MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis

Abstract

Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.

Visualizing protein structures — tools and trends

“…Web delivery of VR contents is possible through WebVR. Several packages have reported VR capacities such as Molecular Rift [49], ChimeraX [50], UnityMol [25,51], Narupa [52], Nanome [53] and CootVR. WebVR-capable molecular viewers are less widespread, possibly due to the currently limited browser-support for this technology.…”

“…VRMol [26] is a complete web-based VR tool available at vrmol.net which has recently been released. UnityMol experiments with WebVR have been reported as well [25].…”

Marine Natural Products from Microalgae: An -Omics Overview

“…These tools are already available in the field of human diseases and of plants [122,123]. To date, the solely integrated approach applied in algae is reported by Maes and colleagues [124]. The authors published an integrated pipeline, called MinOmics (Methods for Integrated analysis of Multiple Omics datasets) to manage various biological data, such as genes, transcripts and proteins, deriving from the freshwater microalga C. reinhardtii [117].…”

Using Computer Simulations and Virtual Reality to Understand, Design and Optimize Artificial Water Channels

“…Advanced visualization is a particularly powerful approach already extensively used to understand biological membrane objects [55]. We will get back to the strengths of novel technological approaches such as using virtual reality gear or high-resolution and large-scale display walls a little later in this discussion [56][57][58][59][60]. The aim of such a visual analysis is to bring novel concepts to the engineering of nanostructured functional systems, together with the understanding of the mechanisms underlying a rational use of water transport functions employed as the nanostructuring tools.…”