相关论文: Uchimata: a toolkit for visualization of 3D genome…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Computational notebooks have gained widespread adoption among researchers from academia and industry as they support reproducible science. These notebooks allow users to combine code, text, and visualizations for easy sharing of experiments…
The wavelet scattering transform is an invariant signal representation suitable for many signal processing and machine learning applications. We present the Kymatio software package, an easy-to-use, high-performance Python implementation of…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
"Computational experiments" use code and interactive visualizations to convey mathematical and physical concepts in an intuitive way, and are increasingly used to support ex cathedra lecturing in scientific and engineering disciplines.…
In the Jupyter ecosystem, data visualization is usually done with "widgets" created as notebook cell outputs. While this mechanism works well in some circumstances, it is not well-suited to presenting interfaces that are long-lived,…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
Sophisticated visualization tools are essential for the presentation and exploration of human neuroimaging data. While two-dimensional orthogonal views of neuroimaging data are conventionally used to display activity and statistical…
The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies - a crucial step…
We present BrainPainter, a software that automatically generates images of highlighted brain structures given a list of numbers corresponding to the output colours of each region. Compared to existing visualisation software (i.e.…
Interactive notebooks are a precious tool for creating graphical user interfaces and teaching materials. Python and Jupyter are becoming increasingly popular in this context, with Jupyter widgets at the core of the interactive…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of…
Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…