DaKS - University of Kassel's research data repository

DaKS is the institutional repository of the University of Kassel for research data. It offers structured storage of research data alongside with descriptive metadata, long-term archiving for at least 10 years and – if requested – the publication of the dataset with a DOI.

DaKS is managed by the university library and the IT Service Centre of the University of Kassel. It is hosted at Philipps-Universität Marburg. We are happy to advise you via daks@uni-kassel.de.

Recent Submissions

Biological data and model Matlab scripts from Zolmon, Trummel, et al., (2026): Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhythms).
(Universität Kassel) Zolmon, Huleg; Trummel, Tabea; Kräling, Lukas; Przybylla, Patrick; Schneider, Anna C.; Stursberg, Olaf; Stengl, Monika
# Biological and simulation data for Zolmon, Trummel, et al., 2026: Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhythms)

## File overview

This repository contains four files: One excel file with biological data and three Matlab files that contain the model code.

## Description Excel file with biological data

This excel file contains the data that is presented in Zolmon, Trummel, et al., 2026: Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhythms)

The data is organized in two sheets:
1. running wheel data,
2. qPCR data.

The sheet "running wheel data" contains 9 lines of metadata, an empty line, one line with column headers followed by the data. The first column is the day relative to dsRNA injection; the second column is the minute of that day, and subsequent columns contain wheel turns in 1 minute bins. Metadata contains (top to bottom): Unique animal identifier (animal ID); light condition as either constant darkness (DD) or constant light (LD); experiment category as either CYC only (CYC), CLK only (CLK), double knockdown (DKD), triple knockdown (TKD); knockdown treatment with the following targets GFP (as control), CLK, CYC, double knockdown (DKD: CLK + CYC), triple knockdown (TKD: PER, TIM1, CRY2) or WT (wild-type, no treatment); experimenter who performed the dsRNA injection and animal care in the running wheels; start date (DD.MM.YYYY) on which the running wheel assay was started; injection date (DD.MM.YYYY) on which dsRNA was injected; indication in which Figure the data from one particular animal was used as an illustrative example; indication as part of which Figure the data is displayed.

The sheet "qPCR data" contains 8 columns. The first column is the experiment ID; second column is the light condition in which the animals were kept, either constant darkness (DD), constant light (LL), or 12:12 hours light:dark (LD); third column is experiment category as either untreated wildtype randomly sampled from the breeding colony (WT), untreated wildtype with age-controlled sampling (WT_age_controlled), CLK knockdown (CLK_KD), CYC knockdown (CYC_KD); fourth column is knockdown treatment with the following targets: none (WT), GFP (as injection control), CLK, CYC, triple knockdown (TKD: PER, TIM1, CRY2); fifth column lists the day or zeitgeber time (ZT) or projected ZT of sacrifice for the qPCR; sixth column lists the target mRNA of the qPCR, seventh column lists the cycle threshold of the qPCR (red values were excluded from their triplets mean calculation); eighth column indicates in which figure the data point was used.

## Description Matlab files

This MATLAB code implements the discussed networks of the computational model to describe the cockroach circadian clock.

The code is divided into three different MATLAB scripts:

1. *clock\_network\_DD\_het.m*: This code simulates the cockroach clock, which is modeled by a heterarchical network. Effects of knockdown are investigated for constant darkness (DD).
2. *clock\_network\_DD\_hier.m*: The cockroach clock is modeled by a hierarchical network in constant darkness (DD).
3. *clock\_network\_LL\_het.m*: To examine the effects of knockdown in constant light (LL), the heterarchical network is adjusted according to LL conditions.

Each script can be run individually. The corresponding networks are represented by matrices using time-varying coupling gains. The parameters of the planar switching affine systems (PSAS), modeling the subsystems' dynamics, are given. The networked system can then be simulated. Finally, the simulation results of the computational model are visualized graphically.

For more details on modeling and discussion, see the corresponding paper.

