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Availabe genome-scale metabolic network reconstructions were collected and listed in [http://gcrg.ucsd.edu/In_Silico_Organisms/Other_Organisms Palsson's Systems Biology Research Group].
Availabe genome-scale metabolic network reconstructions were collected and listed in [http://gcrg.ucsd.edu/In_Silico_Organisms/Other_Organisms Palsson's Systems Biology Research Group].
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Here, we took the adavantage of these reconstructed metabolic networks to demonstrate the availablitity of GEMsME.
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Here, we took the adavantage of these reconstructed metabolic networks to demonstrate the availablitity of GEMSiRV.
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<u>'''Once the reconstructed models imported into the GEMsME, users can start to add, refine and build their own models and run FBA as well in the GEMsME.'''</u>
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<u>'''Once the reconstructed models imported into the GEMSiRV, users can start to add, refine and build their own models and run FBA as well in the GEMSiRV.'''</u>
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Because two kinds of data formats, spreadsheet and xml, are commonly used for reconstructed metabolic models, the GEMsME allows importing both formats.
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Because two kinds of data formats, spreadsheet and xml, are commonly used for reconstructed metabolic models, the GEMSiRV allows importing both formats.
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<font size="2">'''Available models in SBML:'''<font>
<font size="2">'''Available models in SBML:'''<font>
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Models exported from [http://bigg.ucsd.edu/bigg BiGG] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforBiGG.TXT]]) and then imported to GEMsME.
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Models exported from [http://bigg.ucsd.edu/bigg BiGG] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforBiGG.TXT]]) and then imported to GEMSiRV.
<table border="1">
<table border="1">
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Models downloaded from [http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView Model SEED] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforSEED.TXT]]) and then imported to GEMsME. Because the Model SEED provides more than one hundred of draft models, several of them were listed here as examples.
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Models downloaded from [http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView Model SEED] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforSEED.TXT]]) and then imported to GEMSiRV. Because the Model SEED provides more than one hundred of draft models, several of them were listed here as examples.
<table border="1">
<table border="1">
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In addition to the BiGG- and SEED-based models, several published models were made by using the resource of [http://biocyc.org/ BioCyc] and [http://www.genome.jp/kegg/ KEGG]. These models can also be modified and imported into the GEMsME. For example, the SBML file of Haloalkaliphile Natronomonas pharaonis [http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1000799.s003 original release] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforKEGG.TXT]]).
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In addition to the BiGG- and SEED-based models, several published models were made by using the resource of [http://biocyc.org/ BioCyc] and [http://www.genome.jp/kegg/ KEGG]. These models can also be modified and imported into the GEMSiRV. For example, the SBML file of Haloalkaliphile Natronomonas pharaonis [http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1000799.s003 original release] can be modified by [[TextReplacer |TextReplacer]] with the replacing rules ([[Image:RulesforKEGG.TXT]]).
