SB Course
From CSBLwiki
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*Math tutorials | *Math tutorials | ||
**[http://neurotheory.columbia.edu/~ken/math-notes/ Ken Miller's Math Notes - UCSF] | **[http://neurotheory.columbia.edu/~ken/math-notes/ Ken Miller's Math Notes - UCSF] | ||
+ | *Metabolic Control Analysis (MCA) | ||
+ | **[http://buzzard.ups.edu/courses/2007spring/projects/shifton-paper-revised.pdf Introduction] | ||
==Term project== | ==Term project== |
Revision as of 16:51, 27 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
- Metabolic Control Analysis (MCA)
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)