The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Seaver, Samuel D.; Liu, Filipe; Zhang, Qizhi; Jeffryes, James; Faria, José P.; Edirisinghe, Janaka N.; Mundy, Michael; Chia, Nicholas; Noor, Elad; Beber, Moritz E; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; D’haeseleer, Patrik; McCorkle, Sean R.; Bolton, Jay R.; Pearson, Erik; Canon, Shane; Wood-Charlson, Elisha M.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.

doi:10.1093/nar/gkaa746

Title: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Journal Article · 28 September 2020 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkaa746 · OSTI ID:1668123

^[1];

^[1]; Zhang, Qizhi ^[1];

^[1];

^[2];

^[3];

^[4];

^[5];

^[6]; D’haeseleer, Patrik ^[6];

^[7];

^[8];

^[9] more »

Argonne National Lab. (ANL), Lemont, IL (United States)
Mayo Clinic, Rochester, MN (United States)
Eidgenössische Technische Hochschule Zürich, (Switzerland). Inst. of Molecular Systems Biology
Technical University of Denmark, Lyngby (Denmark). Novo Nordisk Foundation Center for Biosustainability
Hope College, Holland, MI (United States)
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Brookhaven National Lab. (BNL), Upton, NY (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

View Journal Article

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Cancer Institute (NCI); National Institutes of Health (NIH); European Union (EU); Mayo Clinic

Grant/Contract Number:: AC05-00OR22725; AC02-06CH11357; AC02-05CH11231; AC52-07NA27344; GEPR-1444202; MCB-1716285; R01CA17924; AC02–05CH11231

OSTI ID:: 1668123

Alternate ID(s):: OSTI ID: 1669770; OSTI ID: 1762244; OSTI ID: 1783779; OSTI ID: 1836207

Report Number(s):: LLNL-JRNL-827856

Journal Information:: Nucleic Acids Research, Vol. 49, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (67)

