Projects
Preamble
Biomedicine raises the most interesting challenges of recent times, and a clever combination of interdisciplinary STEM approaches is the best way to address them. This website is about developing code examples for biological data analysis, gathering knowledge as well as improving your digital everyday workflow…
Excited to see the great advances of this biological century! : )
Project showcase
List of Software Projects including live demos, video manuals and github links – have fun!
Analysis of BioImages
early Summer 2023 – Sept. 2023 (paused)
This is becoming a collection of Python-based example codes focussing on image analysis of biological matter.
Languages: Python (Jupyter Notebook)
keywords: Analysis of fluorescence micrographs (basic) | Cell masking, cell and nuclei segmentation | Cell counting | Center-of-Mass determination | Curvature quantification | Geometric fitting of structures | Time lapse and tissue analysis
Sequence Analysis
early Summer 2023 – Sept. 2023 (paused)
This “Part 1” of the project aims at the principles of analysing (DNA-) sequence data on a very basic level. It is motivated by the many jobs descriptions currently online for genome analysis, next-gen-sequencing (NGS) advances and my fascination towards life science in general. More parts are to come soon…Goal description and example code is presented in a Jupyter-Notebook-(.ipynb-)fileformat. Jupyter-NB or equivalent is required to modify scripts.
Languages: Python (Jupyter Notebook)
keywords: DNA-Seq Analysis (basic) | Graphical Interfaces with TKinter | Sequence Alignment & Needleman-Wunsch-Algorithm | Gene maps & Data visualization
Actionbutton-Dashboard
Spring 2023
Sick and tired of endlessly navigating through directories and bookmark inventories? The Actionbutton-Dashboard-project puts order & efficiency to your everyday digital workflow! An easy-to-configure array of JButtons can open local apps, folders, network drives as well as intranet and internet websites. All you need is to paste the respective paths into spreadsheet files, give the buttons a name and then execute the jar file. Additional configuration parameters can be set such as colors, individual icons and mouseover-comments for each button. Just check out the readme.md on github for further details!
Languages: Java, xml (Maven)
keywords: object oriented programming | swing GUI-Toolkit | building fat jar through xml
POI-ROI-map
Autumn 2022
Life science – an American thing? The SARS-CoV-2 pandemic has shown that European research facilities & companies are very well capable of contributing to the global fight for health. However, it’s fairly easy to lose track of who does what. The original intention of this little POI-ROI-map project was to simplify your job search by enabling you to tag individual points of interest and regions (ROIs & POIs). Nonetheless, this script can also be used for any other purpose! A simple .xlsx spreadsheet-file serves as an easy-to-access “database” and let you define places worth taking a closer look. Available marker elements are ROIs, distance radii as well as POI flags. All elements can be color-coded, the POIs can be further specified by info-popups and are automatically clustered depending on the current zoom setting. Moreover, multiple map representations are available. Have fun while playing around!
Languages: Python, HTML
keywords: folium module | clustering of datapoints | open maps | webdesign