MMinte specifications

Information


Unique identifier OMICS_12841
Name MMinte
Alternative name Microbial Metabolic Interactions
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format TXT, FASTA
Output data Network diagram representing the interactions between the pairs of species.
Operating system Unix/Linux, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.3
Stability Stable
Requirements
BioPython, CherryPy, Cobra, Cycler, DataSpyre, Jinja2, MarkupSafe, Numpy, Pandas, Pyparsing, Python-dateutil, Pytz, Scipy, Six, Wheel
Maintained Yes

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Maintainer


  • person_outline Nicholas Chia <>

Publication for Microbial Metabolic Interactions

MMinte in publications

 (17)
PMCID: 5583593
PMID: 28912798
DOI: 10.3389/fgene.2017.00111

[…] thiele, ; noecker et al., ; shashkova et al., ; magnúsdóttir et al., ). additionally, computational models for human metabolism are also available (thiele et al., ; mardinoglu et al., ), and host-microbial metabolic interactions have been modeled (heinken et al., , ; thiele et al., ; shoaie and nielsen, ; levy et al., ). thus, the final future direction is to update the existing hgm […]

PMCID: 5467172
PMID: 28585563
DOI: 10.1038/ncomms15393

[…] quantitative techniques for identifying and validating specific functions (for example, import and export of metabolites and release of public goods from macromolecule degradation) and microbial metabolic interactions (for example, cross-feeding mechanisms and positive/negative metabolic influences) on a global scale, specifically within in vivo environments. improvements […]

PMCID: 5421297
PMID: 28533768
DOI: 10.3389/fmicb.2017.00791

[…] investigating the biogeography, evolution, and ecology of the beggiatoaceae. abundant and co-occurring sulfate-reducing organisms alongside the lsb suggest tightly coupled sulfur cycling, echoing microbial metabolic interactions that have been well documented in other environments. likewise, the discovery that the sm1 euryarchaeon dominates biofilms and co-occurs with thiothrix […]

PMCID: 5371670
PMID: 28424674
DOI: 10.3389/fmicb.2017.00536

[…] metabolic and immunological disorders is still not well-established., over the last two decades, systems biology has emerged as an important tool to provide insights into the role of mammalian gut microbial metabolic interactions in influencing an individual's susceptibility to health and disease outcomes (martin et al., ). the emergence of systems biology coincides with the completion […]

PMCID: 5147981
PMID: 27936088
DOI: 10.1371/journal.pone.0167788

[…] heterogeneities between and within individual granules that can potentially aid us in better understanding uasb reactors as a biological ecosystem for future operational improvement., networks of microbial metabolic interactions in granules are especially critical as treatment of various compounds frequently found in wastewaters depend on multiple organisms. specifically, to accomplish […]


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MMinte institution(s)
Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Chinahester, MN, USA; Department of Surgery, Mayo Clinic, Chinahester, MN, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Chinahester, MN, USA; Harvard Medical School, Boston, MA, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Chinahester, MN, USA; Department of Surgery, Mayo Clinic, Chinahester, MN, USA; Department of Physiology and Biomedical Engineering, Mayo College, Chinahester, MN, USA
MMinte funding source(s)
This work was supported by the Mayo Clinic Center for Individualized Medicine and the National Institutes of Health under award number R01CA179243.

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