Example Data

Macrophage models in CSML

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Screenshot of MACPAK (Simulatable Macrophage Pathway Knowledgebase) web browser.
Two hundred and twenty-eight csml models are converted to sbml models and uploaded to MACPAK for user's download.

The icons from left to right denote different running applications: Cytoscape, CellDesigner, Cell Illustrator Player and Cell Illustrator Online. For details of these applications on MACPAK the reader is suggested to refer to following publication.

Nagasaki M, Saito A, Fujita A, Tremmel G, Ueno K, Ikeda E, Jeong E, Msiyano S: Systems biology model repository for macrophage pathway simulation. Bioinformatics 2011, 27(11):1591–1593. [pdf]

Following images shows the CSML model underlying C-type lectin receptors in antifungal immunity (Model name: 18160296.csml) and converted SBML model visualized on CellDesigner.

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Simulatable pathway models in the CSML repository

Convertible CSML models:

NoModel nameDownload CSMLDownload SBMLImages on CellDesigner
1Circadian rhythms in DrosophilaCSML 3.0SBML L2V4Click here Larger view
2Circadian rhythms in mutant DrosophilaCSML 3.0 SBML L2V4 Click hereLarger view
3Circadian rhythms in Mus musculusCSML 3.0SBML L2V4Click here Larger view
4Endothelial cell (Extravasation)CSML 3.0SBML L2V4Click here Larger view
5Endothelial cell (Apoptosis)CSML 3.0SBML L2V4Click here Larger view
6Endothelial cell (Angiogenesis)CSML 3.0SBML L2V4Click here Larger view
7Fas-induced apoptosis pathway CSML 3.0 SBML L2V4 Click here Larger view
8Glycolytic pathway and lac operon of E. coliCSML 3.0 SBML L2V4Click here Larger image
9Switching mechanism of lambda phage CSML 3.0 SBML L2V4 Click here Larger view
10p53 (ARF-dependent stabilization pathway) CSML 3.0 SBML L2V4 Click here Larger view
11p53 (CDK-dependent phosphorylation pathway)CSML 3.0 SBML L2V4 Click here Larger view

Unconvertible CSML models:

NoModel nameDownload CSML
1ASE cell fate simulationCSML 3.0
2Extended ASE fate decision modelCSML 3.0
3EGFR signal pathwayCSML 3.0
4VPC fate specificationCSML 3.0

Overview of a conversion from CSML to SBML

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Overview of a conversion from CSML to SBML of circadian rhythm in Mus musculus and the comparison of their simulation results.

(a) CSML model and simulation results of circadian rhythm in Mus musculus using Cell Illustrator.
(b) Converted SBML model and simulation results with CellDesigner (Red curve, per mRNA; blue, Rev/Erv mRNA; green, Bmal mRNA; khaki, REV/ERB; pink, PER/CRY). The converted SBML model can reproduce the same simulation result as CSML’s.