2026 German Conference on Bioinformatics workshop: Turning Python scripts built with Sugar into web apps

Workshop Description: Many bioinformatics tools remain inaccessible to experimental biologists due to their command-line interfaces. This workshop addresses that gap by demonstrating how Python scripts can be transformed into user-friendly web applications. Participants will use the sugar package--a lightweight Python library for sequence and annotation handling--together with NiceGUI to build interactive frontends. Through hands-on exercises, attendees will develop small analysis scripts and convert them into interactive web applications.

Preparation

1. Clone (recommended) or download and unpack this repository. It contains the necessary data files in the data folder and the slides.

git clone https://github.com/rnajena/workshop_gcb2026_webapps.git
cd workshop_gcb2026_webapps

2. Install the necessary tools -- mafft, nicegui, rnajena-sugar. The recommended way is to install these in a new conda environment.

a) Install conda (here mini-forge on Linux, you may use other installers).

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

For Windows and MacOS users check the install instructions.

b) Add bioconda channel (for MAFFT)

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Note: conda-forge is by default already activated in mini-forge, but the above commands guarantee that the conda-forge channel has a higher priority than bioconda.

c) Create new conda environment with conda requirements

conda create -n gcb_webapps "python=3.13" mafft nicegui ipython pip pandas platformdirs pytest requests seaborn

d) Install sugar which is provided via PyPI in the new environment

conda activate gcb_webapps
pip install "rnajena-sugar>=1.2"

e) Test the installation by running

sugar test

f) Activate environment in new terminals

conda activate gcb_webapps

How to

Study the slides. Try out the code snippets from the tutorial in an interactive IPython session inside the data folder. Solve the tasks by creating your scripts in the wd folder. The Sugar and NiceGUI code examples are located in this folder and can be used as a basis for your solutions.

Code solutions

For code solutions or guidance, please contact Tom.