt, Christian. (2020, October 27). SGT-Analyser: A tool to automatically analyse antibiotic-synergism via bacterial growth-curves (checkerboards) (Version v0.10.0). Zenodo. http://doi.org/10.5281/zenodo.4139379

What is SGT-Analyser?

The SGT-Analyser is an tool for the automated analysis of growth-curves of, in an checkerboard-style treated bacteria. The goal is to determine synergistic, additional or antagonistic effects between the two applied antibiotics. For this the so called "Start Growth Time"-method is used.

Getting started

You can use this program either in Google Colab or in your terminal. The use via Google Colab is suited for non-informaticians and provides a graphical interface to interact with. To use the terminal-variant some informatical knowledge is required to setup the modules and use the flags. Further you will need an Excel-file with the data of your growth curves

In the following is described how to use either of this options.

Using SGT_Analyser in Google Colab

• use the link "Open in Colab"
• You will be directed to a Google Colab-site, where the program is setup
• start each block after the preceding, following the instrcutions given at the site

Using SGT-Analyser in the terminal

For the use of SGT-Analyser in your terminal there are two options.

1. Setup on your own system:

• clone this git-repository to your computer using the command

git clone https://github.com/DataSpott/SGT-Analysis.git

• if not already installed use the following command to install pip for python3 in your terminal

sudo apt install python3-pip

• use the following command to set up the necessary python-modules

pip3 install pandas altair xlrd altair_saver selenium scipy tabulate IPython

• to start the SGT-Analyser use the following command in the repository directory

$PWD/sgt_analyser.py --help

2. Use the docker-container:

• make sure docker is installed at your system as described under https://docs.docker.com/get-docker/
• use following command to pull the docker-image to your system, mount all data in the current directory to "/input" in the container and execute it

docker run --rm -it -v $PWD:/input dataspott/sgt_analyser:v0.9.1 sgt_analyser.py -i /input/tecan_infinite_test_data.xlsx

• to get help and see how to use the program use the following command

docker run --rm -it -v $PWD:/input dataspott/sgt_analyser:v0.9.1 sgt_analyser.py --help

Further information

Detailed instructions about the setup and use of "SGT-Analyser" can be found in the manual provided in this repository.