scholarly journals NG-Circos: next-generation Circos for data visualization and interpretation

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Ya Cui ◽  
Zhe Cui ◽  
Jianfeng Xu ◽  
Dapeng Hao ◽  
Jiejun Shi ◽  
...  

Abstract Circos plots are widely used to display multi-dimensional next-generation genomic data, but existing implementations of Circos are not interactive with limited support of data types. Here, we developed next-generation Circos (NG-Circos), a flexible JavaScript-based circular genome visualization tool for designing highly interactive Circos plots using 21 functional modules with various data types. To our knowledge, NG-Circos is the most powerful software to construct interactive Circos plots. By supporting diverse data types in a dynamic browser interface, NG-Circos will accelerate the next-generation data visualization and interpretation, thus promoting the reproducible research in biomedical sciences and beyond. NG-Circos is available at https://wlcb.oit.uci.edu/NG-Circos and https://github.com/YaCui/NG-Circos.

2015 ◽  
Vol 3 (3) ◽  
pp. SX29-SX39 ◽  
Author(s):  
Carl Byers ◽  
Andrew Woo

The ability to integrate diverse data types from multiple live and simulated sources, manipulate them dynamically, and deploy them in integrated, visual formats and in mobile settings provides significant advantages. We have reviewed some of the benefits of volume graphics and the use of big data in the context of 3D visualization case studies, in which inherent features, such as representation efficiencies, dynamic modifications, cross sectioning, and others, could improve interpretation processes and workflows.


2021 ◽  
Author(s):  
Sehi L'Yi ◽  
Qianwen Wang ◽  
Fritz Lekschas ◽  
Nils Gehlenborg

The combination of diverse data types and analysis tasks in genomics has resulted in the development of a wide range of visualization techniques and tools. However, most existing tools are tailored to a specific problem or data type and offer limited customization, making it challenging to optimize visualizations for new analysis tasks or datasets. To address this challenge, we designed Gosling—a grammar for interactive and scalable genomics data visualization. Gosling balances expressiveness for comprehensive multi-scale genomics data visualizations with accessibility for domain scientists. Our accompanying JavaScript toolkit called Gosling.js provides scalable and interactive rendering. Gosling.js is built on top of an existing platform for web-based genomics data visualization to further simplify the visualization of common genomics data formats. We demonstrate the expressiveness of the grammar through a variety of real-world examples. Furthermore, we show how Gosling supports the design of novel genomics visualizations. An online editor and examples of Gosling.js and its source code are available at https://gosling.js.org.


2018 ◽  
pp. 184-194
Author(s):  
Shweta Ramdas ◽  
Jun Z. Li

Next-generation sequencing (NGS) technologies make it possible to efficiently detect DNA variants in either entire genomes or any subsets of the genome, and have dramatically enhanced our ability to search for genetic risk factors of complex psychiatric diseases. While genotyping-based association studies focus on common variants that track extended genomic segments, NGS provides unbiased identification of both common and rare variants, including those that are functionally important but appear in very few families or sporadic cases. Thus NGS directly highlights plausible causal variants, even if such variants are extremely heterogeneous in the population. Meanwhile, such heterogeneity requires new analytical approaches that can aggregate rare variant burden over predefined functional unit such as a gene or a segment of non-coding region with presumed function. Rapid application of NGS technologies also underscored other limits in psychiatric genetics research, including the need for detailed phenotyping and multi-scale integration of diverse data types.


2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.


2021 ◽  
Vol 12 (01) ◽  
pp. 164-169
Author(s):  
Laurie Lovett Novak ◽  
Jonathan Wanderer ◽  
David A. Owens ◽  
Daniel Fabbri ◽  
Julian Z. Genkins ◽  
...  

Abstract Background The data visualization literature asserts that the details of the optimal data display must be tailored to the specific task, the background of the user, and the characteristics of the data. The general organizing principle of a concept-oriented display is known to be useful for many tasks and data types. Objectives In this project, we used general principles of data visualization and a co-design process to produce a clinical display tailored to a specific cognitive task, chosen from the anesthesia domain, but with clear generalizability to other clinical tasks. To support the work of the anesthesia-in-charge (AIC) our task was, for a given day, to depict the acuity level and complexity of each patient in the collection of those that will be operated on the following day. The AIC uses this information to optimally allocate anesthesia staff and providers across operating rooms. Methods We used a co-design process to collaborate with participants who work in the AIC role. We conducted two in-depth interviews with AICs and engaged them in subsequent input on iterative design solutions. Results Through a co-design process, we found (1) the need to carefully match the level of detail in the display to the level required by the clinical task, (2) the impedance caused by irrelevant information on the screen such as icons relevant only to other tasks, and (3) the desire for a specific but optional trajectory of increasingly detailed textual summaries. Conclusion This study reports a real-world clinical informatics development project that engaged users as co-designers. Our process led to the user-preferred design of a single binary flag to identify the subset of patients needing further investigation, and then a trajectory of increasingly detailed, text-based abstractions for each patient that can be displayed when more information is needed.


Author(s):  
Liangjian Chen ◽  
Siyu Chen ◽  
Shengnan Guo ◽  
Yue Yang ◽  
Jianqiu Xu

2012 ◽  
Vol 29 (2) ◽  
pp. 223-234 ◽  
Author(s):  
Awalin Sopan ◽  
Angela Song-Ie Noh ◽  
Sohit Karol ◽  
Paul Rosenfeld ◽  
Ginnah Lee ◽  
...  

2020 ◽  
Author(s):  
Annika Tjuka ◽  
Robert Forkel ◽  
Johann-Mattis List

Psychologists and linguists have collected a great diversity of data for word and concept properties. In psychology, many studies accumulate norms and ratings such as word frequencies or age-of-acquisition often for a large number of words. Linguistics, on the other hand, provides valuable insights into relations of word meanings. We present a collection of those data sets for norms, ratings, and relations that cover different languages: ‘NoRaRe.’ To enable a comparison between the diverse data types, we established workflows that facilitate the expansion of the database. A web application allows convenient access to the data (https://digling.org/norare/). Furthermore, a software API ensures consistent data curation by providing tests to validate the data sets. The NoRaRe collection is linked to the database curated by the Concepticon project (https://concepticon.clld.org) which offers a reference catalog of unified concept sets. The link between words in the data sets and the Concepticon concept sets makes a cross-linguistic comparison possible. In three case studies, we test the validity of our approach, the accuracy of our workflow, and the applicability of our database. The results indicate that the NoRaRe database can be applied for the study of word properties across multiple languages. The data can be used by psychologists and linguists to benefit from the knowledge rooted in both research disciplines.


Sign in / Sign up

Export Citation Format

Share Document