# cy3sbml A Cytoscape App for SBML

The main functions of cy3sbml are accessible from the Cytoscape menu bar above.

| Hide|show panel | Changes the visibility of the cy3sbml panel.
| Import SBML | Load SBML files via the File Import Dialogue. To import multiple files select multiple files.
| Validate SBML | Validate SBML files against the SBML specification. Select the network to validate and click the validation icon.
| SBML Examples | Load SBML examples models.
| BioModel Import | Load SBML files from BioModels.
| Help | Display this help information.
| Cofactor nodes | Manage cofactor nodes in the network.
| Save Layout | Save or load network layout information.
| Load layout | Load network layout information.

## Support

| Forum | https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
| Bug Tracker | https://github.com/matthiaskoenig/cy3sbml/issues
| Source code | https://github.com/matthiaskoenig/cy3sbml
| Email | konigmatt@googlemail.com

## About

Our mission is the visualization of Systems Biology Markup Language (SBML) within the network context.

Our vision is to create a visualization tool for computational models which seamlessly integrates with computational modeling frameworks and workflows.

cy3sbml was developed by Matthias König in cooperation with Andreas Dräger and Nikolas Rodriquez.

### How to cite

Matthias König, Andreas Dräger and Hermann-Georg Holzhütter
CySBML: a Cytoscape plugin for SBML
Bioinformatics. 2012 Jul 5. PubMed

### Funding & Support

This project was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and Virtual Liver Network (VLN, grant number 0315756), and by the National Resource for Network Biology NRNB within the NRNB Academy Summer Session 2015. This project is supported by the Institute for Theoretical Biology (ITB) of the Humboldt University Berlin.

### Attribution

We thank the SBML, Cytoscape, BioModels, BiGG and OLS community for their support.

Cytoscape

- Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
- Cytoscape: a software environment for integrated models of biomolecular interaction networks.
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SBML

- Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
- Bioinformatics. 2003 Mar 1;19(4):524-31. PubMed

JSBML

- Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, and Andreas Dräger.
- JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
- Bioinformatics, 31(20): 3383–3386. PubMed

- Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, and Hucka M.
- JSBML: a flexible Java library for working with SBML.
- Bioinformatics (2011), 27(15):2167–2168. PubMed

MIRIAM registry identifiers.org

- Juty N, Le Novère N, Laibe C.
- Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.
- Nucleic Acids Res. 2012 Jan;40(Database issue):D580-6. doi: 10.1093/nar/gkr1097. Epub 2011 Dec 2. PubMed

- Laibe C, Le Novère N.
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- BMC Syst Biol. 2007 Dec 13;1:58. PubMed

Ontology Lookup Service (OLS)

- Simon Jupp, Tony Burdett, James Malone, Catherine Leroy, Matt Pearce, Julie McMurry, Helen Parkinson.
- A New Ontology Lookup Service at EMBL-EBI
- Malone, J. et al. (eds.) Proceedings of SWAT4LS International Conference 2015

- Côté RG, Jones P, Apweiler R, Hermjakob H.
- The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
- BMC Bioinformatics. 2006 Feb 28;7:97. PubMed

Research Objects

- Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Philip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Danius Michaelides, Stuart Owen, David Newman, Shoaib Sufi, Carole Goble.
- Why linked data is not enough for scientists
- Future Generation Computer Systems 29(2), February 2013, Pages 599-611, ISSN 0167-739X, doi:10.1016/j.future.2011.08.004

COMBINE archive

- F. T. Bergmann, Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., Olivier, B. G., Rodriguez, N., Sauro, H. M., Scharm, M., Soiland-Reyes, S., Waltemath, D., Yvon, F., and Le Novère, N.
- COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
- BMC Systems Biology (2014) 15:369. PubMed

Biomodels

- Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.
- BioModels: Content, Features, Functionality, and Use.
- CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26. PubMed

- Li C, Courtot M, Le Novère N, Laibe C.
- BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
- Brief Bioinform. 2010 May;11(3):270-7. doi: 10.1093/bib/bbp056. PubMed

BiGG Models

- King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.
- BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
- Nucleic Acids Res. 2016 Jan 4;44(D1):D515-22. doi: 10.1093/nar/gkv1049. Epub 2015 Oct 17. PubMed

UniProt

- UniProt Consortium.
- UniProt: a hub for protein information.
- Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12. doi: 10.1093/nar/gku989. Epub 2014 Oct 27. PubMed

- Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R.
- UniProtJAPI: a remote API for accessing UniProt data.
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ChEBI

- Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.
- The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.
- Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24 PubMed