CoNtRol

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Tests:

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✓	Test name	Description
✓	Test name	Description
	DSR	Checks condition (*) for the DSR graph. Implemented using GNU Octave by Casian Pantea, based on M. Banaji and G. Craciun, “Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements.”
	General analysis	Runs a number of tests on the system. These are mainly matrix-tests, and relate to multistationarity, stability and persistence. Implemented by Murad Banaji.
	Endotactic	Tests whether the network is endotactic, strongly endotactic, or not endotactic. Implemented using GLPK and SCIP by Matthew Johnston, Pete Donnell and Casian Pantea, based on “A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems”.
	Convergence to equilibrium in 3D	Tests whether the CRN has a 3D stoichiometric subspace and always converges to equilibrium, based on a theoretical result by Li. Note: this is a work in progress. Implemented by Pete Donnell.
	Jacobian matrix	Pseudo-test: this test calculates the Jacobian matrix and its second additive compound symbolically, but does not perform any analysis on either. Can be useful in spotting CRNs that are cooperative, competitive, otherwise monotone (in forward or backwards time) with respect to an orthant ordering, contractive and/or nonexpansive, or in ruling out Hopf bifurcations via the DSR^[2] condition. Implemented in Maxima by Pete Donnell.
	WRZero Realization for all rate constants.	Checks if there is a WR0 realization for all rate constants. Returns the network of the WR0 realization. This is in the process of being tested.

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Feedback

Please send bug reports, feature requests and other comments to cpantea at math dot wvu dot edu. When reporting bugs, please describe the problem in as much detail as possible, and provide screenshots where relevant.

To submit a CRN with known interesting properties to the CoNtRol database for the isomorphism test, please use the CRN submission form.

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CoNtRol requires the use of temporary session cookies to provide functionality. It does not store any identifiable user information when used in interactive mode (all data displayed in browser).

Some user data is permanently stored when using the batch processing mode, or when submitting new CRNs for the isomorphism test. Data is stored solely for the purposes of providing functionality, security, spam prevention, and attributing submissions. Please do not use batch processing or submit new CRN data if you are concerned about this.

Credits, Acknowledgements & Licensing

Credits

DSR graph Java application: Anca Marginean & Casian Pantea
DSR test: Casian Pantea
General analysis tests: Murad Banaji
Endotacticity test: Matthew Johnston, Pete Donnell & Casian Pantea
Isomorphism test: Pete Donnell, Casian Pantea & Murad Banaji
Graphic design: Pete Donnell & Kitson Consulting
Web interface architecture & programming: Pete Donnell & Kitson Consulting

Acknowledgements

This work was supported by grants F/07 058/BU (Leverhulme, to C.P. and M.B.) and EP/J008826/1 (EPSRC, to P.D. and M.B.) and also by Kitson Consulting Limited.
P.D. wishes to acknowledge Mark Donnell, Polly Hember, Matt Kingston, Olaf Mayer and Casian Pantea for their assistance with typing.

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