Version Differences for Metabolic Models

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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]]). 
 
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]]). 
 
 
 
 
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<font size=2>'''Cellular compartments'''</font>  
+
<font size=2>'''Cellular compartments'''</font> [4]  
 
 
+
{| {{table}}  
 
 
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| align="center" style="background:#f0f0f0;"|'''Localization'''  
 
 
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| align="center" style="background:#f0f0f0;"|'''Label'''  
 
 
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|-  
 
 
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| cytoplasm||[c]  
 
 
+
|-  
 
 
+
| nucleus||[n]  
 
 
+
|-  
 
 
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| mitochondria||[m]  
 
 
+
|-  
 
 
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| extracellular||[e]  
 
 
+
|-  
 
 
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| golgi apparatus||[g]  
 
 
+
|-  
 
 
+
| peroxisome||[x]  
 
 
+
|-  
 
 
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| periplasm||[p]  
 
 
+
|-  
 
 
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| vacuole||[v]  
 
 
+
|-  
 
 
+
| chloroplast||[h]  
 
 
+
|-  
 
 
+
| lysosome||[l]  
 
 
+
|-  
 
 
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| endoplasmic reticulum||[r]  
 
 
+
|-  
 
 
+
| thylakoid||[u]  
 
 
+
|-  
 
 
+
|}  
 
 
 
 
-
cytoplasm [c]  
 
 
-
nucleus [n]  
 
 
-
mitochondria [m]  
 
 
-
extracellular [e]  
 
 
-
golgi apparatus [g]  
 
 
-
peroxisome [x]  
 
 
-
periplasm [p]  
 
 
-
vacuole [v]  
 
 
-
chloroplast [h]  
 
 
-
lysosome [l]  
 
 
-
endoplasmic reticulum [r]  
 
 
-
thylakoid [u]  
 
 
 
 
 
 
 
 
 
 
 
---- 
 
---- 
 
 
 
 
 
[1] Becker, S. A., A. M. Feist, et al. (2007). "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc 2(3): 727-738. 
 
[1] Becker, S. A., A. M. Feist, et al. (2007). "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc 2(3): 727-738.