Bits and Pieces
Small Projects & Other Things
Here’s a list of projects I’ve worked on over the years, mostly in my free time. I’ve tinkered around and experimented with new libraries and front-ends. Most of these tools were built so that I could use them for my work. I’ve also included a few code snippets from old projects that I’ve revived here.
MultispeQ
Python Libraries
The MultispeQ device uses a serial connection for communication with other devices using a USB cable or via Bluetooth®.The first Python library allows to use scripts to control the MultispeQ and create complex measurements and experiments. The second one is a collection of measurement protocols with numerous supporting functions around creating and using protocols.
The development of the libraries also includes the documentation on how to work and develop them. It is implemented using Sphinx in combination with a GitHub workflow to update the documentation automatically when updates are pushed.
Currently both libraries are not on yet added to The Python Package Index (PyPI) pypi.org but can be installed from the Github repo.
JII-MultispeQ on Github JII-MultispeQ-Protocols on GithubData Analysis
React Data Viewer
This data viewer web application lets you bring in data from text, CSV, and JSON files for analysis. You can filter data, set thresholds, define data types, and plot data. You can also perform statistical tests and add data to maps when you have geocoordinates. The analysis can be saved, including the original data, and shared with others for collaboration. Results can be added to a dashboard, which updates automatically when you filter, set thresholds, or change the selection of subsets.
This is a very early version, so if you spot any issues or need any help, please let me know!
Why is React in the title? Well, the application is based on the free and open-source front-end JavaScript library React, but there are many other amazing open libraries like Plotly for visualizing the data making this app possible.
Explore Your Data Source on GitHubPhotosynthesis
Scheme Creator
Creating or modifying the Photosynthetic Scheme for presentations or posters can become time-consuming, including finding figures or previously used files, modifying, labeling, or changing colors. The creator was built to easily add or remove complexes, different pathways, etc., and export the figure as a vector graphic or a regular image file. It also provides a simple figure legend based on the selected elements.
The figure style is based on Kramer, D. M., Avenson, T. J. and Edwards, G. E. (2004) Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions. Trends Plant Sci 9, 349-357
Create a Figure Source on GitHubData Visualization
Calendar Heatmap
When working with time-resolved data, Calendar heatmaps can be a great tool to visualize clusters, outliers,trends, and seasonal cycles over different periods, using a calendar layout with color gradients. This tool makes it easy to create a heatmap from a dataset formatted as a CSV or JSON file. The resulting map can be edited and saved as SVG or PNG.
Create SVG Heatmap Source on GitHubPeriodic Table
Elements
This was a small project to build an interactive Periodic Chart of Elements as part of an application, that never came to be.
The element information is provided by Pubchem.
View ElementsPeriodic Table
Amino Acids
Biologists have a Periodic Chart too! Like the one for Elements, this chart was also intended to be part of an application.
The chart was originally published by Bachem AG.
View Amino AcidsPredict & Calculate
Protein Properties
A future update of the MS/MS database application 2DB was supposed to have numerous little functions helping to quickly characterize proteins identified by mass spectrometry.
The functions, originally in PHP, have found a new home here.
Calculate ParametersPredict & Calculate
Chlorophyll Content
Working with plants or algae provides the option to use either total protein content or chlorophyll content for the planned experiment.
This calculator allows calculating the chlorophyll content according to Porra et al.
Calculate ContentFormatting
FASTA
Formatting a DNA/RNA or AminoAcid sequence can be a pain, especially if you only have to do it occasionally and you don't have those fancy tools.
This tool you allows to quickly format your sequence to fit your needed layout.
Format FASTAFormatting
Citations
Originally part of a simple function made for the PhotosynQ platform to add references, this form can now be used to receive a formatted citation.
No need to fire up your reference manager, a DOI number is enough.
Get CitationFrom Before the New Millenium
Jugend Forscht
Jugend forscht (Youth researches) is a German competition in the areas of science, technology, engineering, and mathematics (STEM) which two friends and I entered in high school back in 1999. This is the work we did on identifying different leaf pigments over the course of a year in Parthenocissus tricuspidata, titled "Die Wilden Farben des Wilden Weins" - "The Various Colors of Boston Ivy".