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks Stanford, Natalie J.; Lubitz, Timo; Smallbone, Kieran PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0079195	journal	November 2013
Metabolic Reconstruction and Modeling Microbial Electrosynthesis Marshall, Christopher W.; Ross, Daniel E.; Handley, Kim M. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-08877-z	journal	August 2017
Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen Marcellin, Esteban; Behrendorff, James B.; Nagaraju, Shilpa Green Chemistry, Vol. 18, Issue 10 https://doi.org/10.1039/C5GC02708J	journal	January 2016
Metabolic engineering of Escherichia coli for the de novo stereospecific biosynthesis of 1,2-propanediol through lactic acid Niu, Wei; Kramer, Levi; Mueller, Joshua Metabolic Engineering Communications, Vol. 8 https://doi.org/10.1016/j.mec.2018.e00082	journal	June 2019
Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement Li, Jian; Sun, Renliang; Ning, Xinjuan Genes, Vol. 9, Issue 7 https://doi.org/10.3390/genes9070364	journal	July 2018
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models King, Zachary A.; Lu, Justin; Dräger, Andreas Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1049	journal	October 2015
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona Journal of Cheminformatics, Vol. 7, Issue 1 https://doi.org/10.1186/s13321-015-0087-1	journal	August 2015
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J. Biophysical Journal, Vol. 95, Issue 3 https://doi.org/10.1529/biophysj.107.124784	journal	August 2008
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H. Genome Biology, Vol. 4, Issue 9, p. R54 https://doi.org/10.1186/gb-2003-4-9-r54	journal	August 2003
Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments Ding, Tong; Case, Kyle A.; Omolo, Morrine A. PLOS ONE, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pone.0149423	journal	February 2016
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage Noor, Elad; Bar-Even, Arren; Flamholz, Avi Bioinformatics, Vol. 28, Issue 15 https://doi.org/10.1093/bioinformatics/bts317	journal	May 2012
In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation Chen, Jin; Henson, Michael A. Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.10.002	journal	November 2016
A systematic assessment of current genome-scale metabolic reconstruction tools Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1769-1	journal	August 2019
Computational analysis of the productivity potential of CAM Shameer, Sanu; Baghalian, Kambiz; Cheung, C. Y. Maurice Nature Plants, Vol. 4, Issue 3 https://doi.org/10.1038/s41477-018-0112-2	journal	February 2018
Data, information, knowledge and principle: back to metabolism in KEGG Kanehisa, Minoru; Goto, Susumu; Sato, Yoko Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1076	journal	November 2013
Towards a genome-scale kinetic model of cellular metabolism Smallbone, Kieran; Simeonidis, Evangelos; Swainston, Neil BMC Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1186/1752-0509-4-6	journal	January 2010
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02947	journal	December 2018
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains Khodayari, Ali; Maranas, Costas D. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13806	journal	December 2016
ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling Zhang, Cheng; Bidkhori, Gholamreza; Benfeitas, Rui Frontiers in Physiology, Vol. 9 https://doi.org/10.3389/fphys.2018.01355	journal	September 2018
Global phenotypic characterization of bacteria Bochner, Barry R. FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00149.x	journal	January 2009
Optimization based automated curation of metabolic reconstructions Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D. BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-212	journal	January 2007
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane Proceedings of the National Academy of Sciences, Vol. 111, Issue 26 https://doi.org/10.1073/pnas.1401329111	journal	June 2014
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets Hartleb, Daniel; Jarre, Florian; Lercher, Martin J. PLOS Computational Biology, Vol. 12, Issue 8 https://doi.org/10.1371/journal.pcbi.1005036	journal	August 2016
MEMOTE for standardized genome-scale metabolic model testing Lieven, Christian; Beber, Moritz E.; Olivier, Brett G. Nature Biotechnology, Vol. 38, Issue 3 https://doi.org/10.1038/s41587-020-0446-y	journal	March 2020
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
Modeling central metabolism and energy biosynthesis across microbial life Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2887-8	journal	August 2016
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Mahadevan, R.; Schilling, C. H. Metabolic Engineering, Vol. 5, Issue 4 https://doi.org/10.1016/j.ymben.2003.09.002	journal	October 2003
A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C ₃ and Crassulacean Acid Metabolism Leaves Cheung, C. Y. Maurice; Poolman, Mark G.; Fell, David. A. Plant Physiology, Vol. 165, Issue 2 https://doi.org/10.1104/pp.113.234468	journal	March 2014
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches Suzek, B. E.; Wang, Y.; Huang, H. Bioinformatics, Vol. 31, Issue 6 https://doi.org/10.1093/bioinformatics/btu739	journal	November 2014
ExplorEnz: the primary source of the IUBMB enzyme list McDonald, A. G.; Boyce, S.; Tipton, K. F. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn582	journal	January 2009
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew P. Genome Biology, Vol. 10, Issue 6 https://doi.org/10.1186/gb-2009-10-6-r69	journal	January 2009
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency Seaver, Samuel M. D.; Lerma‐Ortiz, Claudia; Conrad, Neal The Plant Journal, Vol. 95, Issue 6 https://doi.org/10.1111/tpj.14003	journal	August 2018
Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum Chen, Jin; Daniell, James; Griﬃn, Derek Biochemical Engineering Journal, Vol. 129 https://doi.org/10.1016/j.bej.2017.10.018	journal	January 2018
KEGG as a reference resource for gene and protein annotation Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1070	journal	October 2015
Improving prediction fidelity of cellular metabolism with kinetic descriptions Chowdhury, Anupam; Khodayari, Ali; Maranas, Costas D. Current Opinion in Biotechnology, Vol. 36 https://doi.org/10.1016/j.copbio.2015.08.011	journal	December 2015
Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water Ruiz-Moreno, Héctor Alejandro; López-Tamayo, Ana María; Caro-Quintero, Alejandro Ecological Modelling, Vol. 399 https://doi.org/10.1016/j.ecolmodel.2019.02.001	journal	May 2019
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel PLOS Computational Biology, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pcbi.1006556	journal	November 2018
Network-based metabolic analysis and microbial community modeling Cardona, Cesar; Weisenhorn, Pamela; Henry, Chris Current Opinion in Microbiology, Vol. 31 https://doi.org/10.1016/j.mib.2016.03.008	journal	June 2016
In silico aided metabolic engineering of Klebsiella oxytoca and fermentation optimization for enhanced 2,3-butanediol production Park, Jong Myoung; Song, Hyohak; Lee, Hee Jong Journal of Industrial Microbiology & Biotechnology, Vol. 40, Issue 9 https://doi.org/10.1007/s10295-013-1298-y	journal	June 2013
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology Bordbar, Aarash; Feist, Adam M.; Usaite-Black, Renata BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-180	journal	January 2011
Long-term phenotypic evolution of bacteria Plata, Germán; Henry, Christopher S.; Vitkup, Dennis Nature, Vol. 517, Issue 7534 https://doi.org/10.1038/nature13827	journal	October 2014
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Reframing gene essentiality in terms of adaptive flexibility Guzmán, Gabriela I.; Olson, Connor A.; Hefner, Ying BMC Systems Biology, Vol. 12, Issue 1 https://doi.org/10.1186/s12918-018-0653-z	journal	December 2018
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation Mendoza, Sebastián N.; Cañón, Pablo M.; Contreras, Ángela Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00534	journal	March 2017
Open Babel: An open chemical toolbox O'Boyle, Noel M.; Banck, Michael; James, Craig A. Journal of Cheminformatics, Vol. 3, Issue 1 https://doi.org/10.1186/1758-2946-3-33	journal	October 2011
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela Journal of Cellular Physiology, Vol. 231, Issue 11 https://doi.org/10.1002/jcp.25428	journal	June 2016
Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti diCenzo, George C.; Checcucci, Alice; Bazzicalupo, Marco Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12219	journal	July 2016
Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus Wang, Junhua; Wang, Cheng; Song, Kejing Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0787-5	journal	October 2017
Rewriting yeast central carbon metabolism for industrial isoprenoid production Meadows, Adam L.; Hawkins, Kristy M.; Tsegaye, Yoseph Nature, Vol. 537, Issue 7622 https://doi.org/10.1038/nature19769	journal	September 2016
Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism Jerby, Livnat; Shlomi, Tomer; Ruppin, Eytan Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2010.56	journal	January 2010
Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli Harder, Björn-Johannes; Bettenbrock, Katja; Klamt, Steffen Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.05.008	journal	November 2016
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00142	journal	March 2015
Towards automatic classification within the ChEBI ontology Hastings, Janna; de Matos, Paula; Ennis, Marcus Nature Precedings https://doi.org/10.1038/npre.2009.3525.1	journal	July 2009
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli Alper, Hal; Jin, Yong-Su; Moxley, J. F. Metabolic Engineering, Vol. 7, Issue 3 https://doi.org/10.1016/j.ymben.2004.12.003	journal	May 2005
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K. Proceedings of the National Academy of Sciences, Vol. 113, Issue 26 https://doi.org/10.1073/pnas.1523199113	journal	June 2016
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46249	journal	April 2017
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks Ganter, M.; Bernard, T.; Moretti, S. Bioinformatics, Vol. 29, Issue 6 https://doi.org/10.1093/bioinformatics/btt036	journal	January 2013
Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1) de la Torre, Andrea; Metivier, Aisha; Chu, Frances Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0377-3	journal	November 2015
Combining multiple functional annotation tools increases coverage of metabolic annotation Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5221-9	journal	December 2018
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher Biotechnology Journal, Vol. 8, Issue 9 https://doi.org/10.1002/biot.201300091	journal	August 2013
Using systems biology approaches to elucidate cause and effect in host–microbiome interactions Witherden, Elizabeth A.; Moyes, David L.; Bruce, Kenneth D. Current Opinion in Systems Biology, Vol. 3 https://doi.org/10.1016/j.coisb.2017.05.003	journal	June 2017
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 Milne, Caroline B.; Eddy, James A.; Raju, Ravali BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-130	journal	January 2011
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler Plant Physiology, Vol. 172, Issue 1 https://doi.org/10.1104/pp.16.00593	journal	July 2016
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases Kumar, Akhil; Suthers, Patrick F.; Maranas, Costas D. BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-6	journal	January 2012

