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Editorial
. 2021 Jun 17:1:669186.
doi: 10.3389/fbinf.2021.669186. eCollection 2021.

Grand Challenges in Bioinformatics Data Visualization

Seán I O'Donoghue  1   2   3
Affiliations
Editorial

Grand Challenges in Bioinformatics Data Visualization

Seán I O'Donoghue. Front Bioinform. .
No abstract available

Keywords: bioinformatics; computational biology; data science; data visualization; science communication; visual analytics.

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Conflict of interest statement

The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
The data science cycle. Analysis of newly acquired data increasingly relies on integration with large, accumulating volumes of complex, pre-existing data, and requires frequent re-analysis and re-rendering. Visualization is the main way researchers observe both raw and analysed data; an overarching grand challenge of data visualization is to leverage human visual capabilities—which involve most of the brain and can process ∼10 million bits per second (Koch et al., 2006) to recognize patterns within ∼100 ms (Healey and Enns, 2012) — thereby transforming data into insight. These insights, in turn, lead to new hypotheses, thus continuing the cycle. Unfortunately, the critical step of manually validating derived models by visually comparing raw vs. analysed data (Anscombe, 1973) is often overlooked.
FIGURE 2
FIGURE 2
Six data visualization methods currently used in bioinformatics grand challenges. (A) A molecular-scale, 3D model of the human genome may soon be feasible; in preparation, visualization tools are being developed to enable interactive, multiscale exploration of such models (adapted from Asbury et al. (2010)). (B) t-SNE analysis of scRNA-seq data on breast cancer metastasis (adapted from Valdes-Mora et al. (2019)). (C) Spatiotemporal graph of phosphorylation events in fat cells following insulin stimulation (adapted from Ma et al. (2015), by Jenny Vuong). (D) Here, an interactive, web-based data integration environment is used to explore and curate a molecular-scale model of a subcellular landscape showing HIV-host interactions (Klein et al., 2018; Autin et al., 2020). (E) Portion of spatial transcriptomics analysis showing expression of two genes in an anterior slice from mouse brain (adapted from Vandenbon and Diez (2020)). (F) Disease trajectory graph showing progression from heart pain to cardiac arrest across the entire Danish population (adapted from Jensen et al. (2014)).
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References

    1. Aerts J., Gehlenborg N., Marai G. E., Nieselt K. K. (2018). Visualization of Biological Data - Crossroads (Dagstuhl Semin. 18161). Dagstuhl Rep. 8 (4), 32–71. 10.4230/DAGREP.8.4.32 - DOI
    1. Alqahtani S. (2017). In Silico ADME-Tox Modeling: Progress and Prospects. Expert Opin. Drug Metab. Toxicol. 13, 1147–1158. 10.1080/17425255.2017.1389897 - DOI - PubMed
    1. Altman R. B., Levitt M. (2018). What Is Biomedical Data Science and Do We Need an Annual Review of it? Annu. Rev. Biomed. Data Sci. 1, i–iii. 10.1146/annurev-bd-01-041718-100001 - DOI
    1. Anscombe F. J. (1973). Graphs in Statistical Analysis. Am. Stat. 27, 17–21. 10.1080/00031305.1973.1047896610.2307/2682899 - DOI
    1. Asbury T. M., Mitman M., Tang J., Zheng W. J. (2010). Genome3D: a Viewer-Model Framework for Integrating and Visualizing Multi-Scale Epigenomic Information within a Three-Dimensional Genome. BMC Bioinformatics 11, 444. 10.1186/1471-2105-11-444 - DOI - PMC - PubMed

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