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An architecture for collaboration in systems biology at the age of the Metaverse.

ABSTRACT: As the current state of the Metaverse is largely driven by corporate interests, which may not align with scientific goals and values, academia should play a more active role in its development. Here, we present the challenges and solutions for building a Metaverse that supports systems biology research and collaboration. Our solution consists of two components: Kosmogora, a server ensuring biological data access, traceability, and integrity in the context of a highly collaborative environment such as a metaverse; and ECellDive, a virtual reality application to explore, interact, and build upon the data managed by Kosmogora. We illustrate the synergy between the two components by visualizing a metabolic network and its flux balance analysis. We also argue that the Metaverse of systems biology will foster closer communication and cooperation between experimentalists and modelers in the field.

SUBMITTER: Jacopin E

PROVIDER: S-EPMC10821884 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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An architecture for collaboration in systems biology at the age of the Metaverse.

Jacopin Eliott E Sakamoto Yuki Y Nishida Kozo K Kaizu Kazunari K Takahashi Koichi K

NPJ systems biology and applications 20240127 1

As the current state of the Metaverse is largely driven by corporate interests, which may not align with scientific goals and values, academia should play a more active role in its development. Here, we present the challenges and solutions for building a Metaverse that supports systems biology research and collaboration. Our solution consists of two components: Kosmogora, a server ensuring biological data access, traceability, and integrity in the context of a highly collaborative environment su ...[more]

PMID: 38280851

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Project description:Background: Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium with a great potential to be a consolidated bioprocessing biocatalyst that can ferment cellulose to ethanol. To understand its physiology and genetic targets for future strain development, we have carried out several studies including ethanol-tolerant mutant resequencing and ethanol shock experiments. Methods: In this study, several approaches were applied to enrich mRNA for next-generation sequencing based RNA-Seq and the transcriptomic profiling of C. thermocellum ethanol shock responses was investigated using high-density tiling array and RNA-Seq. Correlations among different transcriptomic platforms of expression array, tiling array, and RNA-Seq were then compared, and data generated from systems biology studies were used for transcriptional architecture improvement. Results: Our results indicate that cloning-based Sanger sequencing can be used for mRNA enrichment ratio determination, and low-copy number plasmid performed better than high-copy one for cDNA library construction. In addition, high correlations were observed among same array platform using different analyses as well as those between two different array platforms of tiling and expression array when probe intensity was compared. Correlations between RNA-Seq and array results especially the one between RNA-Seq and tiling array are also high. Moreover, combining both RNA-Seq and microarray data the transcriptional architecture of C. thermocellum including the prediction and verification of novel transcript (gene), transcriptional start site (TSS), CAZyme genes, ncRNA, and operon were systematically updated and improved. Conclusions: RNA-seq has high correlation with array-based transcriptomic platforms and can provide additional information for transcriptional architecture and genome annotation improvement, which will facilitate future omics-based studies. A twelve array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 30, 60, and 120 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.

Dataset Information

An architecture for collaboration in systems biology at the age of the Metaverse.

Publications

An architecture for collaboration in systems biology at the age of the Metaverse.

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