Version 1.6: Adds 23 new models & more!

Sep. 15, 2019

Version 1.6 introduces a significant number of new models to the repository. We describe the addition of 23 new models that valuably expand the portion of the phylogenetic tree covered by BiGG Models. The models include updates for four E. coli strains, S. aureus, and M. tuberculosis H37Rv and new models for five Plasmodium strains, stage specific models for Trypanosoma cruzi, C. difficile, and A. baumannii. We also expand the functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. These multistrain collections are available for download on the model pages for iYL1228, STM_v1_0, and iCN718.

Github Release

Version 1.5: Introducing Recon3D

Feb. 26, 2018

Version 1.5 introduces Recon3D, the latest genome-scale model of the human metabolic network. Brunk et al. describe how Recon3D incorporates three-dimensional metabolite and protein structure data for integrated analysis of human metabolism. Recon3D includes over 5,000 metabolites, 10,000 reactions, and 2,000 human genes. Additional model details and features are available at http://vmh.life.

Github Release

Version 1.4: Four new models, including the latest for E. coli K-12 MG1655

Oct. 10, 2017

Version 1.4 introduces four models to BiGG, including the latest genome-scale model of Escherichia coli K-12 MG1655 from the Systems Biology Research Group at UCSD. In addition, a new universal model can be downloaded in JSON format from the Data Access page, and a number of bug fixes and improvements are included.

To account for newly discovered metabolic capabilities in E. coli K-12 MG1655, Monk and Lloyd et al. have developed an updated genome-scale model, iML1515, that bridges systems and structural biology. The new model was extensively validated using omics datasets and boasts a 3.7% improvement in gene essentiality predictions over the previous model, iJO1366, along with 184 new genes and 196 new reactions. Check out the manuscript [PDF] to see how this model can be applied to analyze the metabolic capabilities E. coli strains in metagenomic samples or used to build draft reconstructions of freshly sequenced clinical isolates.

Other new models are: iLB1027_lipid for Phaeodactylum tricornutum described by Levering et al., iJB785 for Synechococcus elongatus described by Broddrick et al., and iNF517 for Lactococcus lactis described by Flahaut et al..

Github Release

Version 1.3: Introducing the iCHO model

Nov. 23, 2016

Version 1.3 introduces a new model and includes a number of bug fixes.

To understand the pathways underlying cell growth and protein production in Chinese hamster ovary (CHO) cells, the production cell line for most recombinant protein drugs, Hefzi et al. develop a genome-scale model of all metabolic pathways and use this to analyze the efficacy of common cell treatments used to boost protein production. The model builds off the human genome-scale models RECON1 and RECON2, and has been extensively curated to ensure a high-quality resource for use in studying this model organism. The new model is in BiGG Models with the name iCHOv1.

Github Release