Paint4Net

Visualization of the variable scope of the metabolic network in COBRA Toolbox. 

 

About

 

The Paint4Net is a COBRA Toolbox extension for automatic generation of a hypergraph layout of defined scope with the steady-state rates of reaction fluxes of stoichiometric models. Directionalities and fluxes of reactions are constantly represented in the visualization, while detailed information about the reaction (ID, name and synonyms, and formula) and metabolite (ID, name and synonyms, and charged formula) appears when placing the cursor over the item of interest.

Paint4Net is included in the COBRA Toolbox v3.0 and described in Nature Protocols publication of COBRA Toolbox.

 

Instructions for installing and running Paint4Net HERE.

Tutorial in a PDF format HERE.

More about COBRA Toolbox HERE.

 

Citation

Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S.N., Richelle, A., Heinken, A., Haraldsdottir, H.S., Keating, S.M., Vlasov, V., Wachowiak, J., Magnusdottir, S., Ng, C.Y., Preciat, G., Zagare, A., Chan, S.H.J., Aurich, M.K., Clancy, C.M., Modamio, J., Sauls, J.T., Noronha, A., Bordbar, A., Cousins, B., Assal, D.C. El, Ghaderi, S., Ahookhosh, M., Guebila, M. Ben, Apaolaza, I., Kostromins, A., Le, H.M., Ma, D., Sun, Y., Valcarcel, L. V., Wang, L., Yurkovich, J.T., Vuong, P.T., Assal, L.P. El, Hinton, S., Bryant, W.A., Artacho, F.J.A., Planes, F.J., Stalidzans, E., Maass, A., Vempala, S., Hucka, M., Saunders, M.A., Maranas, C.D., Lewis, N.E., Sauter, T., Palsson, B.Ø., Thiele, I., Fleming, R.M. (2019) Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. Nature Protocols, 14, pp. 639–702. https://doi.org/10.1038/s41596-018-0098-2

Kostromins A., Stalidzans E. (2012) Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism. Biosystems, 109(2), pp. 233–239. https://doi.org/10.1016/j.biosystems.2012.03.002