25 papers · ranked by Valyu relevance
Leonel Merino, Ekaterina Kozlova, Oscar Nierstrasz, Daniel Weiskopf
—Although many tools have been presented in the research literature of software visualization, there is little evidence of their adoption. To choose a suitable visualization tool, practitioners need to analyze various characteristics of tools such as their supported software concerns and level of maturity. Indeed, some…
Murat Cihan Sorkun, Dajt Mullaj, J. M. Vianney A. Koelman, Süleyman Er
Visualizing chemical spaces streamlines the analysis of molecular datasets by reducing the information to human perception level, hence it forms an integral piece of molecular engineering, including chemical library design, high-throughput screening, diversity analysis, and outlier detection. We present here ChemPlot…
Rui Wang, Yasset Perez-Riverol, Henning Hermjakob, Juan Antonio Vizcaíno
Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool…
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…
Wei Zhang, Jonathan A Fine, Christopher Sculley, Jordon McGraw + 1 more
The representation of complex biomolecular structures and interactions is a difficult challenge across life sciences. Researchers and students use unintuitive 2D representations to gain an intuitive understanding of 3D space and molecular interactions. Since this is cumbersome for complex structures, such as…
Georgios A Pavlopoulos, Anna-Lynn Wegener, Reinhard Schneider
The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations…
Johannes Waschke, Mario Hlawitschka, Kerim Anlas, Vikas Trivedi + 3 more
In biology, we are often confronted with information-rich, large-scale trajectory data, but exploring and communicating patterns in such data is often a cumbersome task. Ideally, the data should be wrapped with an interactive visualisation in one concise package that makes it straightforward to create and test…
Noptanit Chotisarn, Leonel Merino, Zheng Xu, Supaporn Lonapalawong + 3 more
'Tianye Zhang' 'Mingliang Xu' 'Wei Chen'] Abstract We report on the state-of-the-art of software visualization. To ensure reproducibility, we adopted the Systematic Literature Review methodology. That is, we analyzed 1440 entries from IEEE Xplore and ACM Digital Library databases. We selected 105 relevant full papers…
Eugenia G Giannopoulou, George Lepouras, Elias S Manolakos
Background The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction…
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…
Annabelle M. Coles, Yuening Liu, Pallav Kosuri
Imaging-based spatial transcriptomics can reveal gene expression in situ by locating and identifying individual RNA molecules at subcellular resolution. These datasets typically contain an abundance of information that when analyzed appropriately can reveal tissue organization across scales from molecules to entire…
Vaja Liluashvili, Selim Kalayci, Eugene Flouder, Manda Wilson + 2 more
Visualizations of biomolecular networks assist in systems-level data exploration in myriad cellular processes in health and disease. While these networks are increasingly informed by data generated from high-throughout (HT) experiments, current tools do not adequately scale with concomitant increase in their size and…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro
Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in…
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.…
Mark S. Keller, Nils Gehlenborg
Tools used for implementing visualization software systems can generally be divided into camps such as static versus interactive and desktop versus web-based. We contribute Pluot, an architecture that bridges these divides, enabling a single software implementation of a visualization to be used regardless of the target…
Aba-Sah Dadzie, Albert Burger
Background Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that…
Zhigang Lu, Yanyan Zhang
In biological research analysis of large data sets, such as RNA-seq gene expression, often involves visualisation of thousands of data points and associated database query. Static charts produced by traditional tools lack the ability to reveal underlying information, and separated database query is laborious and…
Muhammad Tufail, Zahid Halim, Majid Ali Khan
—Modern java programs consist of large number of classes as well as vast amount of objects instantiated during program execution. Software developers are always keen to know the number of objects created for each class. This information is helpful for a developer in understanding the packages/classes of a program and…
Hootan Roshandel, Matthew Shammami, Shiyun Lin, Yin-Pok Wong + 1 more
The rise of virtual and online education in recent years has led to the development and popularization of many online tools, notably 3D models and augmented reality (AR), for visualizing various structures in chemical sciences. The majority of the developed tools focus on either small molecules or biological systems…
Authors not listed
Effective visualization of complex synthesis routes is critical for computeraided synthesis planning (CASP), yet current solutions are limited in scope, integration flexibility, and chemical intuition. We introduce RouteWise, a versatile, containerized web application designed to address these unmet needs. Its modular…
Philippe Youkharibache
During the last decades, 3D Molecular Graphics in Life Sciences has been used almost exclusively by experts through complex software and applications ranging from Structural Biology to Computer Aided Drug Design. The emergence of JavaScript and WebGL as a viable platform has enabled 3D visualization of biomolecular…
Maxim Kolomeets, Vasily Desnitsky, Igor Kotenko, Andrey Chechulin + 3 more
'Brij B. Gupta' 'Guangtao Zhai' 'Alicia García-Holgado'] Currently, the methods and means of human-machine interaction and visualization as its integral part are being increasingly developed. In various fields of scientific knowledge and technology, there is a need to find and select the most effective visualization…
Fernanda I. Saldívar-González, José L. Medina-Franco
Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the…
Seth Johnson, Francesca Samsel, Gregory Abram, Daniel Olson + 5 more
Finding inspiration in our physical world, combining disparate objects in new ways, understanding through hands-on making — for centuries these "low-tech", physical processes have helped us (scientists, artists, architects, doctors, engineers) to investigate, reinterpret, and ultimately make sense of our world.…