Related papers: PEtab-GUI: A graphical user interface to create, e…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
Reliable parameter extraction from experimental data is central to quantitative analysis in spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. We present FitED, a Python-based desktop…
Peptides offer great biomedical potential and serve as promising drug candidates. Currently, the majority of approved peptide drugs are directly derived from well-explored natural human peptides. It is quite necessary to utilize advanced…
The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present…
Understanding mechanistic relationships among genes and their impacts on biological pathways is essential for elucidating disease mechanisms and advancing precision medicine. Despite the availability of extensive molecular interaction and…
Uncovering the underlying causal mechanisms of complex real-world systems remains a significant challenge, as these systems often entail high data collection costs and involve unknown interventions. We introduce MetaCaDI, the first…
Magboltz is widely used to compute electron transport properties in gas mixtures for detector applications. Its text-based workflow, however, can be a barrier for routine use, especially for users who are not already familiar with the…
Probabilistic graphical models (PGMs) serve as a powerful framework for modeling complex systems with uncertainty and extracting valuable insights from data. However, users face challenges when applying PGMs to their problems in terms of…
This project focuses on utilizing a combination of Tkinter for GUI development and Tableauf for data visualization to do sentiment analysis on thread reviews.The main goal is to evaluate and visualize consumer sentiments as they are…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works…
The possibility to create reactive robot programs faster without the need for extensively trained programmers is becoming increasingly important. So far, it has not been explored how various techniques for creating Behavior Tree (BT)…
Data imputation is an effective way to handle missing data, which is common in practical applications. In this study, we propose and test a novel data imputation process that achieve two important goals: (1) preserve the row-wise…
The Parameter-Efficient Fine-Tuning (PEFT) method, which adjusts or introduces fewer trainable parameters to calibrate pre-trained models on downstream tasks, has become a recent research interest. However, existing PEFT methods within the…