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simpheny biopathway predictor software  (Genomatica inc)

 
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    Genomatica inc simpheny biopathway predictor software
    Simpheny Biopathway Predictor 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+biopathway+predictor/pm33026132-252-11-8
    Average 90 stars, based on 1 article reviews
    simpheny biopathway predictor software - by Bioz Stars, 2026-10
    90/100 stars

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    other:

    Article Title: Implementation of Synthetic Pathways to Foster Microbe-Based Production of Non-Naturally Occurring Carboxylic Acids and Derivatives
    Article Snippet: For example, Sympheny Biopathway Predictor (a private tool developed in-house by the Genomatica company [ ]) does this by limiting the allowed size of the molecule along the biochemical pathway, while GEM-PATH verifies in every iteration (reaction step) of the search if the predicted reactions are thermodynamically feasible and if they have a candidate enzyme to catalyze them [ ].

    Article Title: Retrosynthetic design of metabolic pathways to chemicals not found in nature
    Article Snippet: Genomatica used their in-house SimPheny Biopathway Predictor and a set of 50 reaction rules to identify 10,000 pathways between 4-6 genes to produce BDO from E. coli metabolites.

    Article Title: Developed and emerging 1,4-butanediol commercial production strategies: forecasting the current status and future possibility.
    Article Snippet: 1,4-Butanediol (1,4-BDO) is a valuable industrial chemical that is primarily produced via several energy-intensive petrochemical processes based on fossil-based raw materials, leading to issues related to: non-renewability, environmental contamination, and high production costs.. 1,4-BDO is used in many chemical reactions to develop a variety of useful, valuable products, such as: polyurethane, Spandex intermediates, and polyvinyl pyrrolidone (PVP), a water-soluble polymer with numerous personal care and pharmaceutical uses.. In recent years, to satisfy the growing need for 1,4-BDO, there has been a major shift in focus to sustainable bioproduction via microorganisms using: recombinant strains, metabolic engineering, synthetic biology, enzyme engineering, bioinformatics, and artificial intelligence-guided algorithms.

    Software:

    Article Title: Production of C2–C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies
    Article Snippet: .. Genomatica has used their in-house developed software called as SimPheny Biopathway Predictor to identify more than 1000 potential pathways of four to six steps for the synthesis of 1,4-BDO from common central metabolites [ ]. ..

    Article Title: Unlocking Nature's Biosynthetic Power—Metabolic Engineering for the Fermentative Production of Chemicals
    Article Snippet: Biotechnology

    Article Title: Microbial Cell Factories: Biodiversity, Pathway Construction, Robustness, and Industrial Applicability
    Article Snippet: .. The Genomatica’s in-house SimPheny BioPathway Predictor software (http://www.genomatica. com/, accessed on 4 February 2024) has been applied for the production of 1,4-butanediol (BDO) from central metabolites, such as succinyl-CoA, α-ketoglutarate, L-glutamate, and acetyl-CoA. ..


    Functional Assay:

    Article Title: Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae.
    Article Snippet: .. Based on functional groups transfer, Genomatica’s proprietary SimPheny Biopathway Predictor algorithm was successfully used to identify multiple pathways towards 1,4-butanediol from inherent metabolic intermediates in E. coli without being restricted by the known enzymes (Yim et al., 2011). ..



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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