### Software

* Version R2024b of MATLAB was used.
* Toolbox *Communications Toolbox* is requiered.
Agent Home Investment Decisions Stages (AHOIS): Baseline runs of variants DEZ, KWN, WWN, GPJ for Decision Theatre 2 (research project WAERMER)
(Universität Kassel, 2025-04-04) Holzhauer, Sascha; Digel, Ivan; Krebs, Friedrich
The challenge of climate change demands active political interventions. Private building energy retrofitting is one of the main fields such interventions focus on, as in the European Union households consume around a quarter of total produced energy. Finding an efficient way to propose and evaluate policies aiming to stimulate private energy retrofitting is a promising direction approached from different methodical perspectives, among which agent-based modelling is a yet an underdeveloped one.
This dataset is obtained from an agent-based model applying a psychologically grounded multi-stage algorithm to simulate houseowners’ decision-making related to heating system replacements. The model is applied to the district Kiel-Oppendorf to investigate fulfillment for four variants of heat supply (DEZ - decentral supply; KWN - cold local network; WWN - hot local network, GPJ - special hot local network). Plots and slides derived from these data were presented at a so-called decision theatre held on April 4th 2025 in Kiel involving relevant stakeholders such as intallers, house owners, energy advisers, grid operators and city officials.
This dataset contains baseline scenarios for the four variants. A second dataset contain data about application of interventions to increase fulfillment.
Numerical Simulations for ‘Autonomous Circadian Oscillators Intrinsic to Cell Membranes’
(Universität Kassel) Forlino, Mauro Ariel; Garcia, Martin Ezequiel; Piro, Oreste; Stengl, Monika
This repository contains the computational models and simulation code for the membrane-based circadian oscillator described in:

**"Autonomous circadian oscillators intrinsic to cell membranes"**
Mauro A. Forlino, Oreste Piro, Monika Stengl & Martin E. Garcia
https://doi.org/10.21203/rs.3.rs-8788655/v1

Numerical models for "Autonomous circadian oscillators intrinsic to cell membranes" (Forlino, Piro, Stengl, Garcia). Computational models supporting the hypothesis that cell membranes can host autonomous post-translational feedback loops (PTFLs) capable of generating circadian (~24 h) oscillations independently of nuclear transcription-translation feedback. Two cell types are modeled: anucleate red blood cells, using a Goodwin-type feedback architecture, and neurons, using a Hodgkin-Huxley framework with coupled fast positive and delayed negative feedback. Both models produce self-sustained ~24 h oscillations without nuclear input.
Absolute measuring interferometric high-speed profilometer [Dataset]
(Universität Kassel) Eckhardt, Tim; Ziosnki, David; Lehmann, Peter
This dataset contains experimental measurement data obtained for the investigation of high-speed profilometer measurements and absolute surface topography measurement. The dataset comprises measurements acquired with different experimental configurations, including a depth scan with a velocity of 10 µm/s, a lateral scan of a chirp normal, and a measurement of the chirp normal using the GD25 measurement system. The high-speed measurements were recorded with sampling frequencies of 5 MHz and 10 MHz and excitation frequencies of 20 kHz and 19.5 kHz, respectively. The data are provided in HDF5 and text-based formats and include the raw measurement signals as well as example Python scripts for reading and processing the data. The dataset is intended to support the analysis and further development of high-speed profilometry methods, as well as the reproducibility and further investigation of the results presented in the corresponding publication. IMPORTANT: If you use these data, please cite the corresponding article mentioned below.
Navigating the Remanufacturing Trilemma: Balancing Customer, Manufacturer, and Legislator Interests [Repository]
(Universität Kassel, 2025-02-25) Reintanz, Lisa; Wittine, Nicolas; Lange, Kirsten; Wenzel, Sigrid; Refflinghaus, Robert
The associated paper explores the trilemma between different circular economy stakeholders (customer, manufacturer and legislator). The overview database (2019-2024) contains 84 relevant papers (out of 880), which were reduced to 27 through analysis. In addition, findings from expert interviews are used to uncover conflicts and synergies.

The provided Excel file contains the researched literature and documents the process and findings. The main content is found in "References". Each PDF contains an interview protocol, numbered according to the paper’s Table 3. Each protocol contains a description of the expert and a discussion summary.

The provided presentation was used as a guide to conduct the interviews.