14 papers · ranked by Valyu relevance
Leonore Reiser, Erica Bakker, Sabarinath Subramaniam, Xingguo Chen + 5 more
Since 1999, The Arabidopsis Information Resource ([www.arabidopsis.org]()) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce…
Leonore Reiser, Erica Bakker, Sabarinath Subramaniam, Xingguo Chen + 4 more
Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the Arabidopsis thaliana genome. Its primary focus is integrating experimental gene function information from the peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal is to produce a…
Colin Diesh, Garrett Stevens, Scott Cain, Lincoln Stein + 1 more
JBrowse 2 is an open-source genome browser that provides unique features for visualizing syntenic relationships between multiple genomes. This article describes a protocol for setting up synteny views in JBrowse 2, using an assembly-to-assembly whole-genome alignment example. We detail data preparation steps, including…
John L. Portwood, Ethalinda K. Cannon, Olivia C. Haley, Laura E. Tibbs-Cortes + 2 more
Genome visualization has existed for as long as assembled genomes, with an array of tools and approaches to meet researchers’ needs. The genome browser is one of these tools, and it has become a critical analytical resource for geneticists, genome biologists, and breeders. The evolution of genome browser capabilities…
Robert Buels, Eric Yao, Colin M. Diesh, Richard D. Hayes + 7 more
'Monica Munoz-Torres' 'Gregg Helt' 'David M. Goodstein' 'Christine G. Elsik' 'Suzanna E. Lewis' 'Lincoln Stein' 'Ian H. Holmes'] Background JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.…
Shu Tadaka, Junko Kawashima, Eiji Hishinuma, Sakae Saito + 20 more
'Yasunobu Okamura' 'Akihito Otsuki' 'Kaname Kojima' 'Shohei Komaki' 'Yuichi Aoki' 'Takanari Kanno' 'Daisuke Saigusa' 'Jin Inoue' 'Matsuyuki Shirota' 'Jun Takayama' 'Fumiki Katsuoka' 'Atsushi Shimizu' 'Gen Tamiya' 'Ritsuko Shimizu' 'Masahiro Hiratsuka' 'Ikuko\xa0N Motoike' 'Seizo Koshiba' 'Makoto Sasaki' 'Masayuki…
Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett J Stevens + 8 more
JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have been deployed at the end of bioinformatics pipelines, typically decoupled from the analysis…
Eric Yao, Robert Buels, Lincoln Stein, Taner Z. Sen + 2 more
'Aaron E. Darling'] We describe JBrowse Connect, an optional expansion to the JBrowse genome browser, targeted at developers. JBrowse Connect allows live messaging, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present example…
Kez Cleal, Alexander Kearsey, Duncan M. Baird
Genome-Wide (GW) is an interactive genome browser that expedites analysis of aligned sequencing reads and data tracks, and introduces novel interfaces for exploring, annotating and quantifying data. GW’s high-performance design enables rapid rendering of data at speeds approaching the file reading rate, in addition to…
Patrick König, Sebastian Beier, Martin Mascher, Nils Stein + 2 more
In times of ever-increasing quantity and quality of sequencing data that is driven by the ongoing reduction of sequencing costs and simultaneously increasing computing power, an ever-increasing amount of data of genomic diversity is being generated, which is almost impossible to keep track of in its entirety . Rather…
Patrick König, Sebastian Beier, Martin Mascher, Nils Stein + 2 more
The sequencing of whole genomes is becoming increasingly affordable. In this context large-scale sequencing projects are generating ever larger datasets of species-specific genomic diversity. As a consequence, more and more genomic data needs to be made easily accessible and analyzable to the scientific community. We…
Authors not listed
For decades, molecular visualization software has been fundamental to education and research in chemistry, structural biology, and materials science. These tools have enabled the inspection of structures, dynamics, and interactions, yet their reliance on two-dimensional (2D) interfaces imposes persistent limitations.…
Kevin Mildau, Christoph Büschl, Jürgen Zanghellini, Justin J.J. van der Hooft
Computational metabolomics workflows have revolutionized the untargeted metabolomics field. However, the organization and prioritization of metabolite features remains a laborious process. Organizing metabolomics data is often done through mass fragmentation-based spectral similarity grouping, resulting in feature sets…
Amogh Pradeep, Álvaro Feal, Julien Gamba, Ashwin Rao + 3 more
'Martina Lindorfer' 'Narseo Vallina-Rodrìguez' 'David Choffnes'] The privacy-related behavior of mobile browsers has remained widely unexplored by the research community. In fact, as opposed to regular Android apps, mobile browsers may present contradicting privacy behaviors. On the one hand, they can have access to…