11 documents found, page 1 of 2

TranSyT, an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEâs release, software development for the automatic integration of transport reactions into models has stalled.Here, we present the Transport Systems Tracker (TranSyT). Unlike other transpor...

TranSyT, an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEs release, software development for automatic integration of transport reactions into models has stalled. Here we present the Transport Systems Tracker (TranSyT), the next iteration of TRIAGE. ...

MEMOTE for standardized genome-scale metabolic model testing

Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...

Towards the reconstruction of integrated genome-scale models of metabolism and ...

The reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and ...

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Automated reconstruction and comparison of metabolic models for diverse fungal ...

Improving automated model reconstruction across phylogenetically diverse genome...

Methods for automated genome-scale metabolic model reconstruction

In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of ...

Reconciling gene expression data with regulatory network models

The reconstruction of genome-scale metabolic models from genome annotations has become a routine practice in Systems Biology research. The potential of metabolic models for predictive biology is widely accepted by the scientific community, but these same models still lack the capability to account for the effect of gene regulation on metabolic activity. Our focus organism, Bacillus subtilis is most commonly fou...

Enabling comparative modeling of closely related genomes: Example genus Brucella

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this short report, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of met...