SB Course
From CSBLwiki
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==Matlab== | ==Matlab== | ||
*[http://www.mathworks.com/products/simbiology/ SimBiology Toolbox] provided by Mathworks | *[http://www.mathworks.com/products/simbiology/ SimBiology Toolbox] provided by Mathworks | ||
| + | <pre> | ||
| + | M = getstoichmatrix(modelObj) | ||
| + | [M,objSpecies] = getstoichmatrix(modelObj) | ||
| + | [M,objSpecies,objReactions] = getstoichmatrix(modelObj) | ||
| + | </pre> | ||
*[http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] - third party toolbox | *[http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] - third party toolbox | ||
Revision as of 07:04, 4 November 2009
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Biomodel database
Running SBML
- SBML softwares - guide table
- KEGG2SBML - KEGG pathway converter to SBML (written in Perl)
R-project
- R package
- BioConductor - based on R package
- SBMLR package - Manual
- getIncidenceMatrix (get incidence/stoichiometry matrix from model)
- RSBML - quick introduction
- SBMLR package - Manual
Matlab
- SimBiology Toolbox provided by Mathworks
M = getstoichmatrix(modelObj) [M,objSpecies] = getstoichmatrix(modelObj) [M,objSpecies,objReactions] = getstoichmatrix(modelObj)
- Systems Biology Toolbox 2 - third party toolbox
Readings
- Math tutorials
Term project
2009 Fall
- Reconstructing central carbon pathways in target organims
- Shewanella oneidensis MR-1 KEGG pathway map
- Lactate metabolism
- PubMed on flux analysis
- Saccharophagus degradans 2-40 KEGG pathway map
- Glucose to Lactate
- converting KEGG pathway map into 'sbml' by kegg2sbml
- or using Keggconverter
- Example
- glycolysis pathway map - sde0010
- detailed information (content) - sde0010
- download pathway map - KEGG pathway_gif ftp - The final GIF version of KEGG PATHWAY (to be removed)
- Shewanella oneidensis MR-1 KEGG pathway map
library(SBMLR) library(odesolve)
