SB Course
From CSBLwiki
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*[http://www.bioconductor.org BioConductor] - based on ''R'' package | *[http://www.bioconductor.org BioConductor] - based on ''R'' package | ||
**[http://bioconductor.org/packages/2.3/bioc/html/SBMLR.html SBMLR package] - [http://bioconductor.org/packages/2.3/bioc/vignettes/SBMLR/inst/doc/manual.pdf Manual] | **[http://bioconductor.org/packages/2.3/bioc/html/SBMLR.html SBMLR package] - [http://bioconductor.org/packages/2.3/bioc/vignettes/SBMLR/inst/doc/manual.pdf Manual] | ||
| - | ***getIncidenceMatrix (get incidence/stoichiometry matrix from model) | + | ***getIncidenceMatrix <i>(get incidence/stoichiometry matrix from model)</i> |
| - | **RSBML | + | **[http://www.bioconductor.org/packages/2.3/bioc/html/rsbml.html RSBML] - [http://www.bioconductor.org/packages/2.3/bioc/vignettes/rsbml/inst/doc/quick-start.pdf quick introduction] |
==Matlab== | ==Matlab== | ||
Revision as of 14:47, 1 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
- Systems biology 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
