MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format

Forth, Thomas; McConkey, Glenn A.; Westhead, David R.

doi:10.1093/bioinformatics/btq425

Cited by 17 publications

(5 citation statements)

References 12 publications

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“…Many metabolic networks have been reconstructed using various tools, like Pathway Tools. A recent addition to these tools is MetNetMaker (Forth et al 2010). The reactions of the carbohydrate metabolism and N-glycosylation were retrieved from MetNetMaker by simply entering the E.C.…”

Section: Methodsmentioning

confidence: 99%

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

2012

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Pichia pastoris is an efficient expression system for production of recombinant proteins. To understand its physiology for building novel applications it is important to understand and reconstruct its metabolic network. The metabolic reconstruction approach connects genotype with phenotype. Here, we have attempted to reconstruct carbohydrate metabolism pathways responsible for high biomass density and N-glycosylation pathways involved in the post translational modification of proteins of P. pastoris CBS7435. Both these metabolic pathways play a crucial role in heterologous protein production. We report novel, missing and unannotated enzymes involved in the target metabolic pathways. A strong possibility of cellulose and xylose metabolic processes in P. pastoris CBS7435 suggests its use in the area of biofuels. The reconstructed metabolic networks can be used for increased yields and improved product quality, for designing appropriate growth medium, for production of recombinant therapeutics and for making biofuels.

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Section: Methodsmentioning

confidence: 99%

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

2012

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“…Biochemistry books, the metabolic network compilation by Michal and Schomburg [42], and online pathway databanks (KEGG, SGD [http://www.yeastgenome.org], MGI [http://www.informatics.jax.org/], NCBI [http://www.ncbi.nlm.nih.gov/], and TAIR [http://www.arabidopsis.org/]) are good starting points for collecting data [43]. The mathematical model can be built automatically by using software that collects information on reaction networks [44, 45]. Genome‐scale reconstructions [46–49] are excellent starting points for setting up models for MFA.…”

Section: In Vivo Flux Methodsmentioning

confidence: 99%

Eukaryotic metabolism: Measuring compartment fluxes

Wahrheit¹,

Nicolae²,

Heinzle³

2011

Biotechnology Journal

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Metabolic compartmentation represents a major characteristic of eukaryotic cells. The analysis of compartmented metabolic networks is complicated by separation and parallelization of pathways, intracellular transport, and the need for regulatory systems to mediate communication between interdependent compartments. Metabolic flux analysis (MFA) has the potential to reveal compartmented metabolic events, although it is a challenging task requiring demanding experimental techniques and sophisticated modeling. At present no ready-made solution can be provided to cope with the complexity of compartmented metabolic networks, but new powerful tools are emerging. This review gives an overview of different strategies to approach this issue, focusing on different MFA methods and highlighting the additional information that should be included to improve the outcome of an experiment and associate estimation procedures.

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“…To facilitate this collaborative annotation, some tools are available. Other software suites offer manual curation of reconstructed networks (Forth et al, 2010;May et al, 2013). Organism-specific BioCyc databases were created that way and are available online (e.g.…”

Section: Manual Curationmentioning

confidence: 99%

Analysing human metabolic networks using metabolomics

Jourdan¹

2015

Metabolomics as a Tool in Nutrition Research

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MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format

Cited by 17 publications

References 12 publications

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

Eukaryotic metabolism: Measuring compartment fluxes

Analysing human metabolic networks using metabolomics

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