Search · four archives
Search · four archives
15 papers · ranked by Valyu relevance
Jonathan Chacko, Hakan Ozadam, Can Cenik
Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses. In this study, we introduce RiboGraph, a dedicated visualization tool designed to work…
Sanjay Soundarajan, Sachira Kuruppu, Ashutosh Singh, Jongchan Kim + 1 more
The NIH SPARC program seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. SPARC-funded researchers are generating rich datasets from neuromodulation research that are curated and shared according to FAIR (Findable, Accessible, Interoperable…
Oscar O. Ortega, Carlos F. Lopez
Computational models of network-driven processes have become a standard to explain cellular systems-level behavior and predict cellular responses to perturbations. Modern models can span a broad range of biochemical reactions and species that, in principle, comprise the complexity of dynamic cellular processes.…
Anton Stratmann, Martin Beyß, Johann F. Jadebeck, Katharina Nöh
Understanding input-output relationships within multivariate datasets is an ubiquitous task in the life and data sciences. For this, visual analysis is indispensable for providing expressive summaries and preparing decision-making. We present the visual analysis approach and software MooViE, which is designed to strike…
Hamed Rahimi Nasrabadi, Jose-Manuel Alonso
Head-mounted tools for eye/head tracking are increasingly used for assessment of visual behavior in navigation, sports, sociology, and neuroeconomics. Here we introduce an open-source python software (TP3Py) for collection and analysis of portable eye/head tracking signals using Tobii Pro Glasses 3. TP3Py’s modular…
Christian Scheeder, Florian Heigwer, Michael Boutors
The analysis and visualization of arrayed high-throughput screens (HTS), such as cell-based RNAi or small-molecule HTS experiments, requires specialized computational methods. Software packages such as the R/Bioconductor package cellHTS have been developed to support the analysis and are broadly used by the…
Muhammad Zain Butt, Rana Sheraz Ahmad, Eman Fatima, Muhammad Tahir ul Qamar
The application of Large Language Models (LLMs) for generating data visualizations through natural language interaction represents a promising advance in AI-assisted scientific analysis. However, existing LLM-based tools largely emphasize graph generation, while research workflows require not only visualization but…
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P. Telles, Gabriela Vaz Meirelles + 1 more
The advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract…
V. Chiara, A. Buatois, S.-Y. Kim
Video-tracking programs have now become an essential tool for researchers measuring animal behavior across biological fields. The panel of available programs is growing rapidly, providing researchers with numerous specific tools that will match their precise needs. However, their proliferation may complicate…
Renske van Raaphorst, Morten Kjos, Jan-Willem Veening
High-throughput analyses of single-cell microscopy data is a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to…
Nowlan H Freese, Karthik Raveendran, Chaitanya Kintali, Srishti Tiwari + 3 more
Visualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Native, desktop visualization tools like Integrated Genome Browser enable highly interactive data…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
John A. P. Sekar, Jose-Juan Tapia, James R. Faeder
Rule-based modeling frameworks provide a specification format in which kinetic interactions are modeled as “reaction rules”. These rules are specified on phosphorylation motifs, domains, binding sites and other sub-molecular structures, and have proved useful for modeling signal transduction. Visual representations are…
Roger E. Zhu, Xintong Diao, Xiaoyu Liu, Qin Ru + 4 more
Synaptic transmission mediated by various neurotransmitters influences a wide range of behaviors. However, understanding how neuromodulatory transmitters encode diverse behaviors and affect their functions remains challenging. Here, we introduce GESIAP3.0, an advanced, third-generation image analysis program based on…
Yann Spöri, Jean-François Flot
Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is…