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Genomatica inc simpheny™ software
Simpheny™ Software, supplied by Genomatica inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/simpheny+software/simpheny+software/pmc01550432-169-8-7
Average 90 stars, based on 1 article reviews
simpheny™ software - by Bioz Stars, 2026-09
90/100 stars

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Software:

Article Title: Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance
Article Snippet: .. After the draft model was built, a topological map of the reaction subsystems were drawn using SimPheny software (Genomatica, San Diego, CA) (see ). ..

Article Title: SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.
Article Snippet: .. The SimPheny software (www.genomatica.com) is a commercial solution with a database backend providing visualization of numerical results on pathway maps. ..

Article Title: Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
Article Snippet: .. All calculations were done with Simpheny software (Genomatica Inc, San Diego, USA), or with the COBRA Toolbox described in . ..

Article Title: Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180
Article Snippet: .. Data were analyzed using ArrayStar (DNA Star, Madison, WI) and SimPheny software (Genomatica, Inc., San Diego, CA). ..

Article Title: Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1
Article Snippet: .. FBA optimizations were performed on a Dell computer with 2 GB of RAM and a 1.8-GHz Intel Centrino processor linked to a dedicated database server with Simpheny software (Genomatica, Inc.). .. Transposon knockout data were handled in Excel (Microsoft Corp.), and statistical analysis of transposon data was performed in Matlab R2006a (Mathworks, Inc.).

Article Title: Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas
Article Snippet: .. [1- 13 C] Glc , Geobacillus thermoglucosidasius M10EXG , Based on GC-MS data , SimPheny Software from Genomatica , . ..

Article Title: Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain.
Article Snippet: .. As such, an in silico FBA was performed to coarsely predict the optimal cellular metabolism for ethanol production via Simpheny Software from Genomatica (Mahadevan et al., 2006). ..

other:

Article Title: Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
Article Snippet: To visualize the network content we created a map of the ihs TLR v1.0 reconstruction using SimPheny (Genomatica) software.

Combined Bisulfite Restriction Analysis Assay:

Article Title: Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
Article Snippet: .. All calculations were done with Simpheny software (Genomatica Inc, San Diego, USA), or with the COBRA Toolbox described in . ..

Gas Chromatography-Mass Spectrometry:

Article Title: Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas
Article Snippet: .. [1- 13 C] Glc , Geobacillus thermoglucosidasius M10EXG , Based on GC-MS data , SimPheny Software from Genomatica , . ..

In Silico:

Article Title: Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain.
Article Snippet: .. As such, an in silico FBA was performed to coarsely predict the optimal cellular metabolism for ethanol production via Simpheny Software from Genomatica (Mahadevan et al., 2006). ..



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Simpheny Software Platform, supplied by Genomatica inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Metabolic flux methods applied to different organisms. Isotopic tracers used in the experiments, techniques and software for data analysis are reported as well. When authors did not use “omics” software to analyse data the abbreviation “ns” is reported for “not specified” <xref ref-type= a " width="100%" height="100%">

Journal: RSC Advances

Article Title: Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas

doi: 10.1039/d2ra03326g

Figure Lengend Snippet: Metabolic flux methods applied to different organisms. Isotopic tracers used in the experiments, techniques and software for data analysis are reported as well. When authors did not use “omics” software to analyse data the abbreviation “ns” is reported for “not specified” a

Article Snippet: [1- 13 C] Glc , Geobacillus thermoglucosidasius M10EXG , Based on GC-MS data , SimPheny Software from Genomatica , .

Techniques: Software, Labeling, In Vivo