E-cyano is a web-based comprehensive platform for public sharing, annotation, analysis, and visualization of dynamical models and wet-lab experiments related to cyanobacteria. Includes modelling repository with partial dynamical models of clock, photosynthesis, metabolism and other processes, and experiments module containing a set of relevant wet-lab time-series data. The models are accompanied with precise annotations in terms of a compact logical rule-based description of involved reactions. Online simulation is available.
How to cite this tool:
- Troják, M., Šafránek, D., Hrabec, J., Šalagovič, J., Romanovská, F., & Červený, J. (2016, September). E-Cyanobacterium. org: A Web-Based Platform for Systems Biology of Cyanobacteria. In International Conference on Computational Methods in Systems Biology (pp. 316-322). Springer International Publishing.
Conditions of use:
Access to public models and experimental data is available to all users. Registered users can create their own parameter sets that can be simulated online. Publication of new models requires to contact the e-cyano team (see Task 2 in Workflow).
Task 1: Browsing and downloading models.
Go to Model repository, click on the particular model in the left panel, browse the information in the tabs below the model scheme, run the simulation or export the model as SBML file on the Simulation tab.
Task 2: Browsing and downloading experimental data.
Go to Experiments repository, click on the particular experiment in the list, browse the information in the tabs, display or download the data on the Data tab.
Task 3: Submitting a new model.
Make sure your model is in good agreement with the consortium-agreed biochemical space of cyanobacteria and is compliant with SBML level 2 standard. Then contact the development team by filling in the form below:
- Purpose of the model: …
- E-cyanobacterium processes covered: …
- Relation to existing models: …
- Publication where the model has been described: …
- A link to the SBML level 2 compliant XML model file: …
Task 4: Requesting experimental model validation.
Make sure your model has been successfully deployed to e-cyanobacterium.org and is functioning well. Contact the experimental team by filling in the form below:
- Purpose of the experiments:
- E-cyanobacterium model to be validated:
- Klement, M., Děd, T., Šafránek, D., Červený, J., Müller, S., & Steuer, R. (2014). Biochemical space: a framework for systemic annotation of biological models. Electronic Notes in Theoretical Computer Science, 306, 31-44.
- Klement, M., Šafránek, D., Děd, T., Pejznoch, A., Nedbal, L., Steuer, R., … & Müller, S. (2013). A comprehensive web-based platform for domain-specific biological models. Electronic Notes in Theoretical Computer Science, 299, 61-67.
- Šafránek, D., Červený, J., Klement, M., Pospíšilová, J., Brim, L., Lazár, D., & Nedbal, L. (2011). E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. Biosystems, 103(2), 115-124.