ECOMICS specifications


Unique identifier OMICS_23108
Alternative name ECosystem trans-OMICS investigation
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • Bm-Char
  • E-class
  • FT2B
  • HetMap


  • person_outline Jun Kikuchi <>

Publication for ECosystem trans-OMICS investigation

ECOMICS in publications

PMCID: 5059772
PMID: 27713404
DOI: 10.1038/ncomms13090

[…] cell models is the lack of integrated data sources. we develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create ecomics, a consistent, quality-controlled multi-omics compendium for escherichia coli with cohesive meta-data information. we then use this resource to train a multi-scale model that integrates four […]

PMCID: 3686774
PMID: 23840554
DOI: 10.1371/journal.pone.0066919

[…] and microbial degradability characterization using thermogravimetric analysis, solution-state nmr, and denaturing gradient gel electrophoresis. these measured data were further analyzed using an “ecomics” web-based toolkit. from the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose […]

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ECOMICS institution(s)
Plant Science Center, RIKEN, Yokohama, Japan; Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan; Advanced Science Institute, RIKEN, Wako, Japan; Bioinformatics and Systems Engineering Division, RIKEN, Yokohama, Japan; Biomass Engineering Program, RIKEN Cluster for Innovation, Wako, Japan; Graduate School of Bioagriculture Sciences, Nagoya University, Nagoya, Japan
ECOMICS funding source(s)
Supported, in part, by Grants-in-Aid for Scientific Research for challenging exploratory research, and Scientific Research (A) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan, and, in part, by grants from Research and Development Program for New Bio-industry Initiatives of the Bio-oriented Technology Research Advancement Institution (BRAIN), and the New Energy and Industrial Technology Development Organization (NEDO).

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