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. 2020 Oct 9;1(7):100122.
doi: 10.1016/j.patter.2020.100122.

Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration

Dain R Brademan  1   2 , Ian J Miller  3 , Nicholas W Kwiecien  1 , David J Pagliarini  2   3   4   5   6 , Michael S Westphall  3 , Joshua J Coon  1   2   3 , Evgenia Shishkova  3   7
Affiliations

Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration

Dain R Brademan et al. Patterns (N Y). .

Abstract

Researchers now generate large multi-omic datasets using increasingly mature mass spectrometry techniques at an astounding pace, facing new challenges of "Big Data" dissemination, visualization, and exploration. Conveniently, web-based data portals accommodate the complexity of multi-omic experiments and the many experts involved. However, developing these tailored companion resources requires programming expertise and knowledge of web server architecture-a substantial burden for most. Here, we describe Argonaut, a simple, code-free, and user-friendly platform for creating customizable, interactive data-hosting websites. Argonaut carries out real-time statistical analyses of the data, which it organizes into easily sharable projects. Collaborating researchers worldwide can explore the results, visualized through popular plots, and modify them to streamline data interpretation. Increasing the pace and ease of access to multi-omic data, Argonaut aims to propel discovery of new biological insights. We showcase the capabilities of this tool using a published multi-omics dataset on the large mitochondrial protease deletion collection.

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Conflict of interest statement

DECLARATION OF INTERESTS N.W.K., M.S.W., and J.J.C. filed a patent, entitled “Web-Based Data Upload and Visualization Platform Enabling Creation of Code-Free Exploration of MS-Based Omics Data” (US20190034047A1; status 9.6.2020 “Pending”), related to the work described in this manuscript. The other authors declare no competing financial interest. SUPPLEMENTAL INFORMATION Supplemental Information can be found online at https://doi.org/10.1016/j.patter.2020.100122.

Figures

None
Graphical abstract
Figure 1
Figure 1
The Argonaut Workflow Argonaut is designed as a portable platform to share multi-omics data in an online environment using customizable interactive visualizations. Processed quantitative measurements from case/control-style experiments are uploaded to the online platform in a variety of text-based formats. Uploaded data are then categorized according to the uploader's experimental design. Common data transformations, such as missing value imputation, filtering missing values, control normalization, or log2 transformations, can be conducted. Inferential statistics are used to determine the significance of molecular perturbations. Data portals can be customized in a variety of ways, allowing detailed project and data descriptions, selection of visualization options, and project management. Data portal access can also be shared directly with collaborators using a secure permission sharing scheme, allowing multiple laboratories to concurrently explore large datasets to rapidly generate biological insight.
Figure 2
Figure 2
Bioinformatic Analyses Visualized by Argonaut The website generated using the multi-omic data from the Veling et al. study features a set of six analyses that are commonly used in omics experiments. All visualizations are fully interactive and generated on-demand using queries from the uploaded data. Significance and fold-change thresholds for data highlighting can be adjusted as desired. Visualizations and data can be exported from the portal as vector graphics, such as the ones used to produce this figure, and text-based spreadsheets, respectively.
See this image and copyright information in PMC

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