Siddharth Chauhan

TL;DR: A community effort to develop a test suite named MEMOTE (for metabolic model tests) to assess GEM quality, and advocate adoption of the latest version of the Systems Biology Markup Language level 3 flux balance constraints (SBML3FBC) package as the primary description and exchange format.

TL;DR: For example, Memote as mentioned in this paper is an open-source software containing a community-maintained, standardized set of metabolic model tests, which can be extended to include experimental datasets for automatic model validation.

TL;DR: Memote is presented, an open-source software containing a community-maintained, standardized set of metabolic model tests that provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.

TL;DR: In this paper, the authors introduce a workflow that converts all public gene expression data for a microbe into a dynamic representation of the organism's transcriptional regulatory network, which can be used to predict new regulons and analyze datasets in the context of all published data.

TL;DR: In this article, independent component analysis was applied to 95 high-quality Sulfolobus acidocaldarius RNA-seq datasets and extract 45 independently modulated gene sets, or iModulons.