Cited By (9)

Additional file 9 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Garza, Daniel R.; von Meijenfeldt, F. A. Bastiaan; van Dijk, Bram figshare https://doi.org/10.6084/m9.figshare.20499832	dataset	January 2022
KBase Narrative - kb_DRAM P. normanii annotation with model Flynn, Rory; Faria, José U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/128174.5/1893104	dataset	January 2022
Additional file 7 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Garza, Daniel R.; von Meijenfeldt, F. A. Bastiaan; van Dijk, Bram figshare https://doi.org/10.6084/m9.figshare.20499826	dataset	January 2022
Additional file 8 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Garza, Daniel R.; von Meijenfeldt, F. A. Bastiaan; van Dijk, Bram figshare https://doi.org/10.6084/m9.figshare.20499829	dataset	January 2022
KBase Narrative - kb_DRAM E. coli annotation Shaffer, Michael U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/103341.23/1893106	dataset	January 2022
Additional file 10 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Garza, Daniel R.; von Meijenfeldt, F. A. Bastiaan; van Dijk, Bram figshare https://doi.org/10.6084/m9.figshare.20499802.v1	dataset	January 2022
eQuilibrator 3.0 -- a platform for the estimation of thermodynamic constants Beber, Moritz E.; Gollub, Mattia G.; Mozaffari, Dana arXiv https://doi.org/10.48550/arxiv.2103.00621	preprint	January 2021
Additional file 11 of Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes Garza, Daniel R.; von Meijenfeldt, F. A. Bastiaan; van Dijk, Bram figshare https://doi.org/10.6084/m9.figshare.20499805.v1	dataset	January 2022
DRAM example narrative Shaffer, Michael Colorado State Univ., Fort Collins, CO (United States) https://doi.org/10.25982/88325.84/1855758	dataset	January 2021

Figures / Tables (10)

Similar Records

Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models

Technical Report · 2010 · OSTI ID:1234257

Stevens, Rick

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

Journal Article · 2018 · The Plant Journal · OSTI ID:1463753

Seaver, Samuel M. D.; Lerma‐Ortiz, Claudia; Conrad, Neal; +4 more

Integration of a constraint-based metabolic model of Brassica napus developing seeds with ¹³C-metabolic flux analysis

Journal Article · 2014 · Frontiers in Plant Science · OSTI ID:1178233

Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biological and medical sciences