SB Course
From CSBLwiki
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**''Saccharophagus degradans'' 2-40 [http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=sde KEGG pathway map] | **''Saccharophagus degradans'' 2-40 [http://www.genome.jp/kegg-bin/show_organism?menu_type=pathway_maps&org=sde KEGG pathway map] | ||
***Glucose to Lactate | ***Glucose to Lactate | ||
| + | ***converting KEGG pathway map into 'sbml' by [http://sbml.org/Software/KEGG2SBML kegg2sbml] | ||
| + | ****Example | ||
| + | *****glycolysis pathway map - [http://www.genome.jp/kegg-bin/show_pathway?sde00010 sde0010] | ||
| + | *****detailed information (content) - [http://www.genome.jp/dbget-bin/www_bget?pathway+sde00010 sde0010] | ||
| + | *****download pathway map - [ftp://ftp.genome.jp/pub/kegg/release/current/ KEGG ftp] | ||
==Readings== | ==Readings== | ||
Revision as of 04:21, 30 October 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
- RSBML
Matlab
- Systems biology toolbox
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
- Shewanella oneidensis MR-1 KEGG pathway map
