KBase: The United States Department of Energy Systems Biology Knowledgebase

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Stodden V, McNutt M, Bailey D, Deelman E, Gil Y, Hanson B . Enhancing reproducibility for computational methods. Science. 2016; 354(6317):1240-1241. DOI: 10.1126/science.aah6168. View

Faria J, Davis J, Edirisinghe J, Taylor R, Weisenhorn P, Olson R . Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. Front Microbiol. 2016; 7:1819. PMC: 5121216. DOI: 10.3389/fmicb.2016.01819. View

Edirisinghe J, Weisenhorn P, Conrad N, Xia F, Overbeek R, Stevens R . Modeling central metabolism and energy biosynthesis across microbial life. BMC Genomics. 2016; 17:568. PMC: 4977884. DOI: 10.1186/s12864-016-2887-8. View

Bochner B . Global phenotypic characterization of bacteria. FEMS Microbiol Rev. 2008; 33(1):191-205. PMC: 2704929. DOI: 10.1111/j.1574-6976.2008.00149.x. View

Prlic A, Procter J . Ten simple rules for the open development of scientific software. PLoS Comput Biol. 2012; 8(12):e1002802. PMC: 3516539. DOI: 10.1371/journal.pcbi.1002802. View

Goodstein D, Shu S, Howson R, Neupane R, Hayes R, Fazo J . Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2011; 40(Database issue):D1178-86. PMC: 3245001. DOI: 10.1093/nar/gkr944. View

Pruitt K, Tatusova T, Maglott D . NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2006; 35(Database issue):D61-5. PMC: 1716718. DOI: 10.1093/nar/gkl842. View

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Caspi R, Foerster H, Fulcher C, Hopkinson R, Ingraham J, Kaipa P . MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2005; 34(Database issue):D511-6. PMC: 1347490. DOI: 10.1093/nar/gkj128. View

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Henry C, Bernstein H, Weisenhorn P, Taylor R, Lee J, Zucker J . Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction. J Cell Physiol. 2016; 231(11):2339-45. PMC: 5132105. DOI: 10.1002/jcp.25428. View

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Magnusdottir S, Heinken A, Kutt L, Ravcheev D, Bauer E, Noronha A . Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2016; 35(1):81-89. DOI: 10.1038/nbt.3703. View